Characterization of antimicrobial peptides in anuran genomes through orthologs and phylogenetic analysis

Antimicrobial peptides (AMPs) are vital components of the innate immune system, with cathelicidins standing out due to their broad-spectrum antimicrobial properties. This study explores the diversity and molecular evolution of cathelicidins across 27 anuran species, spanning 13 families. Utilizing d...

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Autores:
Dix Polo, Juliana
Tipo de recurso:
Trabajo de grado de pregrado
Fecha de publicación:
2024
Institución:
Universidad de los Andes
Repositorio:
Séneca: repositorio Uniandes
Idioma:
eng
OAI Identifier:
oai:repositorio.uniandes.edu.co:1992/74998
Acceso en línea:
https://hdl.handle.net/1992/74998
Palabra clave:
Anuran phylogeny
Cathelicidins
Antimicrobial peptides
Gene duplication
Phylogenetic diversification
Immune defense
Biología
Rights
openAccess
License
Attribution-NonCommercial-NoDerivatives 4.0 International
id UNIANDES2_5d60266a52ad8bd49f89b1d0417dbced
oai_identifier_str oai:repositorio.uniandes.edu.co:1992/74998
network_acronym_str UNIANDES2
network_name_str Séneca: repositorio Uniandes
repository_id_str
dc.title.eng.fl_str_mv Characterization of antimicrobial peptides in anuran genomes through orthologs and phylogenetic analysis
title Characterization of antimicrobial peptides in anuran genomes through orthologs and phylogenetic analysis
spellingShingle Characterization of antimicrobial peptides in anuran genomes through orthologs and phylogenetic analysis
Anuran phylogeny
Cathelicidins
Antimicrobial peptides
Gene duplication
Phylogenetic diversification
Immune defense
Biología
title_short Characterization of antimicrobial peptides in anuran genomes through orthologs and phylogenetic analysis
title_full Characterization of antimicrobial peptides in anuran genomes through orthologs and phylogenetic analysis
title_fullStr Characterization of antimicrobial peptides in anuran genomes through orthologs and phylogenetic analysis
title_full_unstemmed Characterization of antimicrobial peptides in anuran genomes through orthologs and phylogenetic analysis
title_sort Characterization of antimicrobial peptides in anuran genomes through orthologs and phylogenetic analysis
dc.creator.fl_str_mv Dix Polo, Juliana
dc.contributor.advisor.none.fl_str_mv Crawford, Andrew Jackson
dc.contributor.author.none.fl_str_mv Dix Polo, Juliana
dc.subject.keyword.eng.fl_str_mv Anuran phylogeny
Cathelicidins
Antimicrobial peptides
Gene duplication
Phylogenetic diversification
Immune defense
topic Anuran phylogeny
Cathelicidins
Antimicrobial peptides
Gene duplication
Phylogenetic diversification
Immune defense
Biología
dc.subject.themes.spa.fl_str_mv Biología
description Antimicrobial peptides (AMPs) are vital components of the innate immune system, with cathelicidins standing out due to their broad-spectrum antimicrobial properties. This study explores the diversity and molecular evolution of cathelicidins across 27 anuran species, spanning 13 families. Utilizing data from extensive genomic initiatives like the Vertebrate Genomes Project (VGP), 187 cathelicidin-like sequences within a single orthogroup were identified , highlighting significant gene duplication events that have driven the diversification of this gene family. Also, phylogenetic analyses, supported by both maximum likelihood and Bayesian inference methods, indicate that cathelicidins have evolved under intense evolutionary pressures, leading to diversification that may enhance anurans' ability to combat pathogens. The study underscores the value of large-scale genomic projects in providing the high-quality data necessary for in-depth evolutionary research. Future directions should include the functional characterization of these peptides, further species inclusion, and experimental validation of conserved domains to deepen our understanding of their roles in immune defense.
