Entendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitifera

ilustraciones, diagramas

Autores:: Rodríguez Riascos, Yamile Andrea

Tipo de recurso:

Fecha de publicación:: 2023

Institución:: Universidad Nacional de Colombia

Repositorio:: Universidad Nacional de Colombia

Idioma:: spa

id	UNACIONAL2_d636cca28e86655a15ded6ee396db8e3
oai_identifier_str	oai:repositorio.unal.edu.co:unal/84620
network_acronym_str	UNACIONAL2
network_name_str	Universidad Nacional de Colombia
repository_id_str
dc.title.spa.fl_str_mv	Entendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitifera
dc.title.translated.eng.fl_str_mv	The role of lncRNA during gastrulation in Acropora species: A. tenuis and A. digitifera
title	Entendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitifera
spellingShingle	Entendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitifera 570 - Biología Antozoos Anthozoa Corales LncRNA Transcriptoma Genómica comparativa Ortología Estructura secundaria conservada
title_short	Entendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitifera
title_full	Entendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitifera
title_fullStr	Entendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitifera
title_full_unstemmed	Entendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitifera
title_sort	Entendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitifera
dc.creator.fl_str_mv	Rodríguez Riascos, Yamile Andrea
dc.contributor.advisor.none.fl_str_mv	Clara Isabel, Bermúdez Santana
dc.contributor.author.none.fl_str_mv	Rodríguez Riascos, Yamile Andrea
dc.contributor.editor.none.fl_str_mv	Reyes Bermúdez, Alejandro
dc.contributor.researchgroup.spa.fl_str_mv	Grupo de Investigación: RN´omica teórica y computacional
dc.subject.ddc.spa.fl_str_mv	570 - Biología
topic	570 - Biología Antozoos Anthozoa Corales LncRNA Transcriptoma Genómica comparativa Ortología Estructura secundaria conservada
dc.subject.decs.spa.fl_str_mv	Antozoos
dc.subject.decs.eng.fl_str_mv	Anthozoa
dc.subject.lemb.spa.fl_str_mv	Corales
dc.subject.proposal.spa.fl_str_mv	LncRNA Transcriptoma Genómica comparativa Ortología Estructura secundaria conservada
description	ilustraciones, diagramas
publishDate	2023
dc.date.accessioned.none.fl_str_mv	2023-08-31T16:44:23Z
dc.date.available.none.fl_str_mv	2023-08-31T16:44:23Z
dc.date.issued.none.fl_str_mv	2023
dc.type.spa.fl_str_mv	Trabajo de grado - Maestría
dc.type.driver.spa.fl_str_mv	info:eu-repo/semantics/masterThesis
dc.type.version.spa.fl_str_mv	info:eu-repo/semantics/acceptedVersion
dc.type.content.spa.fl_str_mv	DataPaper
dc.type.redcol.spa.fl_str_mv	http://purl.org/redcol/resource_type/TM
status_str	acceptedVersion
dc.identifier.uri.none.fl_str_mv	https://repositorio.unal.edu.co/handle/unal/84620
dc.identifier.instname.spa.fl_str_mv	Universidad Nacional de Colombia
dc.identifier.reponame.spa.fl_str_mv	Repositorio Institucional Universidad Nacional de Colombia
dc.identifier.repourl.spa.fl_str_mv	https://repositorio.unal.edu.co/
url	https://repositorio.unal.edu.co/handle/unal/84620 https://repositorio.unal.edu.co/
identifier_str_mv	Universidad Nacional de Colombia Repositorio Institucional Universidad Nacional de Colombia
dc.language.iso.spa.fl_str_mv	spa
language	spa
dc.relation.references.spa.fl_str_mv	J. A. Schwarz, P. B. Brokstein, C. Voolstra, A. Y. Terry, D. J. Miller, A. M. Szmant, M. A. Coffroth, and M. Medina, “Coral life history and symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata.,” BMC genomics, vol. 9, p. 97, 2008. D. G. Fautin, “Structural diversity, systematics, and evolution of cnidae,” Toxicon, vol. 54, no. 8, pp. 1054–1064, 2009. A. Reyes-Bermudez, A. Villar-Briones, C. Ramirez-Portilla, M. Hidaka, and A. S. Mikheyev, “Developmental progression in the coral acropora digitifera is controlled by differential expression of distinct regulatory gene networks,” Genome Biology and Evolution, vol. 8, no. 3, pp. 851–870, 2016. Z.-Q. Zhang et al., “Animal biodiversity: an introduction to higher-level classification and taxonomic richness,” Zootaxa, vol. 3148, no. 1, pp. 7–12, 2011. S. Takahashi-Kariyazono, K. Sakai, and Y. Terai, “Presence–absence polymorphisms of single-copy genes in the stony coral acropora digitifera,” BMC genomics, vol. 21, no. 1, pp. 1–13, 2020. V. Chazottes, P. Hutchings, and A. Osorno, “Impact of an experimental eutrophication on the processes of bioerosion on the reef: One tree island, great barrier reef, australia,” Marine Pollution Bulletin, vol. 118, no. 1-2, pp. 125–130, 2017. A. Reyes-Bermudez, D. J. Miller, and S. Sprungala, “The neuronal calcium sensor protein acrocalcin: a potential target of calmodulin regulation during development in the coral acropora millepora,” PloS one, vol. 7, no. 12, p. e51689, 2012. A. Riesgo, S. Andrade, P. P. Sharma, M. Novo, A. R. P´erez-Porro, V. Vahtera, V. L. Gonz´alez, G. Y. Kawauchi, and G. Giribet, “Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa,” Frontiers in zoology, vol. 9, no. 1, pp. 1–24, 2012. G. Plickert, V. Jacoby, U. Frank, W. A. M¨uller, and O. Mokady, “Wnt signaling in hydroid development: formation of the primary body axis in embryogenesis and its subsequent patterning,” Developmental biology, vol. 298, no. 2, pp. 368–378, 2006. F. Gaiti, W. L. Hatleberg, M. Tanurdˇzi´c, and B. M. Degnan, “Sponge long non-coding rnas are expressed in specific cell types and conserved networks,” Non-coding RNA, vol. 4, no. 1, p. 6, 2018. F. Gaiti, B. Sc, and M. Sc, “Origin and evolution of the metazoan non-coding regulatory genome Insights from the sponge Amphimedon queenslandica,” 2017. J. Veron and M. Stafford-Smith, “Corals of the world (townsville mc, australian institute of marine science),” Mitochondrial DNA part B, vol. 913, 2000. L. Hern´andez-Fern´andez, R. G. de Zayas, Y. M. Olivera, F. P. Amarg´os, C. B. L´opez, L. B. D. Sotolongo, F. Bretos, T. F. Mart´ın, D. L. Cabrera, and F. S. Moret, “Distribution and status of living colonies of acropora spp. in the reef crests of a protected marine area of the caribbean (jardines de la reina national park, cuba),” PeerJ, vol. 7, p. e6470, 2019. C. Shinzato, K. Khalturin, J. Inoue, Y. Zayasu, M. Kanda, M. Kawamitsu, Y. Yoshioka, H. Yamashita, G. Suzuki, and N. Satoh, “Eighteen coral genomes reveal the evolutionary origin of acropora strategies to accommodate environmental changes,” Molecular biology and evolution, vol. 38, no. 1, pp. 16–30, 2021. K. Sakai, T. Singh, and A. Iguchi, “Bleaching and post-bleaching mortality of acropora corals on a heat-susceptible reef in 2016,” PeerJ, vol. 7, p. e8138, 2019. D. D. Licatalosi and R. B. Darnell, “RNA processing and its regulation: Global insights into biological networks,” Nature Reviews Genetics, vol. 11, no. 1, pp. 75–87, 2010. C. Huang, D. Leng, S. Sun, and X. D. Zhang, “Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection,” BMC Genomics, vol. 20, no. 1, pp. 1–15, 2019. V. Costa, C. Angelini, I. De Feis, and A. Ciccodicola, “Uncovering the complexity of transcriptomes with RNA-Seq,” Journal of Biomedicine and Biotechnology, pp. 1–19, 2010. E. E. Schadt, J. Lamb, X. Yang, J. Zhu, S. Edwards, S. K. Sieberts, S. Monks, M. Reitman, P. Y. Lum, A. Leonardson, R. Thieringer, J. M. Metzger, J. Castle, H. Zhu, S. F. Kash, T. A. Drake, A. Sachs, and R. Inpharmatics, “An integrative genomics approach to infer causal associations between gene expression and disease,” Nat Genet., vol. 37, no. 7, pp. 710–717, 2005. S. Riquier, M. Mathieu, C. Bessiere, A. Boureux, F. Ruffle, J.-m. Lemaitre, F. Djouad, N. Gilbert, and T. Commes, “Long non-coding RNA exploration for mesenchymal stem cell characterisation,” BMC Genomics, vol. 22, pp. 1–23, 2021. Z. C. Dong and Y. Chen, “Transcriptomics: Advances and approaches,” Science China Life Sciences, vol. 56, no. 10, pp. 960–967, 2013. F. Ozsolak and P. M. Milos, “Rna sequencing: advances, challenges and opportunities,” Nature reviews genetics, vol. 12, no. 2, pp. 87–98, 2011. Y. Han, S. Gao, K. Muegge, W. Zhang, and B. Zhou, “Advanced applications of rna sequencing and challenges,” Bioinformatics and biology insights, vol. 9, pp. BBI– S28991, 2015. M. R. Bakhtiarizadeh and A. A. Alamouti, “Rna-seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep,” Scientific Reports, vol. 10, no. 1, pp. 1–13, 2020. A. Oshlack and M. Robinson, “Youngmd (2010) from rna-seq reads to differential expression results,” Genome Biol, vol. 11, no. 12, p. 220. M. Pertea, D. Kim, G. M. Pertea, J. T. Leek, and S. L. Salzberg, “Transcript-level expression analysis of rna-seq experiments with hisat, stringtie and ballgown,” Nature protocols, vol. 11, no. 9, pp. 1650–1667, 2016. F. Seyednasrollah, A. Laiho, and L. L. Elo, “Comparison of software packages for detecting differential expression in rna-seq studies,” Briefings in bioinformatics, vol. 16, no. 1, pp. 59–70, 2015. F. Rapaport, R. Khanin, Y. Liang, M. Pirun, A. Krek, P. Zumbo, C. E. Mason, N. D. Socci, and D. Betel, “Comprehensive evaluation of differential gene expression analysis methods for rna-seq data,” Genome biology, vol. 14, no. 9, pp. 1–13, 2013. C. Soneson and M. Delorenzi, “A comparison of methods for differential expression analysis of rna-seq data,” BMC bioinformatics, vol. 14, no. 1, pp. 1–18, 2013. D. Bhattacharya and Agrawal, “Comparative genomics explains the evolutionary success of reef-forming corals,” eLife, vol. 5, no. MAY2016, pp. 1–26, 2016. J. Alf¨oldi and K. Lindblad-Toh, “Comparative genomics as a tool to understand evolution and disease,” Genome Research, vol. 23, no. 7, pp. 1063–1068, 2013. A. M. Altenhoff, M. Gil, G. H. Gonnet, and C. Dessimoz, “Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs,” PLoS ONE, vol. 8, no. 1, 2013. D. W. Mount, “Bioinformatics: Sequence and Genome Analysis,” in Cold Spring Harbor Laboratory Press, ch. 11, p. 692, 2004. R. R. de la Haba, C. L´opez-Hermoso, C. S´anchez-Porro, K. T. Konstantinidis, and A. Ventosa, “Comparative Genomics and Phylogenomic Analysis of the Genus Salinivibrio,” Frontiers in Microbiology, vol. 10, no. September, pp. 1–15, 2019. M. Lechner, M. Hernandez-rosales, D. Doerr, N. Wieseke, J. Stoye, R. K. Hartmann, and S. J. Prohaska, “Orthology Detection Combining Clustering and Synteny for Very Large Datasets,” vol. 9, no. 8, 2014. A. M. Altenhoff, M. Gil, G. H. Gonnet, and C. Dessimoz, “Inferring hierarchical orthologous groups from orthologous gene pairs,” PloS one, vol. 8, no. 1, p. e53786, 2013 K. Trachana, T. A. Larsson, S. Powell, W.