publishDate 2024
dc.date.accessioned.none.fl_str_mv 2024-08-05T19:16:46Z
dc.date.available.none.fl_str_mv 2024-08-05T19:16:46Z
dc.date.issued.none.fl_str_mv 2024-08-02
dc.type.none.fl_str_mv Trabajo de grado - Pregrado
dc.type.driver.none.fl_str_mv info:eu-repo/semantics/bachelorThesis
dc.type.version.none.fl_str_mv info:eu-repo/semantics/acceptedVersion
dc.type.coar.none.fl_str_mv http://purl.org/coar/resource_type/c_7a1f
dc.type.content.none.fl_str_mv Text
dc.type.redcol.none.fl_str_mv http://purl.org/redcol/resource_type/TP
format http://purl.org/coar/resource_type/c_7a1f
status_str acceptedVersion
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/1992/74998
dc.identifier.instname.none.fl_str_mv instname:Universidad de los Andes
dc.identifier.reponame.none.fl_str_mv reponame:Repositorio Institucional Séneca
dc.identifier.repourl.none.fl_str_mv repourl:https://repositorio.uniandes.edu.co/
url https://hdl.handle.net/1992/74998
identifier_str_mv instname:Universidad de los Andes
reponame:Repositorio Institucional Séneca
repourl:https://repositorio.uniandes.edu.co/
dc.language.iso.none.fl_str_mv eng
language eng
dc.relation.references.none.fl_str_mv Duellman, W. E. & Trueb, L. Biology of Amphibians. (JHU Press, 1994).
Zweifel, R. G. Encyclopedia of Reptiles & Amphibians. (Academic Press, 1998).
Benítez-Prián, M. et al. Diversity and Molecular Evolution of Antimicrobial Peptides in Caecilian Amphibians. Toxins 16, 150 (2024).
Ling, G. et al. Cathelicidins from the Bullfrog Rana catesbeiana Provides Novel Template for Peptide Antibiotic Design. PLOS ONE 9, e93216 (2014).
Hancock, R. E. W., Haney, E. F. & Gill, E. E. The immunology of host defence peptides: beyond antimicrobial activity. Nat Rev Immunol 16, 321–334 (2016).
Rollins-Smith, L. A. The importance of antimicrobial peptides (AMPs) in amphibian skin defense. Developmental & Comparative Immunology 142, 104657 (2023).
Hao, X. et al. Amphibian cathelicidin fills the evolutionary gap of cathelicidin in vertebrate. Amino Acids 43, 677–685 (2012).
Nguyen, L. T., Haney, E. F. & Vogel, H. J. The expanding scope of antimicrobial peptide structures and their modes of action. Trends in Biotechnology 29, 464–472 (2011).
Soltaninejad, H. et al. Antimicrobial Peptides from Amphibian Innate Immune System as Potent Antidiabetic Agents: A Literature Review and Bioinformatics Analysis. Journal of Diabetes Research 2021, e2894722 (2021).
Mu, L. et al. The first identified cathelicidin from tree frogs possesses anti-inflammatory and partial LPS neutralization activities. Amino Acids 49, 1571–1585 (2017).
Huang, N. et al. Pyramiding of bacterial blight resistance genes in rice: marker-assisted selection using RFLP and PCR. Theor Appl Genet 95, 313–320 (1997).
Nell, M. J. et al. Development of novel LL-37 derived antimicrobial peptides with LPS and LTA neutralizing and antimicrobial activities for therapeutic application. Peptides 27, 649–660 (2006).
Koczulla, R. et al. An angiogenic role for the human peptide antibiotic LL-37/hCAP-18. J Clin Invest 111, 1665–1672 (2003).
Steinstraesser, L. et al. Host Defense Peptides in Wound Healing. Mol Med 14, 528–537 (2008).
Sang, Y. et al. Canine cathelicidin (K9CATH): Gene cloning, expression, and biochemical activity of a novel pro-myeloid antimicrobial peptide. Developmental & Comparative Immunology 31, 1278–1296 (2007).