-H. Chen, T. Doerks, J. Muller, and P. Bork, “Orthology prediction methods: a quality assessment using curated protein families,” Bioessays, vol. 33, no. 10, pp. 769–780, 2011. A. Kuzniar, R. C. van Ham, S. Pongor, and J. A. Leunissen, “The quest for orthologs: finding the corresponding gene across genomes,” Trends in Genetics, vol. 24, no. 11, pp. 539–551, 2008. A. Azad, G. A. Pavlopoulos, C. A. Ouzounis, N. C. Kyrpides, and A. Bulu¸c, “Hipmcl: a high-performance parallel implementation of the markov clustering algorithm for large-scale networks,” Nucleic acids research, vol. 46, no. 6, pp. e33–e33, 2018. I. A. Vergara and N. Chen, “Large synteny blocks revealed between caenorhabditis elegans and caenorhabditis briggsae genomes using orthocluster,” BMC genomics, vol. 11, no. 1, pp. 1–13, 2010. J. Graf and M. Kretz, “From structure to function: Route to understanding lncrna mechanism,” Bioessays, vol. 42, no. 12, p. 2000027, 2020. K. Mishra and C. Kanduri, “Understanding long noncoding rna and chromatin interactions: what we know so far,” Non-coding RNA, vol. 5, no. 4, p. 54, 2019. S. R. Atkinson, S. Marguerat, and J. B¨ahler, “Exploring long non-coding rnas through sequencing,” in Seminars in cell & developmental biology, vol. 23, pp. 200–205, Elsevier, 2012. J. Liu, L.-Z. Yang, and L.-L. Chen, “Understanding lncrna–protein assemblies with imaging and single-molecule approaches,” Current Opinion in Genetics & Development, vol. 72, pp. 128–137, 2022. W. A. MacDonald and M. R. Mann, “Long noncoding rna functionality in imprinted domain regulation,” PLoS Genetics, vol. 16, no. 8, p. e1008930, 2020. R.-W. Yao, Y. Wang, and L.-L. Chen, “Cellular functions of long noncoding rnas,” Nature cell biology, vol. 21, no. 5, pp. 542–551, 2019. R. Li, H. Zhu, and Y. Luo, “Understanding the functions of long non-coding rnas through their higher-order structures,” International journal of molecular sciences, vol. 17, no. 5, p. 702, 2016. K. Sanbonmatsu, “Getting to the bottom of lncrna mechanism: structure–function relationships,” Mammalian Genome, vol. 33, no. 2, pp. 343–353, 2022. J. Iwakiri, M. Hamada, and K. Asai, “Bioinformatics tools for lncrna research,” Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, vol. 1859, no. 1, pp. 23–30, 2016. Q. Zhao, Z. Zhao, X. Fan, Z. Yuan, Q. Mao, and Y. Yao, “Review of machine learning methods for rna secondary structure prediction,” PLoS computational biology, vol. 17, no. 8, p. e1009291, 2021. M. Cao, J. Zhao, and G. Hu, “Genome-wide methods for investigating long noncoding rnas,” Biomedicine & Pharmacotherapy, vol. 111, pp. 395–401, 2019. G. M. Cruz-Miranda, A. Hidalgo-Miranda, D. A. B´arcenas-L´opez, J. C. N´u˜nezEnr´ıquez, J. Ram´ırez-Bello, J. M. Mej´ıa-Arangur´e, and S. Jim´enez-Morales, “Long noncoding rna and acute leukemia,” International journal of molecular sciences, vol. 20, no. 3, p. 735, 2019. K. C. Wang and H. Y. Chang, “Molecular mechanisms of long noncoding rnas,” Molecular cell, vol. 43, no. 6, pp. 904–914, 2011. J. Chen, H. Wang, and Y. Yao, “Experimental study of nonlinear ultrasonic behavior of soil materials during the compaction,” Ultrasonics, vol. 69, pp. 19–24, 2016. L. Yang, J. E. Froberg, and J. T. Lee, “Long noncoding rnas: fresh perspectives into the rna world,” Trends in biochemical sciences, vol. 39, no. 1, pp. 35–43, 2014. D. H. Mathews, “How to benchmark rna secondary structure prediction accuracy,” Methods, vol. 162, pp. 60–67, 2019. N. Aghaeepour and H. H. Hoos, “Ensemble-based prediction of rna secondary structures,” BMC bioinformatics, vol. 14, no. 1, pp. 1–16, 2013. I. Tinoco Jr and C. Bustamante, “How rna folds,” Journal of molecular biology, vol. 293, no. 2, pp. 271–281, 1999. Y. Wan, M. Kertesz, R. C. Spitale, E. Segal, and H. Y. Chang, “Understanding the transcriptome through rna structure,” Nature Reviews Genetics, vol. 12, no. 9, pp. 641– 655, 2011. S. Bellaousov and D. H. Mathews, “Probknot: fast prediction of rna secondary structure including pseudoknots,” Rna, vol. 16, no. 10, pp. 1870–1880, 2010. C. W. Leonard, C. E. Hajdin, F. Karabiber, D. H. Mathews, O. V. Favorov, N. V. Dokholyan, and K. M. Weeks, “Principles for understanding the accuracy of shapedirected rna structure modeling,” vol. 52, no. 4, pp. 588–595, 2013. I. L. Hofacker, “Vienna rna secondary structure server,” Nucleic acids research, vol. 31, no. 13, pp. 3429–3431, 2003. J. I. Horabin, “Long noncoding rnas as metazoan developmental regulators,” Chromosome research, vol. 21, no. 6, pp. 673–684, 2013 A. Pauli, E. Valen, M. F. Lin, M. Garber, N. L. Vastenhouw, J. Z. Levin, L. Fan, A. Sandelin, J. L. Rinn, A. Regev, and A. F. Schier, “Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis,” Genome Research, vol. 22, no. 3, pp. 577–591, 2012. S. Haque, K. Kaushik, V. E. Leonard, S. Kapoor, A. Sivadas, A. Joshi, V. Scaria, and S. Sivasubbu, “Short stories on zebrafish long noncoding RNAs,” Zebrafish, vol. 11, no. 6, pp. 499–508, 2014. E. Forouzmand, N. D. L. Owens, I. L. Blitz, K. D. Paraiso, M. K. Khokha, M. J. Gilchrist, X. Xie, and K. W. Y. Cho, “Developmentally regulated long non-coding RNAs in Xenopus tropicalis,” Developmental Biology, vol. 426, no. 2, pp. 401–408, 2017. A. Akay, D. Jordan, I. C. Navarro, T. Wrzesinski, C. P. Ponting, E. A. Miska, and W. Haerty, “Identification of functional long non-coding RNAs in C. elegans,” bioRxiv, pp. 1–14, 2018. J. W. Nam and D. P. Bartel, “Long noncoding RNAs in C. elegans,” Genome Research, vol. 22, no. 12, pp. 2529–2540, 2012. F. Gaiti, S. L. Fernandez-Valverde, N. Nakanishi, A. D. Calcino, I. Yanai, M. Tanurdzic, and B. M. Degnan, “Dynamic and widespread lncrna expression in a sponge and the origin of animal complexity,” Molecular biology and evolution, vol. 32, no. 9, pp. 2367– 2382, 2015. A. E. Kornienko, P. M. Guenzl, D. P. Barlow, and F. M. Pauler, “Gene regulation by the act of long non-coding rna transcription,” BMC biology, vol. 11, no. 1, pp. 1–14, 2013. A. Pauli, J. L. Rinn, and A. F. Schier, “Non coding RNAs regulation in embryogenesis,” Nat Rev Genet., vol. 12, no. 2, pp. 136–149, 2011. J. Ponjavic, C. P. Ponting, and G. Lunter, “Functionality or transcriptional noise? evidence for selection within long noncoding rnas,” Genome research, vol. 17, no. 5, pp. 556–565, 2007. X.-D. Huang, J.-g. Dai, K.-t. Lin, M. Liu, H.-t. Ruan, H. Zhang, W.-g. Liu, M.-X. He, and M. Zhao, “Regulation of il-17 by lncrna of irf-2 in the pearl oyster,” Fish & shellfish immunology, vol. 81, pp. 108–112, 2018. B. Gourbal, S. Pinaud, G. J. Beckers, J. W. Van Der Meer, U. Conrath, and M. G. Netea, “Innate immune memory: An evolutionary perspective,” Immunological reviews, vol. 283, no. 1, pp. 21–40, 2018. V. Valenzuela-Mu˜noz, P. Pereiro, M. Alvarez-Rodr´ıguez, C. Gallardo-Esc´arate, A. Fi- ´ gueras, and B. Novoa, “Comparative modulation of lncrnas in wild-type and rag1- heterozygous mutant zebrafish exposed to immune challenge with sp N. Wei, W. Pang, Y. Wang, Y. Xiong, R. Xu, W. Wu, C. Zhao, and G. Yang, “Knockdown of pu. 1 mrna and as lncrna regulates expression of immune-related genes in zebrafish danio rerio,” Developmental & Comparative Immunology, vol. 44, no. 2, pp. 315– 319, 2014. P. Pereiro, R. Moreira, B. Novoa, and A. Figueras, “Differential expression of long non-coding rna (lncrna) in mediterranean mussel (mytilus galloprovincialis) hemocytes under immune stimuli,” Genes, vol. 12, no. 9, p. 1393, 2021. Z. Hongkuan, T. Karsoon, L. Shengkang, M. Hongyu, and Z. Huaiping, “The functional roles of the non-coding rnas in molluscs,” Gene, vol. 768, p. 145300, 2021. D. Feng, Q. Li, H. Yu, L. Kong, and S. Du, “Transcriptional profiling of long non-coding rnas in mantle of crassostrea gigas and their association with shell pigmentation,” Scientific Reports, vol. 8, no. 1, p. 1436, 2018. A. Fatica and I. Bozzoni, “Long non-coding rnas: new players in cell differentiation and development,” Nature Reviews Genetics, vol. 15, no. 1, pp. 7–21, 2014. W. Kim, C. Miguel-Rojas, J. Wang, J. P. Townsend, and F. Trail, “Developmental dynamics of long noncoding RNA expression during sexual fruiting body formation in Fusarium graminearum,” mBio, vol. 9, no. 4, pp. 1–17, 2018. S. Frank, A. Aguirre, J. Hescheler, and L. Kurian, “A lncRNA Perspective into (Re)building the heart,” Frontiers in Cell and Developmental Biology, vol. 4, no. NOV, pp. 1–11, 2016. F. Darbellay and A. Necsulea, “Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs,” Molecular Biology and Evolution, vol. 37, no. 1, pp. 240–259, 2020. L. Kurian, A. Aguirre, I. Sancho-Martinez, C. Benner, T. Hishida, T. B. Nguyen, P. Reddy, E. Nivet, M. N. Krause, D. A. Nelles, C. R. Esteban, J. M. Campistol, G. W. Yeo, and J. C. I. Belmonte, “Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development,” Circulation, vol. 131, no. 14, pp. 1278–1290, 2015. W. Jiang, Y. Liu, R. Liu, K. Zhang, and Y. Zhang, “LncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression,” cell Rep, vol. 11, no. 1, pp. 137–148, 2015. I. C. Welsh, H. Kwak, F. L. Chen, M. Werner, L. S. Shopland, C. G. Danko, J. T. Lis, M. Zhang, J. F. Martin, and N. A. Kurpios, “Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality,” Cell Reports, vol. 13, no. 2, pp. 337–349, 2015. L. A. Goff, A. F. Groff, M. Sauvageau, Z. Trayes-Gibson, D. B. Sanchez-Gomez, M. Morse, R. D. Martin, L. E. Elcavage, S. C. Liapis, M. Gonzalez-Celeiro, O. Plana, E. Li, C. Gerhardinger, G. S. Tomassy, P. Arlotta, and J. L. Rinn, “Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain,” Proceedings of the National Academy of Sciences of the United States of America, vol. 112, no. 22, pp. 6855–6862, 2015. M. Kretz, D. E. Webster, R. J. Flockhart, C. S. Lee, A. Zehnder, V. Lopez-Pajares, K. Qu, G. X. Zheng, J. Chow, G. E. Kim, J. L. Rinn, H. Y. Chang, Z. Siprashvili, and P. A. Khavari, “Suppression of progenitor differentiation requires the long noncoding RNA ANCR,” Genes and Development, vol. 26, no. 4, pp. 338–343, 2012. P. Grote and B. G. Herrmann, “Long noncoding RNAs in organogenesis: Making the difference,” Trends in Genetics, vol. 31, no. 6, pp. 329–335, 2015. P. Cartwright and A. Collins, “Fossils and phylogenies: Integrating multiple lines of evidence to investigate the origin of early major metazoan lineages,” Integrative and Comparative Biology, vol. 47, no. 5, pp. 744–751, 2007. M. Inoue, R. Suwa, A. Suzuki, K. Sakai, and H. Kawahata, “Effects of seawater pH on growth and skeletal U/Ca ratios of Acropora digitifera coral polyps,” Geophysical Research Letters, vol. 38, no. 12, pp. 2–5, 2011. N. J. Strausfeld and F. Hirth, “Introduction to ’Origin and evolution of the nervous system’.,” Philosophical transactions of the Royal Society of London. Series B, Biological sciences, vol. 370, dec 2015. H. V. A. N. Iten, A. C. Marques, J. D. E. Moraes, M. L. A. F. Pacheco, M. Guimaraes, and S. I. M. Oes, “Frontiers in palaeontology origin and early diversification of the phylum cnidaria verrill : major developments in the analysis of the taxon ’ s proterozoic ˆa€“ cambrian history,” Frontiers in Palaeontology, vol. 57, pp. 677–690, 2014 C. W. Dunn, A. Hejnol, D. Q. Matus, K. Pang, W. E. Browne, S. A. Smith, E. Seaver, G. W. Rouse, M. Obst, G. D. Edgecombe, M. V. Sørensen, S. H. D. Haddock, A. Schmidt-Rhaesa, A. Okusu, R. M. Kristensen, W. C. Wheeler, M. Q. Martindale, and G. Giribet, “Broad phylogenomic sampling improves resolution of the animal tree of life,” Nature, vol. 452, pp. 745–749, apr 2008. A. L. Fidler, R. M. Vanacore, S. V. Chetyrkin, V. K. Pedchenko, G. Bhave, V. P. Yin, C. L. Stothers, K. L. Rose, W. H. McDonald, T. A. Clark, D.-B. Borza, R. E. Steele, M. T. Ivy, T. Aspirnauts, J. K. Hudson, and B. G. Hudson, “A unique covalent bond in basement membrane is a primordial innovation for tissue evolution.,” Proceedings of the National Academy of Sciences of the United States of America, vol. 111, pp. 331–6, jan 2014. A. G. Collins, “Phylogeny of medusozoa and the evolution of cnidarian life cycles,” Journal of Evolutionary Biology, vol. 15, no. 3, pp. 418–432, 2002. I. Fiorillo, S. Rossi, V. Alva, J. M. Gili, and P. J. L´opez-Gonz´alez, “Seasonal cycle of sexual reproduction of the Mediterranean soft coral Alcyonium acaule (Anthozoa, Octocorallia),” Marine Biology, vol. 160, no. 3, pp. 719–728, 2013. S. Goffredo, J. Radetic’, V. Airi, and F. Zaccanti, “Sexual reproduction of the solitary sunset cup coral¡i¿Leptopsammia pruvoti¡/i¿(Scleractinia: Dendrophylliidae) in the Mediterranean. 1. Morphological aspects of gametogenesis and ontogenesis,” Marine Biology, vol. 147, no. 2, pp. 485–495, 2005. W. A. M¨uller and T. Leitz, “Metamorphosis in the Cnidaria,” Canadian Journal of Zoology, vol. 80, no. 10, pp. 1755–1771, 2002. L. C. Grasso, J. Maindonald, S. Rudd, D. C. Hayward, R. Saint, D. J. Miller, and E. E. Ball, “Microarray analysis identifies candidate genes for key roles in coral development.,” BMC genomics, vol. 9, p. 540, 2008. X. Yuan, T. Yuan, H. Huang, L. Jiang, W. Zhou, and S. Liu, “Elevated CO2 delays the early development of scleractinian coral Acropora gemmifera,” Scientific Reports, vol. 8, no. 1, p. 2787, 2018. E. M. Hemond, S. T. Kaluziak, and S. V. Vollmer, “The genetics of colony form and function in Caribbean Acropora corals,” BMC Genomics, vol. 15, no. 1, pp. 1–21, 2014. A. M. Kerr, A. H. Baird, and T. P. Hughes, “Correlated evolution of sex and reproductive mode in corals (Anthozoa: Scleractinia),” Proceedings of the Royal Society B: Biological Sciences, vol. 278, no. 1702, pp. 75–81, 2011. Q. M. Heather and Q. M. Mark, “Embryonic development in two species of scleractinian coral embryos: Symbiodinium localization and mode of gastrulation,” Evolution Development, vol. 9, no. 4, pp. 355–367, 2007. C. Marchini, V. Airi, R. Fontana, G. Tortorelli, M. Rocchi, G. Falini, O. Levy, Z. Dubinsky, and S. Goffredo, “Annual reproductive cycle and unusual embryogenesis of a temperate coral in the Mediterranean Sea,” PLoS ONE, vol. 10, no. 10, pp. 1–17, 2015. D. J. Miller, D. C. Hayward, J. S. Reece-Hoyes, I. Scholten, J. Catmull, W. J. Gehring, P. Callaerts, J. E. Larsen, and E. E. Ball, “Pax gene diversity in the basal cnidarian Acropora millepora (Cnidaria, Anthozoa): implications for the evolution of the Pax gene family.,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 9, pp. 4475–80, 2000. E. E. Ball, D. C. Hayward, J. Catmull, J. S. Reece-Hoyes, N. R. Hislop, P. L. Harrison, and D. J. Miller, “Molecular control of development in the reef coral, Acropora millepora,” Proceedings of the 9th International Coral Reef Symposium, vol. 1, no. October, pp. 395–402, 2000. J. H. Vandermeulen, “Studies on reef corals. II. Fine structure of planktonic planula larva of Pocillopora damicornis, with emphasis on the aboral epidermis,” Marine Biology, vol. 27, no. 3, pp. 239–249, 1974. D. C. Hayward, S. Hetherington, C. A. Behm, L. C. Grasso, S. Foret, D. J. Miller, and E. E. Ball, “Differential gene expression at coral settlement and metamorphosis - A subtractive hybridization study,” PLoS ONE, vol. 6, no. 10, 2011. J. H. Vandermeulen, “Studies on reef corals. III. Fine structural changes of calicoblast cells in Pocillopora damicornis during settling and calcification,” Marine Biology, vol. 31, no. 1, pp. 69–77, 1975. X. Chen, Y. Sun, R. Cai, G. Wang, X. Shu, and W. Pang, “Long noncoding rna: multiple players in gene expression,” BMB reports, vol. 51, no. 6, p. 280, 2018. X. Yan, L. Ma, and M. Yang, “Identification and characterization of long non-coding rna (lncrna) in the developing seeds of jatropha curcas,” Scientific reports, vol. 10, no. 1, pp. 1–10, 2020. V. Eldem, G. Zararsiz, T. Ta¸s¸ci, I. P. Duru, Y. Bakir, and M. Erkan, “Transcriptome analysis for non-model organism: Current status and best-practices,” Applications of RNA-Seq and Omics Strategies-From Microorganisms to Human Health, vol. 1, no. 2, pp. 1–19, 2017. H.-L. V. Wang and J. A. Chekanova, “Long noncoding rnas in plants,” Long non coding RNA biology, pp. 133–154, 2017. J. Kang, A. Chung, S. Suresh, L. L. Bonzi, J. M. Sourisse, S. Ramirez, D. Romeo, N. Petit-Marty, C. Pegueroles, and C. Schunter, “Environmental regulation of gene expression mediated by long non-coding rnas,” bioRxiv, pp. 2022–06, 2022. C. Huang, J.-E. R. Morlighem, J. Cai, Q. Liao, C. D. Perez, P. B. Gomes, M. Guo, ´ G. R´adis-Baptista, and S. M.-Y. Lee, “Identification of long non-coding rnas in two anthozoan species and their possible implications for coral bleaching,” Scientific reports, vol. 7, no. 1, pp. 1–18, 2017. X. Zhou, H. Lindsay, and M. D. Robinson, “Robustly detecting differential expression in rna sequencing data using observation weights,” Nucleic acids research, vol. 42, no. 11, pp. e91–e91, 2014. C. I. Ortega Peñaloza and C. I. Bermúdez, Identification of neurodevelopmental genes in the coral species Acropora digitifera ( Acroporidae ). PhD thesis, 2022. M. D. Robinson, D. J. McCarthy, and G. K. Smyth, “edger: a bioconductor package for differential expression analysis of digital gene expression data,” bioinformatics, vol. 26, no. 1, pp. 139–140, 2010. J. T. Kung, D. Colognori, and J. T. Lee, “Long noncoding rnas: past, present, and future,” Genetics, vol. 193, no. 3, pp. 651–669, 2013. M. K. Iyer, Y. S. Niknafs, R. Malik, U. Singhal, A. Sahu, Y. Hosono, T. R. Barrette, J. R. Prensner, J. R. Evans, S. Zhao, et al., “The landscape of long noncoding rnas in the human transcriptome,” Nature genetics, vol. 47, no. 3, pp. 199–208, 2015. L. Solnica-Krezel and D. S. Sepich, “Gastrulation: making and shaping germ layers,” Annual review of cell and developmental biology, vol. 28, no. 1, pp. 687–717, 2012. Y. A. Kraus and A. V. Markov, “The gastrulation in cnidaria: A key to understanding phylogeny or the chaos of secondary modifications?,” Obshch. Biol, vol. 77, no. 1, pp. 83–105, 2016. N. Nakanishi, S. Sogabe, and B. M. Degnan, “Evolutionary origin of gastrulation: Insights from sponge development,” BMC Biology, vol. 12, pp. 1–9, 2014. L. S. Babonis and M. Q. Martindale, “Phylogenetic evidence for the modular evolution of metazoan signalling pathways,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 372, no. 1713, p. 20150477, 2017. G. Zhang, B. Li, C. Li, M. T. P. Gilbert, E. D. Jarvis, J. Wang, and A. G. Consortium, “Comparative genomic data of the avian phylogenomics project,” GigaScience, vol. 3, no. 1, pp. 2047–217X, 2014. S. Brenner, J. H. Miller, and W. Broughton, Encyclopedia of genetics. No. Sirsi) i9780122270802, 2002. J. B. Ahrens, K. J. Wade, and D. D. Pollock, “A fast, general synteny detection engine,” bioRxiv, 2021. H. Tang, M. D. Bomhoff, E. Briones, L. Zhang, J. C. Schnable, and E. Lyons, “Synfind: compiling syntenic regions across any set of genomes on demand,” Genome biology and