Yu, H. et al. Identification and polymorphism discovery of the cathelicidins, Lf-CATHs in ranid amphibian (Limnonectes fragilis). The FEBS Journal 280, 6022–6032 (2013).
Zanetti, M. Cathelicidins, multifunctional peptides of the innate immunity. Journal of Leukocyte Biology 75, 39–48 (2004).
Lewin, H. A. et al. Earth BioGenome Project: Sequencing life for the future of life. Proceedings of the National Academy of Sciences 115, 4325–4333 (2018).
Paez, S. et al. Reference genomes for conservation. Science 377, 364–366 (2022).
Portik, D. M., Streicher, J. W. & Wiens, J. J. Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species. Molecular Phylogenetics and Evolution 188, 107907 (2023).
Womack, M. C. & Bell, R. C. Two-hundred million years of anuran body-size evolution in relation to geography, ecology and life history. Journal of Evolutionary Biology 33, 1417–1432 (2020).
Blackburn, D. C. & Wake, D. B. Class Amphibia Gray, 1825. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classi­fication and survey of taxonomic richness. Zootaxa 3148, (2011).
de Queiroz, K. & Gauthier, J. Phylogeny as a Central Principle in Taxonomy: Phylogenetic Definitions of Taxon Names. Systematic Biology 39, 307–322 (1990).
Duellman, W. E. & Trueb, L. Biology of Amphibians. (McGraw-Hill, New York, 670 pp, 1986).
Faivovitch, J. et al. Systematic review of the frog family Hylidae, with special reference to Hylinae: phylogenetic analysis and taxonomic revision. Bull Amer Mus Nat Hist 294, 1–240 (2005).
Amphibian Species of the World. A Taxonomic and Geographical Reference. Allen Press and Association of Systematics Collections, Lawrence, Kansas 732 pp, (1985).
Frost, D. R. et al. The Amphibian Tree of Life. Bull Amer Mus Nat Hist 297, 1–370 (2006).
Pyron, A. & Wiens, J. J. A large-scale phylogeny of Amphibia with over 2,800 species, and a revised classification of extant frogs, salamanders, and caecilians. Mol Phy Evol 61, 543–583 (2011).
Bickham, J. et al. Turtle taxonomy: methodology, recommendations, and guidelines. in Defining turtle diversity: Proceedings of a workshop on genetics, ethics, and taxonomy of freshwater turtles and tortoises. Chelonian Research Monographs, 4. Lunenburg (eds. Shaffer, H. B., FitzSimmons, N. N., Georges, A. & Agj, R.) 73–84 (Chelonian Research Foundation, MA), 2007).
Qi, R.-H. et al. Identification and characterization of two novel cathelicidins from the frog Odorrana livida. Zool Res 40, 94–101 (2019).
Emms, D. M. & Kelly, S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology 16, 157 (2015).
Emms, D. davidemms/OrthoFinder. (2024).
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20, 238 (2019).
Madeira, F. et al. The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024. Nucleic Acids Research gkae241 (2024) doi:10.1093/nar/gkae241.
Wang, X., Duan, H., Li, M., Xu, W. & Wei, L. Characterization and mechanism of action of amphibian-derived wound-healing-promoting peptides. Front. Cell Dev. Biol. 11, (2023).
Lu, S. et al. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res 48, D265–D268 (2020).
Marchler-Bauer, A. et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res 45, D200–D203 (2017).
Zanetti, M. The Role of Cathelicidins in the Innate Host Defenses of Mammals. Current Issues in Molecular Biology 7, 179–196 (2005).
Hughes, A. L. & Friedman, R. Gene Duplication and the Properties of Biological Networks. J Mol Evol 61, 758–764 (2005).
Zelezetsky, I. et al. Evolution of the primate cathelicidin. Correlation between structural variations and antimicrobial activity. J Biol Chem 281, 19861–19871 (2006).
Efron, B., Halloran, E. & Holmes, S. Bootstrap confidence levels for phylogenetic trees. Proceedings of the National Academy of Sciences 93, 13429–13429 (1996).