evolution, vol. 7, no. 12, pp. 3286–3298, 2015. K. Vandepoele, Y. Saeys, C. Simillion, J. Raes, and Y. Van de Peer, “The automatic detection of homologous regions (adhore) and its application to microcolinearity between arabidopsis and rice,” Genome Research, vol. 12, no. 11, pp. 1792–1801, 2002. C. G. Ghiurcuta and B. M. Moret, “Evaluating synteny for improved comparative studies,” Bioinformatics, vol. 30, no. 12, pp. i9–i18, 2014. F. Wu, L. A. Mueller, D. Crouzillat, V. P´etiard, and S. D. Tanksley, “Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (cosii) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade,” Genetics, vol. 174, no. 3, pp. 1407–1420, 2006. B. Lenhard, A. Sandelin, L. Mendoza, P. Engstr¨om, N. Jareborg, and W. W. Wasserman, “Identification of conserved regulatory elements by comparative genome analysis,” Journal of biology, vol. 2, no. 2, pp. 1–11, 2003. T. Hachiya, Y. Osana, K. Popendorf, and Y. Sakakibara, “Accurate identification of orthologous segments among multiple genomes,” Bioinformatics, vol. 25, no. 7, pp. 853–860, 2009. Y. Yoshioka, G. Suzuki, Y. Zayasu, H. Yamashita, and C. Shinzato, “Comparative genomics highlight the importance of lineage-specific gene families in evolutionary divergence of the coral genus, montipora,” BMC Ecology and Evolution, vol. 22, no. 1, pp. 1–16, 2022 S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of molecular biology, vol. 215, no. 3, pp. 403–410, 1990. W. J. Kent, “The blast-like alignment tool,” Genome research, vol. 12, no. 4, pp. 656–664, 2002. A. Moya, L. Huisman, E. Ball, D. Hayward, L. Grasso, C. Chua, H. Woo, J.-P. Gattuso, S. Foret, and D. J. Miller, “Whole transcriptome analysis of the coral acropora millepora reveals complex responses to co2-driven acidification during the initiation of calcification,” Molecular ecology, vol. 21, no. 10, pp. 2440–2454, 2012. D. Charif, J. R. Lobry, A. Necsulea, L. Palmeira, S. Penel, G. Perriere, and M. S. Penel, “Package ‘seqinr’,” 2022. H. Pages, P. Aboyoun, R. Gentleman, S. DebRoy, M. H. Pages, D. DataImport, S. BSgenome, R. XStringSet-class, R. MaskedXString-class, and R. XStringSet-io, “Package ‘biostrings’,” R, 2013. E. Neuwirth and M. E. Neuwirth, “Package ‘rcolorbrewer’,” ColorBrewer Palettes, 2014. H. Wickham, M. H. Wickham, and I. RColorBrewer, “Package ‘scales’,” 2016. T. Mailund, “Manipulating data frames: dplyr,” in R Data Science Quick Reference, pp. 109–160, Springer, 2019. H. Wickham and M. H. Wickham, “Package ‘tidyr’,” Easily Tidy Data with spread and gather Functions, 2017. H. Wickham, W. Chang, and M. H. Wickham, “Package ‘ggplot2’,” Create elegant data visualisations using the grammar of graphics. Version, vol. 2, no. 1, pp. 1–189, 2016. Z. Gu, L. Gu, R. Eils, M. Schlesner, and B. Brors, “Circlize implements and enhances circular visualization in r,” Bioinformatics, vol. 30, no. 19, pp. 2811–2812, 2014. S. Han, Y. Liang, Q. Ma, Y. Xu, Y. Zhang, W. Du, C. Wang, and Y. Li, “Lncfinder: an integrated platform for long non-coding rna identification utilizing sequence intrinsic composition, structural information and physicochemical property,” Briefings in bioinformatics, vol. 20, no. 6, pp. 2009–2027, 2019. A. C. Darling, B. Mau, F. R. Blattner, and N. T. Perna, “Mauve: multiple alignment of conserved genomic sequence with rearrangements,” Genome research, vol. 14, no. 7, pp. 1394–1403, 2004 R. Achawanantakun, J. Chen, Y. Sun, and Y. Zhang, “Lncrna-id: Long non-coding rna identification using balanced random forests,” Bioinformatics, vol. 31, no. 24, pp. 3897– 3905, 2015. Y. Liu, X. Liao, T. Han, A. Su, Z. Guo, N. Lu, C. He, and Z. Lu, “Full-length transcriptome sequencing of the scleractinian coral montipora foliosa reveals the gene expression profile of coral–zooxanthellae holobiont,” Biology, vol. 10, no. 12, p. 1274, 2021. C. Shinzato, E. Shoguchi, T. Kawashima, M. Hamada, K. Hisata, M. Tanaka, M. Fujie, M. Fujiwara, R. Koyanagi, T. Ikuta, A. Fujiyama, D. J. Miller, and N. Satoh, “Using the Acropora digitifera genome to understand coral responses to environmental change,” Nature, vol. 476, no. 7360, pp. 320–323, 2011. C. Shinzato, K. Khalturin, J. Inoue, Y. Zayasu, M. Kanda, M. Kawamitsu, Y. Yoshioka, H. Yamashita, G. Suzuki, and N. Satoh, “Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes,” Molecular Biology and Evolution, vol. 38, no. 1, pp. 16–30, 2021. C. P. Ponting, “The functional repertoires of metazoan genomes,” Nature Reviews Genetics, vol. 9, no. 9, pp. 689–698, 2008. N. H. Putnam, M. Srivastava, U. Hellsten, B. Dirks, J. Chapman, A. Salamov, A. Terry, H. Shapiro, E. Lindquist, V. V. Kapitonov, et al., “Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization,” science, vol. 317, no. 5834, pp. 86–94, 2007. J. A. Chapman, E. F. Kirkness, O. Simakov, S. E. Hampson, T. Mitros, T. Weinmaier, T. Rattei, P. G. Balasubramanian, J. Borman, D. Busam, et al., “The dynamic genome of hydra,” Nature, vol. 464, no. 7288, pp. 592–596, 2010. C. R. Voolstra, Y. Li, Y. J. Liew, S. Baumgarten, D. Zoccola, J.-F. Flot, S. Tambutt´e, D. Allemand, and M. Aranda, “Comparative analysis of the genomes of stylophora pistillata and acropora digitifera provides evidence for extensive differences between species of corals,” Scientific reports, vol. 7, no. 1, pp. 1–14, 2017. E. Rivas, J. Clements, and S. R. Eddy, “A statistical test for conserved rna structure shows lack of evidence for structure in lncrnas,” Nature methods, vol. 14, no. 1, pp. 45– 48, 2017. K. Khalturin, C. Shinzato, M. Khalturina, M. Hamada, M. Fujie, R. Koyanagi, M. Kanda, H. Goto, F. Anton-Erxleben, M. Toyokawa, et al., “Medusozoan genomes inform the evolution of the jellyfish body plan,” Nature Ecology & Evolution, vol. 3, no. 5, pp. 811–822, 2019. O. R. Salazar, P. N. Arun, G. Cui, L. K. Bay, M. J. van Oppen, N. S. Webster, and M. Aranda, “The coral acropora loripes genome reveals an alternative pathway for cysteine biosynthesis in animals,” Science advances, vol. 8, no. 38, p. eabq0304, 2022. Y. Zhang, H. Huang, D. Zhang, J. Qiu, J. Yang, K. Wang, L. Zhu, J. Fan, and J. Yang, “A review on recent computational methods for predicting noncoding rnas,” BioMed research international, vol. 2017, 2017. F. Salabi, H. Jafari, S. Navidpour, and A. S. Sadr, “Systematic and computational identification of androctonus crassicauda long non-coding rnas,” Scientific reports, vol. 11, no. 1, pp. 1–14, 2021. V. Maracaja-Coutinho, A. R. Paschoal, J. C. Caris-Maldonado, P. V. Borges, A. J. Ferreira, and A. M. Durham, “Noncoding rnas databases: current status and trends,” Computational Biology of Non-Coding RNA, pp. 251–285, 2019. H. Ma, Y. Hao, X. Dong, Q. Gong, J. Chen, J. Zhang, and W. Tian, “Molecular mechanisms and function prediction of long noncoding rna,” The Scientific World Journal, vol. 2012, 2012. J. T. Low and K. M. Weeks, “Shape-directed rna secondary structure prediction,” Methods, vol. 52, no. 2, pp. 150–158, 2010. S. Washietl, I. L. Hofacker, and P. F. Stadler, “Fast and reliable prediction of noncoding rnas,” Proceedings of the National Academy of Sciences, vol. 102, no. 7, pp. 2454–2459, 2005. A. R. Gruber, S. Findeiß, S. Washietl, I. L. Hofacker, and P. F. Stadler, “Rnaz 2.0: improved noncoding rna detection,” in Biocomputing 2010, pp. 69–79, World Scientific, 2010. I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, and P. Schuster, “Fast folding and comparison of rna secondary structures,” Monatshefte f¨ur Chemie/Chemical Monthly, vol. 125, no. 2, pp. 167–188, 1994. L. Fontana, L. Partridge, and V. D. Longo, “Extending healthy life span from yeast to humans,” science, vol. 328, no. 5976, pp. 321–326, 2010. J.-H. Yoon, K. Abdelmohsen, and M. Gorospe, “Posttranscriptional gene regulation by long noncoding rna,” Journal of molecular biology, vol. 425, no. 19, pp. 3723–3730, 2013. S. Sweta, T. Dudnakova, S. Sudheer, A. H. Baker, and R. Bhushan, “Importance of long non-coding rnas in the development and disease of skeletal muscle and cardiovascular lineages,” Frontiers in Cell and Developmental Biology, vol. 7, p. 228, 2019. J. Harrow, A. Frankish, J. M. Gonzalez, E. Tapanari, M. Diekhans, F. Kokocinski, B. L. Aken, D. Barrell, A. Zadissa, S. Searle, et al., “Gencode: the reference human genome annotation for the encode project,” Genome research, vol. 22, no. 9, pp. 1760–1774, 2012. T. Derrien, R. Johnson, G. Bussotti, A. Tanzer, S. Djebali, H. Tilgner, G. Guernec, D. Martin, A. Merkel, D. G. Knowles, et al., “The gencode v7 catalog of human long noncoding rnas: analysis of their gene structure, evolution, and expression,” Genome research, vol. 22, no. 9, pp. 1775–1789, 2012. H. Naora and D. J. Montell, “Ovarian cancer metastasis: integrating insights from disparate model organisms,” Nature reviews cancer, vol. 5, no. 5, pp. 355–366, 2005. M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. Mcgettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson, and D. G. Higgins, “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007 R. Lorenz, S. H. Bernhart, C. H¨oner zu Siederdissen, H. Tafer, C. Flamm, P. F. Stadler, and I. L. Hofacker, “Viennarna package 2.0,” Algorithms for molecular biology, vol. 6, pp. 1–14, 2011. F. Li, Q. Zheng, P. Ryvkin, I. Dragomir, Y. Desai, S. Aiyer, O. Valladares, J. Yang, S. Bambina, L. R. Sabin, et al., “Global analysis of rna secondary structure in two metazoans,” Cell reports, vol. 1, no. 1, pp. 69–82, 2012. D. H. Mathews, D. H. Turner, and M. Zuker, “Rna secondary structure prediction,” Current protocols in nucleic acid chemistry, vol. 28, no. 1, pp. 11–2, 2007. K. A. Leamy, S. M. Assmann, D. H. Mathews, and P. C. Bevilacqua, “Bridging the gap between in vitro and in vivo rna folding,” Quarterly reviews of biophysics, vol. 49, p. e10, 2016.
dc.rights.coar.fl_str_mv	http://purl.org/coar/access_right/c_abf2
dc.rights.license.spa.fl_str_mv	Reconocimiento 4.0 Internacional
dc.rights.uri.spa.fl_str_mv	http://creativecommons.org/licenses/by/4.0/
dc.rights.accessrights.spa.fl_str_mv	info:eu-repo/semantics/openAccess
rights_invalid_str_mv	Reconocimiento 4.0 Internacional http://creativecommons.org/licenses/by/4.0/ http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv	openAccess
dc.format.extent.spa.fl_str_mv	xv, 80 páginas
dc.format.mimetype.spa.fl_str_mv	application/pdf
dc.publisher.spa.fl_str_mv	Universidad Nacional de Colombia
dc.publisher.program.spa.fl_str_mv	Bogotá - Ciencias - Maestría en Ciencias - Biología
dc.publisher.faculty.spa.fl_str_mv	Facultad de Ciencias
dc.publisher.place.spa.fl_str_mv	Bogotá, Colombia
dc.publisher.branch.spa.fl_str_mv	Universidad Nacional de Colombia - Sede Bogotá
institution	Universidad Nacional de Colombia
bitstream.url.fl_str_mv	https://repositorio.unal.edu.co/bitstream/unal/84620/3/license.txt https://repositorio.unal.edu.co/bitstream/unal/84620/4/3957420077.2023.pdf https://repositorio.unal.edu.co/bitstream/unal/84620/5/3957420077.2023.pdf.jpg
bitstream.checksum.fl_str_mv	eb34b1cf90b7e1103fc9dfd26be24b4a 331c0c9bdaef2a69013c1647465313fa 5c6dcefb3630bdf0578e67f5e2822bce
bitstream.checksumAlgorithm.fl_str_mv	MD5 MD5 MD5
repository.name.fl_str_mv	Repositorio Institucional Universidad Nacional de Colombia
repository.mail.fl_str_mv	repositorio_nal@unal.edu.co
_version_	1806886581804466176
spelling	Reconocimiento 4.0 Internacionalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Clara Isabel, Bermúdez Santanaac7e6426971ef745c06f9be60a974224Rodríguez Riascos, Yamile Andreaeb837cf5d34c8e4323d0d24b0f8336d4Reyes Bermúdez, AlejandroGrupo de Investigación: RN´omica teórica y computacional2023-08-31T16:44:23Z2023-08-31T16:44:23Z2023https://repositorio.unal.edu.co/handle/unal/84620Universidad Nacional de ColombiaRepositorio Institucional Universidad Nacional de Colombiahttps://repositorio.unal.edu.co/ilustraciones, diagramasLos ARN largos no codificantes (lncRNA) desempeñan funciones reguladoras en una amplia gama de procesos biológicos bien definidos como la regulación génica, la epigenética y el anda- miaje molecular. Sin embargo, para muchas especies de corales, la ausencia de un ensamblaje del genomas y transcriptomas completos, impide la identificación integral de los lncRNA. Gracias a los avances recientes en la tecnologı́a de secuenciación Existe nueva información en datos que respectan a genomas borrares y transcriptomas con niveles de ensamblajes que van hasta cromosomas, sentando las bases para la identificación y caracterización de lncRNA de su expresión en diversos tejidos. El objetivo de este estudio fue entender el papel de los lncRNA en la gastrulación de tres especies del género Acropora incluyendo datos de expre- sión de las fases del desarrollo de Acropora digitifera, Acropora tenuis y anotar los lncRNA resultantes en función de su potencial para la ortologı́a con lncRNA conocidos entre estas especies, además de validar por estructura conservada estas moléculas. Para dar respuesta a esta necesidad y usando el ensamblaje del transcriptoma de novo, se logro identificar 4.326 lncRNA potenciales con expresión diferencial para A. digitifera y 3.375 lncRNA en A. tenuis de los cuales detectaron lncRNAs sobreregulados y especie-especı́ficos para gástrula con un total de 56 en A. digitifera y 21 en A. tenuis, de de lncRNA de alta confianza, 25 se encuentran en homologı́a de secuencia en las dos especies mencinadas anteriormente y 74 tienen ortólogos entre las tres especies de Acropora. Además a estos lncRNA en términos de las relaciones de estabilidad termodinámica y conservación estructural, se detectaron 2258 estructuras, se las cuales se identificaron 56 estructuras en A. digitifera y 21 en A. tenuis que poseen expresión diferencial en la etapa de gástrula, pero que no están en ortologı́a y que son considerados especie-especı́ficos en esta etapa del desarrollo. En conjunto, este trabajo proporciona un recurso valioso para el estudio comparativo, funcional y estructural de los lncRNA lo que facilitarı́a la comprensión del papel de estas moléculas en procesos del desarrollo de corales. (Texto tomado de la fuente)Long non-coding RNAs (lncRNAs) play regulatory roles in a wide range of well-defined bio- logical processes such as gene regulation, epigenetics, and molecular scaffolding. However, for many coral species, the absence of a complete genome and transcriptome assembly prevents the comprehensive identification of lncRNAs. Recent advances in sequencing technology re- veal new information data regarding deletion genomes and transcriptomes with assembly levels ranging up to chromosomes, laying the foundation for lncRNA identification and cha- racterization of their expression in various tissues. This study aimed to understand the role of lncRNAs in the gastrulation of three species of the Acropora genus including expression data from the developmental stages of Acropora digitifera, and Acropora tenuis and to anno- tate the resulting lncRNAs according to their potential for orthology with known lncRNAs among these species, in addition to validating by conserved structure these molecules. In response to this need and using de novo transcriptome assembly, we identified 4,326 diffe- rentially expressed potential lncRNAs for A. digitifera and 3,375 lncRNAs in A. tenuis of which we detected over-regulated and species-specific lncRNAs for gastrula with a total of 56 in A. digitifera and 21 in A. tenuis, of the high-confidence lncRNAs, 25 are in sequen- ce homology in the two species mentioned above and 74 have orthologs among the three Acropora species. In addition to these lncRNAs in terms of thermodynamic stability and structural conservation relationships, 2258 structures were detected, of which 56 structures were identified in A. digitifera and 21 inA. tenuis that possesses differential expression at the gastrula stage, but is not in ortholog and is considered species-specific at this stage of development. Taken together, this work provides a valuable resource for the comparative, functional, and structural study of lncRNAs that will facilitate understanding these mole- cules’ role in coral developmental processes.MaestríaMagíster en Ciencias - BiologíaGenómica Comparativaxv, 80 páginasapplication/pdfspaUniversidad Nacional de ColombiaBogotá - Ciencias - Maestría en Ciencias - BiologíaFacultad de CienciasBogotá, ColombiaUniversidad Nacional de Colombia - Sede Bogotá570 - BiologíaAntozoosAnthozoaCoralesLncRNATranscriptomaGenómica comparativaOrtologíaEstructura secundaria conservadaEntendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitiferaThe role of lncRNA during gastrulation in Acropora species: A. tenuis and A. digitiferaTrabajo de grado - Maestríainfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/acceptedVersionDataPaperhttp://purl.org/redcol/resource_type/TMJ. A. Schwarz, P. B. Brokstein, C. Voolstra, A. Y. Terry, D. J. Miller, A. M. Szmant, M. A. Coffroth, and M. Medina, “Coral life history and symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata.,” BMC genomics, vol. 9, p. 97, 2008.D. G. Fautin, “Structural diversity, systematics, and evolution of cnidae,” Toxicon, vol. 54, no. 8, pp. 1054–1064, 2009.A. Reyes-Bermudez, A. Villar-Briones, C. Ramirez-Portilla, M. Hidaka, and A. S. Mikheyev, “Developmental progression in the coral acropora digitifera is controlled by differential expression of distinct regulatory gene networks,” Genome Biology and Evolution, vol. 8, no. 3, pp. 851–870, 2016.Z.-Q. Zhang et al., “Animal biodiversity: an introduction to higher-level classification and taxonomic richness,” Zootaxa, vol. 3148, no. 1, pp. 7–12, 2011.S. Takahashi-Kariyazono, K. Sakai, and Y. Terai, “Presence–absence polymorphisms of single-copy genes in the stony coral acropora digitifera,” BMC genomics, vol. 21, no. 1, pp. 1–13, 2020.V. Chazottes, P. Hutchings, and A. Osorno, “Impact of an experimental eutrophication on the processes of bioerosion on the reef: One tree island, great barrier reef, australia,” Marine Pollution Bulletin, vol. 118, no. 1-2, pp. 125–130, 2017.A. Reyes-Bermudez, D. J. Miller, and S. Sprungala, “The neuronal calcium sensor protein acrocalcin: a potential target of calmodulin regulation during development in the coral acropora millepora,” PloS one, vol. 7, no. 12, p. e51689, 2012.A. Riesgo, S. Andrade, P. P. Sharma, M. Novo, A. R. P´erez-Porro, V. Vahtera, V. L. Gonz´alez, G. Y. Kawauchi, and G. Giribet, “Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa,” Frontiers in zoology, vol. 9, no. 1, pp. 1–24, 2012.G. Plickert, V. Jacoby, U. Frank, W. A. M¨uller, and O. Mokady, “Wnt signaling in hydroid development: formation of the primary body axis in embryogenesis and its subsequent patterning,” Developmental biology, vol. 298, no. 2, pp. 368–378, 2006.F. Gaiti, W. L. Hatleberg, M. Tanurdˇzi´c, and B. M. Degnan, “Sponge long non-coding rnas are expressed in specific cell types and conserved networks,” Non-coding RNA, vol. 4, no. 1, p. 6, 2018.F. Gaiti, B. Sc, and M. Sc, “Origin and evolution of the metazoan non-coding regulatory genome Insights from the sponge Amphimedon queenslandica,” 2017.J. Veron and M. Stafford-Smith, “Corals of the world (townsville mc, australian institute of marine science),” Mitochondrial DNA part B, vol. 913, 2000.L. Hern´andez-Fern´andez, R. G. de Zayas, Y. M. Olivera, F. P. Amarg´os, C. B. L´opez, L. B. D. Sotolongo, F. Bretos, T. F. Mart´ın, D. L. Cabrera, and F. S. Moret, “Distribution and status of living colonies of acropora spp. in the reef crests of a protected marine area of the caribbean (jardines de la reina national park, cuba),” PeerJ, vol. 7, p. e6470, 2019.C. Shinzato, K. Khalturin, J. Inoue, Y. Zayasu, M. Kanda, M. Kawamitsu, Y. Yoshioka, H. Yamashita, G. Suzuki, and N. Satoh, “Eighteen coral genomes reveal the evolutionary origin of acropora strategies to accommodate environmental changes,” Molecular biology and evolution, vol. 38, no. 1, pp. 16–30, 2021.K. Sakai, T. Singh, and A. Iguchi, “Bleaching and post-bleaching mortality of acropora corals on a heat-susceptible reef in 2016,” PeerJ, vol. 7, p. e8138, 2019.D. D. Licatalosi and R. B. Darnell, “RNA processing and its regulation: Global insights into biological networks,” Nature Reviews Genetics, vol. 11, no. 1, pp. 75–87, 2010.C. Huang, D. Leng, S. Sun, and X. D. Zhang, “Re-analysis of the coral Acropora digitifera transcriptome reveals a complex lncRNAs-mRNAs interaction network implicated in Symbiodinium infection,” BMC Genomics, vol. 20, no. 1, pp. 1–15, 2019.V. Costa, C. Angelini, I. De Feis, and A. Ciccodicola, “Uncovering the complexity of transcriptomes with RNA-Seq,” Journal of Biomedicine and Biotechnology, pp. 1–19, 2010.E. E. Schadt, J. Lamb, X. Yang, J. Zhu, S. Edwards, S. K. Sieberts, S. Monks, M. Reitman, P. Y. Lum, A. Leonardson, R. Thieringer, J. M. Metzger, J. Castle, H. Zhu, S. F. Kash, T. A. Drake, A. Sachs, and R. Inpharmatics, “An integrative genomics approach to infer causal associations between gene expression and disease,” Nat Genet., vol. 37, no. 7, pp. 710–717, 2005.S. Riquier, M. Mathieu, C. Bessiere, A. Boureux, F. Ruffle, J.-m. Lemaitre, F. Djouad, N. Gilbert, and T. Commes, “Long non-coding RNA exploration for mesenchymal stem cell characterisation,” BMC Genomics, vol. 22, pp. 1–23, 2021.Z. C. Dong and Y. Chen, “Transcriptomics: Advances and approaches,” Science China Life Sciences, vol. 56, no. 10, pp. 960–967, 2013.F. Ozsolak and P. M. Milos, “Rna sequencing: advances, challenges and opportunities,” Nature reviews genetics, vol. 12, no. 2, pp. 87–98, 2011.Y. Han, S. Gao, K. Muegge, W. Zhang, and B. Zhou, “Advanced applications of rna sequencing and challenges,” Bioinformatics and biology insights, vol. 9, pp. BBI– S28991, 2015.M. R. Bakhtiarizadeh and A. A. Alamouti, “Rna-seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep,” Scientific Reports, vol. 10, no. 1, pp. 1–13, 2020.A. Oshlack and M. Robinson, “Youngmd (2010) from rna-seq reads to differential expression results,” Genome Biol, vol. 11, no. 12, p. 220.M. Pertea, D. Kim, G. M. Pertea, J. T. Leek, and S. L. Salzberg, “Transcript-level expression analysis of rna-seq experiments with hisat, stringtie and ballgown,” Nature protocols, vol. 11, no. 9, pp. 1650–1667, 2016.F. Seyednasrollah, A. Laiho, and L. L. Elo, “Comparison of software packages for detecting differential expression in rna-seq studies,” Briefings in bioinformatics, vol. 16, no. 1, pp. 59–70, 2015.F. Rapaport, R. Khanin, Y. Liang, M. Pirun, A. Krek, P. Zumbo, C. E. Mason, N. D. Socci, and D. Betel, “Comprehensive evaluation of differential gene expression analysis methods for rna-seq data,” Genome biology, vol. 14, no. 9, pp. 1–13, 2013.C. Soneson and M. Delorenzi, “A comparison of methods for differential expression analysis of rna-seq data,” BMC bioinformatics, vol. 14, no. 1, pp. 1–18, 2013.D. Bhattacharya and Agrawal, “Comparative genomics explains the evolutionary success of reef-forming corals,” eLife, vol. 5, no. MAY2016, pp. 1–26, 2016.J. Alf¨oldi and K. Lindblad-Toh, “Comparative genomics as a tool to understand evolution and disease,” Genome Research, vol. 23, no. 7, pp. 1063–1068, 2013.A. M. Altenhoff, M. Gil, G. H. Gonnet, and C. Dessimoz, “Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs,” PLoS ONE, vol. 8, no. 1, 2013.D. W. Mount, “Bioinformatics: Sequence and Genome Analysis,” in Cold Spring Harbor Laboratory Press, ch. 11, p. 692, 2004.R. R. de la Haba, C. L´opez-Hermoso, C. S´anchez-Porro, K. T. Konstantinidis, and A. Ventosa, “Comparative Genomics and Phylogenomic Analysis of the Genus Salinivibrio,” Frontiers in Microbiology, vol. 10, no. September, pp. 1–15, 2019.M. Lechner, M. Hernandez-rosales, D. Doerr, N. Wieseke, J. Stoye, R. K. Hartmann, and S. J. Prohaska, “Orthology Detection Combining Clustering and Synteny for Very Large Datasets,” vol. 9, no. 8, 2014.A. M. Altenhoff, M. Gil, G. H. Gonnet, and C. Dessimoz, “Inferring hierarchical orthologous groups from orthologous gene pairs,” PloS one, vol. 8, no. 1, p. e53786, 2013K. Trachana, T. A. Larsson, S. Powell, W.-H. Chen, T. Doerks, J. Muller, and P. Bork, “Orthology prediction methods: a quality assessment using curated protein families,” Bioessays, vol. 33, no. 10, pp. 769–780, 2011.A. Kuzniar, R. C. van Ham, S. Pongor, and J. A. Leunissen, “The quest for orthologs: finding the corresponding gene across genomes,” Trends in Genetics, vol. 24, no. 11, pp. 539–551, 2008.A. Azad, G. A. Pavlopoulos, C. A. Ouzounis, N. C. Kyrpides, and A. Bulu¸c, “Hipmcl: a high-performance parallel implementation of the markov clustering algorithm for large-scale networks,” Nucleic acids research, vol. 46, no. 6, pp. e33–e33, 2018.I. A. Vergara and N. Chen, “Large synteny blocks revealed between caenorhabditis elegans and caenorhabditis briggsae genomes using orthocluster,” BMC genomics, vol. 11, no. 1, pp. 1–13, 2010.J. Graf and M. Kretz, “From structure to function: Route to understanding lncrna mechanism,” Bioessays, vol. 42, no. 12, p. 2000027, 2020.K. Mishra and C. Kanduri, “Understanding long noncoding rna and chromatin interactions: what we know so far,” Non-coding RNA, vol. 5, no. 4, p. 54, 2019.S. R. Atkinson, S. Marguerat, and J. B¨ahler, “Exploring long non-coding rnas through sequencing,” in Seminars in cell & developmental biology, vol. 23, pp. 200–205, Elsevier, 2012.J. Liu, L.-Z. Yang, and L.-L. Chen, “Understanding lncrna–protein assemblies with imaging and single-molecule approaches,” Current Opinion in Genetics & Development, vol. 72, pp. 128–137, 2022.W. A. MacDonald and M. R. Mann, “Long noncoding rna functionality in imprinted domain regulation,” PLoS Genetics, vol. 16, no. 8, p. e1008930, 2020.R.-W. Yao, Y. Wang, and L.-L. Chen, “Cellular functions of long noncoding rnas,” Nature cell biology, vol. 21, no. 5, pp. 542–551, 2019.R. Li, H. Zhu, and Y. Luo, “Understanding the functions of long non-coding rnas through their higher-order structures,” International journal of molecular sciences, vol. 17, no. 5, p. 702, 2016.K. Sanbonmatsu, “Getting to the bottom of lncrna mechanism: structure–function relationships,” Mammalian Genome, vol. 33, no. 2, pp. 343–353, 2022.J. Iwakiri, M. Hamada, and K. Asai, “Bioinformatics tools for lncrna research,” Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, vol. 1859, no. 1, pp. 23–30, 2016.Q. Zhao, Z. Zhao, X. Fan, Z. Yuan, Q. Mao, and Y. Yao, “Review of machine learning methods for rna secondary structure prediction,” PLoS computational biology, vol. 17, no. 8, p. e1009291, 2021.M. Cao, J. Zhao, and G. Hu, “Genome-wide methods for investigating long noncoding rnas,” Biomedicine & Pharmacotherapy, vol. 111, pp. 395–401, 2019.G. M. Cruz-Miranda, A. Hidalgo-Miranda, D. A. B´arcenas-L´opez, J. C. N´u˜nezEnr´ıquez, J. Ram´ırez-Bello, J. M. Mej´ıa-Arangur´e, and S. Jim´enez-Morales, “Long noncoding rna and acute leukemia,” International journal of molecular sciences, vol. 20, no. 3, p. 735, 2019.K. C. Wang and H. Y. Chang, “Molecular mechanisms of long noncoding rnas,” Molecular cell, vol. 43, no. 6, pp. 904–914, 2011.J. Chen, H. Wang, and Y. Yao, “Experimental study of nonlinear ultrasonic behavior of soil materials during the compaction,” Ultrasonics, vol. 69, pp. 19–24, 2016.L. Yang, J. E. Froberg, and J. T. Lee, “Long noncoding rnas: fresh perspectives into the rna world,” Trends in biochemical sciences, vol. 39, no. 1, pp. 35–43, 2014.D. H. Mathews, “How to benchmark rna secondary structure prediction accuracy,” Methods, vol. 162, pp. 60–67, 2019.N. Aghaeepour and H. H. Hoos, “Ensemble-based prediction of rna secondary structures,” BMC bioinformatics, vol. 14, no. 1, pp. 1–16, 2013.I. Tinoco Jr and C. Bustamante, “How rna folds,” Journal of molecular biology, vol. 293, no. 2, pp. 271–281, 1999.Y. Wan, M. Kertesz, R. C. Spitale, E. Segal, and H. Y. Chang, “Understanding the transcriptome through rna structure,” Nature Reviews Genetics, vol. 12, no. 9, pp. 641– 655, 2011.S. Bellaousov and D. H. Mathews, “Probknot: fast prediction of rna secondary structure including pseudoknots,” Rna, vol. 16, no. 10, pp. 1870–1880, 2010.C. W. Leonard, C. E. Hajdin, F. Karabiber, D. H. Mathews, O. V. Favorov, N. V. Dokholyan, and K. M. Weeks, “Principles for understanding the accuracy of shapedirected rna structure modeling,” vol. 52, no. 4, pp. 588–595, 2013.I. L. Hofacker, “Vienna rna secondary structure server,” Nucleic acids research, vol. 31, no. 13, pp. 3429–3431, 2003.J. I. Horabin, “Long noncoding rnas as metazoan developmental regulators,” Chromosome research, vol. 21, no. 6, pp. 673–684, 2013A. Pauli, E. Valen, M. F. Lin, M. Garber, N. L. Vastenhouw, J. Z. Levin, L. Fan, A. Sandelin, J. L. Rinn, A. Regev, and A. F. Schier, “Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis,” Genome Research, vol. 22, no. 3, pp. 577–591, 2012.S. Haque, K. Kaushik, V. E. Leonard, S. Kapoor, A. Sivadas, A. Joshi, V. Scaria, and S. Sivasubbu, “Short stories on zebrafish long noncoding RNAs,” Zebrafish, vol. 11, no. 6, pp. 499–508, 2014.E. Forouzmand, N. D. L. Owens, I. L. Blitz, K. D. Paraiso, M. K. Khokha, M. J. Gilchrist, X. Xie, and K. W. Y. Cho, “Developmentally regulated long non-coding RNAs in Xenopus tropicalis,” Developmental Biology, vol. 426, no. 2, pp. 401–408, 2017.A. Akay, D. Jordan, I. C. Navarro, T. Wrzesinski, C. P. Ponting, E. A. Miska, and W. Haerty, “Identification of functional long non-coding RNAs in C. elegans,” bioRxiv, pp. 1–14, 2018.J. W. Nam and D. P. Bartel, “Long noncoding RNAs in C. elegans,” Genome Research, vol. 22, no. 12, pp. 2529–2540, 2012.F. Gaiti, S. L. Fernandez-Valverde, N. Nakanishi, A. D. Calcino, I. Yanai, M. Tanurdzic, and B. M. Degnan, “Dynamic and widespread lncrna expression in a sponge and the origin of animal complexity,” Molecular biology and evolution, vol. 32, no. 9, pp. 2367– 2382, 2015.A. E. Kornienko, P. M. Guenzl, D. P. Barlow, and F. M. Pauler, “Gene regulation by the act of long non-coding rna transcription,” BMC biology, vol. 11, no. 1, pp. 1–14, 2013.A. Pauli, J. L. Rinn, and A. F. Schier, “Non coding RNAs regulation in embryogenesis,” Nat Rev Genet., vol. 12, no. 2, pp. 136–149, 2011.J. Ponjavic, C. P. Ponting, and G. Lunter, “Functionality or transcriptional noise? evidence for selection within long noncoding rnas,” Genome research, vol. 17, no. 5, pp. 556–565, 2007.X.-D. Huang, J.-g. Dai, K.-t. Lin, M. Liu, H.-t. Ruan, H. Zhang, W.-g. Liu, M.-X. He, and M. Zhao, “Regulation of il-17 by lncrna of irf-2 in the pearl oyster,” Fish & shellfish immunology, vol. 81, pp. 108–112, 2018.B. Gourbal, S. Pinaud, G. J. Beckers, J. W. Van Der Meer, U. Conrath, and M. G. Netea, “Innate immune memory: An evolutionary perspective,” Immunological reviews, vol. 283, no. 1, pp. 21–40, 2018.V. Valenzuela-Mu˜noz, P. Pereiro, M. Alvarez-Rodr´ıguez, C. Gallardo-Esc´arate, A. Fi- ´ gueras, and B. Novoa, “Comparative modulation of lncrnas in wild-type and rag1- heterozygous mutant zebrafish exposed to immune challenge with spN. Wei, W. Pang, Y. Wang, Y. Xiong, R. Xu, W. Wu, C. Zhao, and G. Yang, “Knockdown of pu. 1 mrna and as lncrna regulates expression of immune-related genes in zebrafish danio rerio,” Developmental & Comparative Immunology, vol. 44, no. 2, pp. 315– 319, 2014.P. Pereiro, R. Moreira, B. Novoa, and A. Figueras, “Differential expression of long non-coding rna (lncrna) in mediterranean mussel (mytilus galloprovincialis) hemocytes under immune stimuli,” Genes, vol. 12, no. 9, p. 1393, 2021.Z. Hongkuan, T. Karsoon, L. Shengkang, M. Hongyu, and Z. Huaiping, “The functional roles of the non-coding rnas in molluscs,” Gene, vol. 768, p. 145300, 2021.D. Feng, Q. Li, H. Yu, L. Kong, and S. Du, “Transcriptional profiling of long non-coding rnas in mantle of crassostrea gigas and their association with shell pigmentation,” Scientific Reports, vol. 8, no. 1, p. 1436, 2018.A. Fatica and I. Bozzoni, “Long non-coding rnas: new players in cell differentiation and development,” Nature Reviews Genetics, vol. 15, no. 1, pp. 7–21, 2014.W. Kim, C. Miguel-Rojas, J. Wang, J. P. Townsend, and F. Trail, “Developmental dynamics of long noncoding RNA expression during sexual fruiting body formation in Fusarium graminearum,” mBio, vol. 9, no. 4, pp. 1–17, 2018.S. Frank, A. Aguirre, J. Hescheler, and L. Kurian, “A lncRNA Perspective into (Re)building the heart,” Frontiers in Cell and Developmental Biology, vol. 4, no. NOV, pp. 1–11, 2016.F. Darbellay and A. Necsulea, “Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs,” Molecular Biology and Evolution, vol. 37, no. 1, pp. 240–259, 2020.L. Kurian, A. Aguirre, I. Sancho-Martinez, C. Benner, T. Hishida, T. B. Nguyen, P. Reddy, E. Nivet, M. N. Krause, D. A. Nelles, C. R. Esteban, J. M. Campistol, G. W. Yeo, and J. C. I. Belmonte, “Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development,” Circulation, vol. 131, no. 14, pp. 1278–1290, 2015.W. Jiang, Y. Liu, R. Liu, K. Zhang, and Y. Zhang, “LncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression,” cell Rep, vol. 11, no. 1, pp. 137–148, 2015.I. C. Welsh, H. Kwak, F. L. Chen, M. Werner, L. S. Shopland, C. G. Danko, J. T. Lis, M. Zhang, J. F. Martin, and N. A. Kurpios, “Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality,” Cell Reports, vol. 13, no. 2, pp. 337–349, 2015.L. A. Goff, A. F. Groff, M. Sauvageau, Z. Trayes-Gibson, D. B. Sanchez-Gomez, M. Morse, R. D. Martin, L. E. Elcavage, S. C. Liapis, M. Gonzalez-Celeiro, O. Plana, E. Li, C. Gerhardinger, G. S. Tomassy, P. Arlotta, and J. L. Rinn, “Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain,” Proceedings of the National Academy of Sciences of the United States of America, vol. 112, no. 22, pp. 6855–6862, 2015.M. Kretz, D. E. Webster, R. J. Flockhart, C. S. Lee, A. Zehnder, V. Lopez-Pajares, K. Qu, G. X. Zheng, J. Chow, G. E. Kim, J. L. Rinn, H. Y. Chang, Z. Siprashvili, and P. A. Khavari, “Suppression of progenitor differentiation requires the long noncoding RNA ANCR,” Genes and Development, vol. 26, no. 4, pp. 338–343, 2012.P. Grote and B. G. Herrmann, “Long noncoding RNAs in organogenesis: Making the difference,” Trends in Genetics, vol. 31, no. 6, pp. 329–335, 2015.P. Cartwright and A. Collins, “Fossils and phylogenies: Integrating multiple lines of evidence to investigate the origin of early major metazoan lineages,” Integrative and Comparative Biology, vol. 47, no. 5, pp. 744–751, 2007.M. Inoue, R. Suwa, A. Suzuki, K. Sakai, and H. Kawahata, “Effects of seawater pH on growth and skeletal U/Ca ratios of Acropora digitifera coral polyps,” Geophysical Research Letters, vol. 38, no. 12, pp. 2–5, 2011.N. J. Strausfeld and F. Hirth, “Introduction to ’Origin and evolution of the nervous system’.,” Philosophical transactions of the Royal Society of London. Series B, Biological sciences, vol. 370, dec 2015.H. V. A. N. Iten, A. C. Marques, J. D. E. Moraes, M. L. A. F. Pacheco, M. Guimaraes, and S. I. M. Oes, “Frontiers in palaeontology origin and early diversification of the phylum cnidaria verrill : major developments in the analysis of the taxon ’ s proterozoic ˆa€“ cambrian history,” Frontiers in Palaeontology, vol. 57, pp. 677–690, 2014C. W. Dunn, A. Hejnol, D. Q. Matus, K. Pang, W. E. Browne, S. A. Smith, E. Seaver, G. W. Rouse, M. Obst, G. D. Edgecombe, M. V. Sørensen, S. H. D. Haddock, A. Schmidt-Rhaesa, A. Okusu, R. M. Kristensen, W. C. Wheeler, M. Q. Martindale, and G. Giribet, “Broad phylogenomic sampling improves resolution of the animal tree of life,” Nature, vol. 452, pp. 745–749, apr 2008.A. L. Fidler, R. M. Vanacore, S. V. Chetyrkin, V. K. Pedchenko, G. Bhave, V. P. Yin, C. L. Stothers, K. L. Rose, W. H. McDonald, T. A. Clark, D.-B. Borza, R. E. Steele, M. T. Ivy, T. Aspirnauts, J. K. Hudson, and B. G. Hudson, “A unique covalent bond in basement membrane is a primordial innovation for tissue evolution.,” Proceedings of the National Academy of Sciences of the United States of America, vol. 111, pp. 331–6, jan 2014.A. G. Collins, “Phylogeny of medusozoa and the evolution of cnidarian life cycles,” Journal of Evolutionary Biology, vol. 15, no. 3, pp. 418–432, 2002.I. Fiorillo, S. Rossi, V. Alva, J. M. Gili, and P. J. L´opez-Gonz´alez, “Seasonal cycle of sexual reproduction of the Mediterranean soft coral Alcyonium acaule (Anthozoa, Octocorallia),” Marine Biology, vol. 160, no. 3, pp. 719–728, 2013.S. Goffredo, J. Radetic’, V. Airi, and F. Zaccanti, “Sexual reproduction of the solitary sunset cup coral¡i¿Leptopsammia pruvoti¡/i¿(Scleractinia: Dendrophylliidae) in the Mediterranean. 1. Morphological aspects of gametogenesis and ontogenesis,” Marine Biology, vol. 147, no. 2, pp. 485–495, 2005.W. A. M¨uller and T. Leitz, “Metamorphosis in the Cnidaria,” Canadian Journal of Zoology, vol. 80, no. 10, pp. 1755–1771, 2002.L. C. Grasso, J. Maindonald, S. Rudd, D. C. Hayward, R. Saint, D. J. Miller, and E. E. Ball, “Microarray analysis identifies candidate genes for key roles in coral development.,” BMC genomics, vol. 9, p. 540, 2008.X. Yuan, T. Yuan, H. Huang, L. Jiang, W. Zhou, and S. Liu, “Elevated CO2 delays the early development of scleractinian coral Acropora gemmifera,” Scientific Reports, vol. 8, no. 1, p. 2787, 2018.E. M. Hemond, S. T. Kaluziak, and S. V. Vollmer, “The genetics of colony form and function in Caribbean Acropora corals,” BMC Genomics, vol. 15, no. 1, pp. 1–21, 2014.A. M. Kerr, A. H. Baird, and T. P. Hughes, “Correlated evolution of sex and reproductive mode in corals (Anthozoa: Scleractinia),” Proceedings of the Royal Society B: Biological Sciences, vol. 278, no. 1702, pp. 75–81, 2011.Q. M. Heather and Q. M. Mark, “Embryonic development in two species of scleractinian coral embryos: Symbiodinium localization and mode of gastrulation,” Evolution Development, vol. 9, no. 4, pp. 355–367, 2007.C. Marchini, V. Airi, R. Fontana, G. Tortorelli, M. Rocchi, G. Falini, O. Levy, Z. Dubinsky, and S. Goffredo, “Annual reproductive cycle and unusual embryogenesis of a temperate coral in the Mediterranean Sea,” PLoS ONE, vol. 10, no. 10, pp. 1–17, 2015.D. J. Miller, D. C. Hayward, J. S. Reece-Hoyes, I. Scholten, J. Catmull, W. J. Gehring, P. Callaerts, J. E. Larsen, and E. E. Ball, “Pax gene diversity in the basal cnidarian Acropora millepora (Cnidaria, Anthozoa): implications for the evolution of the Pax gene family.,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 9, pp. 4475–80, 2000.E. E. Ball, D. C. Hayward, J. Catmull, J. S. Reece-Hoyes, N. R. Hislop, P. L. Harrison, and D. J. Miller, “Molecular control of development in the reef coral, Acropora millepora,” Proceedings of the 9th International Coral Reef Symposium, vol. 1, no. October, pp. 395–402, 2000.J. H. Vandermeulen, “Studies on reef corals. II. Fine structure of planktonic planula larva of Pocillopora damicornis, with emphasis on the aboral epidermis,” Marine Biology, vol. 27, no. 3, pp. 239–249, 1974.D. C. Hayward, S. Hetherington, C. A. Behm, L. C. Grasso, S. Foret, D. J. Miller, and E. E. Ball, “Differential gene expression at coral settlement and metamorphosis - A subtractive hybridization study,” PLoS ONE, vol. 6, no. 10, 2011.J. H. Vandermeulen, “Studies on reef corals. III. Fine structural changes of calicoblast cells in Pocillopora damicornis during settling and calcification,” Marine Biology, vol. 31, no. 1, pp. 69–77, 1975.X. Chen, Y. Sun, R. Cai, G. Wang, X. Shu, and W. Pang, “Long noncoding rna: multiple players in gene expression,” BMB reports, vol. 51, no. 6, p. 280, 2018.X. Yan, L. Ma, and M. Yang, “Identification and characterization of long non-coding rna (lncrna) in the developing seeds of jatropha curcas,” Scientific reports, vol. 10, no. 1, pp. 1–10, 2020.V. Eldem, G. Zararsiz, T. Ta¸s¸ci, I. P. Duru, Y. Bakir, and M. Erkan, “Transcriptome analysis for non-model organism: Current status and best-practices,” Applications of RNA-Seq and Omics Strategies-From Microorganisms to Human Health, vol. 1, no. 2, pp. 1–19, 2017.H.-L. V. Wang and J. A. Chekanova, “Long noncoding rnas in plants,” Long non coding RNA biology, pp. 133–154, 2017.J. Kang, A. Chung, S. Suresh, L. L. Bonzi, J. M. Sourisse, S. Ramirez, D. Romeo, N. Petit-Marty, C. Pegueroles, and C. Schunter, “Environmental regulation of gene expression mediated by long non-coding rnas,” bioRxiv, pp. 2022–06, 2022.C. Huang, J.-E. R. Morlighem, J. Cai, Q. Liao, C. D. Perez, P. B. Gomes, M. Guo, ´ G. R´adis-Baptista, and S. M.-Y. Lee, “Identification of long non-coding rnas in two anthozoan species and their possible implications for coral bleaching,” Scientific reports, vol. 7, no. 1, pp. 1–18, 2017.X. Zhou, H. Lindsay, and M. D. Robinson, “Robustly detecting differential expression in rna sequencing data using observation weights,” Nucleic acids research, vol. 42, no. 11, pp. e91–e91, 2014.C. I. Ortega Peñaloza and C. I. Bermúdez, Identification of neurodevelopmental genes in the coral species Acropora digitifera ( Acroporidae ). PhD thesis, 2022.M. D. Robinson, D. J. McCarthy, and G. K. Smyth, “edger: a bioconductor package for differential expression analysis of digital gene expression data,” bioinformatics, vol. 26, no. 1, pp. 139–140, 2010.J. T. Kung, D. Colognori, and J. T. Lee, “Long noncoding rnas: past, present, and future,” Genetics, vol. 193, no. 3, pp. 651–669, 2013.M. K. Iyer, Y. S. Niknafs, R. Malik, U. Singhal, A. Sahu, Y. Hosono, T. R. Barrette, J. R. Prensner, J. R. Evans, S. Zhao, et al., “The landscape of long noncoding rnas in the human transcriptome,” Nature genetics, vol. 47, no. 3, pp. 199–208, 2015.L. Solnica-Krezel and D. S. Sepich, “Gastrulation: making and shaping germ layers,” Annual review of cell and developmental biology, vol. 28, no. 1, pp. 687–717, 2012.Y. A. Kraus and A. V. Markov, “The gastrulation in cnidaria: A key to understanding phylogeny or the chaos of secondary modifications?,” Obshch. Biol, vol. 77, no. 1, pp. 83–105, 2016.N. Nakanishi, S. Sogabe, and B. M. Degnan, “Evolutionary origin of gastrulation: Insights from sponge development,” BMC Biology, vol. 12, pp. 1–9, 2014.L. S. Babonis and M. Q. Martindale, “Phylogenetic evidence for the modular evolution of metazoan signalling pathways,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 372, no. 1713, p. 20150477, 2017.G. Zhang, B. Li, C. Li, M. T. P. Gilbert, E. D. Jarvis, J. Wang, and A. G. Consortium, “Comparative genomic data of the avian phylogenomics project,” GigaScience, vol. 3, no. 1, pp. 2047–217X, 2014.S. Brenner, J. H. Miller, and W. Broughton, Encyclopedia of genetics. No. Sirsi) i9780122270802, 2002.J. B. Ahrens, K. J. Wade, and D. D. Pollock, “A fast, general synteny detection engine,” bioRxiv, 2021.H. Tang, M. D. Bomhoff, E. Briones, L. Zhang, J. C. Schnable, and E. Lyons, “Synfind: compiling syntenic regions across any set of genomes on demand,” Genome biology and evolution, vol. 7, no. 12, pp. 3286–3298, 2015.K. Vandepoele, Y. Saeys, C. Simillion, J. Raes, and Y. Van de Peer, “The automatic detection of homologous regions (adhore) and its application to microcolinearity between arabidopsis and rice,” Genome Research, vol. 12, no. 11, pp. 1792–1801, 2002.C. G. Ghiurcuta and B. M. Moret, “Evaluating synteny for improved comparative studies,” Bioinformatics, vol. 30, no. 12, pp. i9–i18, 2014.F. Wu, L. A. Mueller, D. Crouzillat, V. P´etiard, and S. D. Tanksley, “Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (cosii) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade,” Genetics, vol. 174, no. 3, pp. 1407–1420, 2006.B. Lenhard, A. Sandelin, L. Mendoza, P. Engstr¨om, N. Jareborg, and W. W. Wasserman, “Identification of conserved regulatory elements by comparative genome analysis,” Journal of biology, vol. 2, no. 2, pp. 1–11, 2003.T. Hachiya, Y. Osana, K. Popendorf, and Y. Sakakibara, “Accurate identification of orthologous segments among multiple genomes,” Bioinformatics, vol. 25, no. 7, pp. 853–860, 2009.Y. Yoshioka, G. Suzuki, Y. Zayasu, H. Yamashita, and C. Shinzato, “Comparative genomics highlight the importance of lineage-specific gene families in evolutionary divergence of the coral genus, montipora,” BMC Ecology and Evolution, vol. 22, no. 1, pp. 1–16, 2022S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of molecular biology, vol. 215, no. 3, pp. 403–410, 1990.W. J. Kent, “The blast-like alignment tool,” Genome research, vol. 12, no. 4, pp. 656–664, 2002.A. Moya, L. Huisman, E. Ball, D. Hayward, L. Grasso, C. Chua, H. Woo, J.-P. Gattuso, S. Foret, and D. J. Miller, “Whole transcriptome analysis of the coral acropora millepora reveals complex responses to co2-driven acidification during the initiation of calcification,” Molecular ecology, vol. 21, no. 10, pp. 2440–2454, 2012.D. Charif, J. R. Lobry, A. Necsulea, L. Palmeira, S. Penel, G. Perriere, and M. S. Penel, “Package ‘seqinr’,” 2022.H. Pages, P. Aboyoun, R. Gentleman, S. DebRoy, M. H. Pages, D. DataImport, S. BSgenome, R. XStringSet-class, R. MaskedXString-class, and R. XStringSet-io, “Package ‘biostrings’,” R, 2013.E. Neuwirth and M. E. Neuwirth, “Package ‘rcolorbrewer’,” ColorBrewer Palettes, 2014.H. Wickham, M. H. Wickham, and I. RColorBrewer, “Package ‘scales’,” 2016.T. Mailund, “Manipulating data frames: dplyr,” in R Data Science Quick Reference, pp. 109–160, Springer, 2019.H. Wickham and M. H. Wickham, “Package ‘tidyr’,” Easily Tidy Data with spread and gather Functions, 2017.H. Wickham, W. Chang, and M. H. Wickham, “Package ‘ggplot2’,” Create elegant data visualisations using the grammar of graphics. Version, vol. 2, no. 1, pp. 1–189, 2016.Z. Gu, L. Gu, R. Eils, M. Schlesner, and B. Brors, “Circlize implements and enhances circular visualization in r,” Bioinformatics, vol. 30, no. 19, pp. 2811–2812, 2014.S. Han, Y. Liang, Q. Ma, Y. Xu, Y. Zhang, W. Du, C. Wang, and Y. Li, “Lncfinder: an integrated platform for long non-coding rna identification utilizing sequence intrinsic composition, structural information and physicochemical property,” Briefings in bioinformatics, vol. 20, no. 6, pp. 2009–2027, 2019.A. C. Darling, B. Mau, F. R. Blattner, and N. T. Perna, “Mauve: multiple alignment of conserved genomic sequence with rearrangements,” Genome research, vol. 14, no. 7, pp. 1394–1403, 2004R. Achawanantakun, J. Chen, Y. Sun, and Y. Zhang, “Lncrna-id: Long non-coding rna identification using balanced random forests,” Bioinformatics, vol. 31, no. 24, pp. 3897– 3905, 2015.Y. Liu, X. Liao, T. Han, A. Su, Z. Guo, N. Lu, C. He, and Z. Lu, “Full-length transcriptome sequencing of the scleractinian coral montipora foliosa reveals the gene expression profile of coral–zooxanthellae holobiont,” Biology, vol. 10, no. 12, p. 1274, 2021.C. Shinzato, E. Shoguchi, T. Kawashima, M. Hamada, K. Hisata, M. Tanaka, M. Fujie, M. Fujiwara, R. Koyanagi, T. Ikuta, A. Fujiyama, D. J. Miller, and N. Satoh, “Using the Acropora digitifera genome to understand coral responses to environmental change,” Nature, vol. 476, no. 7360, pp. 320–323, 2011.C. Shinzato, K. Khalturin, J. Inoue, Y. Zayasu, M. Kanda, M. Kawamitsu, Y. Yoshioka, H. Yamashita, G. Suzuki, and N. Satoh, “Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes,” Molecular Biology and Evolution, vol. 38, no. 1, pp. 16–30, 2021.C. P. Ponting, “The functional repertoires of metazoan genomes,” Nature Reviews Genetics, vol. 9, no. 9, pp. 689–698, 2008.N. H. Putnam, M. Srivastava, U. Hellsten, B. Dirks, J. Chapman, A. Salamov, A. Terry, H. Shapiro, E. Lindquist, V. V. Kapitonov, et al., “Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization,” science, vol. 317, no. 5834, pp. 86–94, 2007.J. A. Chapman, E. F. Kirkness, O. Simakov, S. E. Hampson, T. Mitros, T. Weinmaier, T. Rattei, P. G. Balasubramanian, J. Borman, D. Busam, et al., “The dynamic genome of hydra,” Nature, vol. 464, no. 7288, pp. 592–596, 2010.C. R. Voolstra, Y. Li, Y. J. Liew, S. Baumgarten, D. Zoccola, J.-F. Flot, S. Tambutt´e, D. Allemand, and M. Aranda, “Comparative analysis of the genomes of stylophora pistillata and acropora digitifera provides evidence for extensive differences between species of corals,” Scientific reports, vol. 7, no. 1, pp. 1–14, 2017.E. Rivas, J. Clements, and S. R. Eddy, “A statistical test for conserved rna structure shows lack of evidence for structure in lncrnas,” Nature methods, vol. 14, no. 1, pp. 45– 48, 2017.K. Khalturin, C. Shinzato, M. Khalturina, M. Hamada, M. Fujie, R. Koyanagi, M. Kanda, H. Goto, F. Anton-Erxleben, M. Toyokawa, et al., “Medusozoan genomes inform the evolution of the jellyfish body plan,” Nature Ecology & Evolution, vol. 3, no. 5, pp. 811–822, 2019.O. R. Salazar, P. N. Arun, G. Cui, L. K. Bay, M. J. van Oppen, N. S. Webster, and M. Aranda, “The coral acropora loripes genome reveals an alternative pathway for cysteine biosynthesis in animals,” Science advances, vol. 8, no. 38, p. eabq0304, 2022.Y. Zhang, H. Huang, D. Zhang, J. Qiu, J. Yang, K. Wang, L. Zhu, J. Fan, and J. Yang, “A review on recent computational methods for predicting noncoding rnas,” BioMed research international, vol. 2017, 2017.F. Salabi, H. Jafari, S. Navidpour, and A. S. Sadr, “Systematic and computational identification of androctonus crassicauda long non-coding rnas,” Scientific reports, vol. 11, no. 1, pp. 1–14, 2021.V. Maracaja-Coutinho, A. R. Paschoal, J. C. Caris-Maldonado, P. V. Borges, A. J. Ferreira, and A. M. Durham, “Noncoding rnas databases: current status and trends,” Computational Biology of Non-Coding RNA, pp. 251–285, 2019.H. Ma, Y. Hao, X. Dong, Q. Gong, J. Chen, J. Zhang, and W. Tian, “Molecular mechanisms and function prediction of long noncoding rna,” The Scientific World Journal, vol. 2012, 2012.J. T. Low and K. M. Weeks, “Shape-directed rna secondary structure prediction,” Methods, vol. 52, no. 2, pp. 150–158, 2010.S. Washietl, I. L. Hofacker, and P. F. Stadler, “Fast and reliable prediction of noncoding rnas,” Proceedings of the National Academy of Sciences, vol. 102, no. 7, pp. 2454–2459, 2005.A. R. Gruber, S. Findeiß, S. Washietl, I. L. Hofacker, and P. F. Stadler, “Rnaz 2.0: improved noncoding rna detection,” in Biocomputing 2010, pp. 69–79, World Scientific, 2010.I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, and P. Schuster, “Fast folding and comparison of rna secondary structures,” Monatshefte f¨ur Chemie/Chemical Monthly, vol. 125, no. 2, pp. 167–188, 1994.L. Fontana, L. Partridge, and V. D. Longo, “Extending healthy life span from yeast to humans,” science, vol. 328, no. 5976, pp. 321–326, 2010.J.-H. Yoon, K. Abdelmohsen, and M. Gorospe, “Posttranscriptional gene regulation by long noncoding rna,” Journal of molecular biology, vol. 425, no. 19, pp. 3723–3730, 2013.S. Sweta, T. Dudnakova, S. Sudheer, A. H. Baker, and R. Bhushan, “Importance of long non-coding rnas in the development and disease of skeletal muscle and cardiovascular lineages,” Frontiers in Cell and Developmental Biology, vol. 7, p. 228, 2019.J. Harrow, A. Frankish, J. M. Gonzalez, E. Tapanari, M. Diekhans, F. Kokocinski, B. L. Aken, D. Barrell, A. Zadissa, S. Searle, et al., “Gencode: the reference human genome annotation for the encode project,” Genome research, vol. 22, no. 9, pp. 1760–1774, 2012.T. Derrien, R. Johnson, G. Bussotti, A. Tanzer, S. Djebali, H. Tilgner, G. Guernec, D. Martin, A. Merkel, D. G. Knowles, et al., “The gencode v7 catalog of human long noncoding rnas: analysis of their gene structure, evolution, and expression,” Genome research, vol. 22, no. 9, pp. 1775–1789, 2012.H. Naora and D. J. Montell, “Ovarian cancer metastasis: integrating insights from disparate model organisms,” Nature reviews cancer, vol. 5, no. 5, pp. 355–366, 2005.M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. Mcgettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson, and D. G. Higgins, “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007R. Lorenz, S. H. Bernhart, C. H¨oner zu Siederdissen, H. Tafer, C. Flamm, P. F. Stadler, and I. L. Hofacker, “Viennarna package 2.0,” Algorithms for molecular biology, vol. 6, pp. 1–14, 2011.F. Li, Q. Zheng, P. Ryvkin, I. Dragomir, Y. Desai, S. Aiyer, O. Valladares, J. Yang, S. Bambina, L. R. Sabin, et al., “Global analysis of rna secondary structure in two metazoans,” Cell reports, vol. 1, no. 1, pp. 69–82, 2012.D. H. Mathews, D. H. Turner, and M. Zuker, “Rna secondary structure prediction,” Current protocols in nucleic acid chemistry, vol. 28, no. 1, pp. 11–2, 2007.K. A. Leamy, S. M. Assmann, D. H. Mathews, and P. C. Bevilacqua, “Bridging the gap between in vitro and in vivo rna folding,” Quarterly reviews of biophysics, vol. 49, p. e10, 2016.LICENSElicense.txtlicense.txttext/plain; charset=utf-85879https://repositorio.unal.edu.co/bitstream/unal/84620/3/license.txteb34b1cf90b7e1103fc9dfd26be24b4aMD53ORIGINAL3957420077.2023.pdf3957420077.2023.pdfTesis de Maestría en Ciencias - Biologíaapplication/pdf2594749https://repositorio.unal.edu.co/bitstream/unal/84620/4/3957420077.2023.pdf331c0c9bdaef2a69013c1647465313faMD54THUMBNAIL3957420077.2023.pdf.jpg3957420077.2023.pdf.jpgGenerated Thumbnailimage/jpeg3917https://repositorio.unal.edu.co/bitstream/unal/84620/5/3957420077.2023.pdf.jpg5c6dcefb3630bdf0578e67f5e2822bceMD55unal/84620oai:repositorio.unal.edu.co:unal/846202024-08-05 23:10:24.272Repositorio Institucional Universidad Nacional de Colombiarepositorio_nal@unal.edu.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

Entendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitifera

Publicaciones similares