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Molecular Biology and Evolution 32, 268–274 (2015).
Pamilo, P. & Nei, M. Relationships between gene trees and species trees. Molecular Biology and Evolution 5, 568–583 (1988).
Swenson, K. M. & El-Mabrouk, N. Gene trees and species trees: irreconcilable differences. BMC Bioinformatics 13, S15 (2012).
Wei, L. et al. Structure and function of a potent lipopolysaccharide-binding antimicrobial and anti-inflammatory peptide. J Med Chem 56, 3546–3556 (2013).
Roelants, K. et al. Global patterns of diversification in the history of modern amphibians. Proceedings of the National Academy of Sciences 104, 887–892 (2007).
Lu, B. Evolutionary Insights into the Relationship of Frogs, Salamanders, and Caecilians and Their Adaptive Traits, with an Emphasis on Salamander Regeneration and Longevity. Animals (Basel) 13, 3449 (2023).
Tennessen, J. A. Molecular evolution of animal antimicrobial peptides: widespread moderate positive selection. J Evol Biol 18, 1387–1394 (2005).
Koonin, E. V. & Novozhilov, A. S. Origin and evolution of the genetic code: the universal enigma. IUBMB Life 61, 99–111 (2009).
Ohno, S. Duplication for the Sake of Producing More of the Same. in Evolution by Gene Duplication (ed. Ohno, S.) 59–65 (Springer, Berlin, Heidelberg, 1970). doi:10.1007/978-3-642-86659-3_11.
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spelling Crawford, Andrew Jacksonvirtual::19790-1Dix Polo, Juliana2024-08-05T19:16:46Z2024-08-05T19:16:46Z2024-08-02https://hdl.handle.net/1992/74998instname:Universidad de los Andesreponame:Repositorio Institucional Sénecarepourl:https://repositorio.uniandes.edu.co/Antimicrobial peptides (AMPs) are vital components of the innate immune system, with cathelicidins standing out due to their broad-spectrum antimicrobial properties. This study explores the diversity and molecular evolution of cathelicidins across 27 anuran species, spanning 13 families. Utilizing data from extensive genomic initiatives like the Vertebrate Genomes Project (VGP), 187 cathelicidin-like sequences within a single orthogroup were identified , highlighting significant gene duplication events that have driven the diversification of this gene family. Also, phylogenetic analyses, supported by both maximum likelihood and Bayesian inference methods, indicate that cathelicidins have evolved under intense evolutionary pressures, leading to diversification that may enhance anurans' ability to combat pathogens. The study underscores the value of large-scale genomic projects in providing the high-quality data necessary for in-depth evolutionary research. Future directions should include the functional characterization of these peptides, further species inclusion, and experimental validation of conserved domains to deepen our understanding of their roles in immune defense.PregradoBioinformatics26 páginasapplication/pdfengUniversidad de los AndesBiologíaFacultad de CienciasDepartamento de Ciencias BiológicasAttribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Characterization of antimicrobial peptides in anuran genomes through orthologs and phylogenetic analysisTrabajo de grado - Pregradoinfo:eu-repo/semantics/bachelorThesisinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_7a1fTexthttp://purl.org/redcol/resource_type/TPAnuran phylogenyCathelicidinsAntimicrobial peptidesGene duplicationPhylogenetic diversificationImmune defenseBiologíaDuellman, W. E. & Trueb, L. Biology of Amphibians. (JHU Press, 1994).Zweifel, R. G. Encyclopedia of Reptiles & Amphibians. (Academic Press, 1998).Benítez-Prián, M. et al. Diversity and Molecular Evolution of Antimicrobial Peptides in Caecilian Amphibians. Toxins 16, 150 (2024).Ling, G. et al. Cathelicidins from the Bullfrog Rana catesbeiana Provides Novel Template for Peptide Antibiotic Design. PLOS ONE 9, e93216 (2014).Hancock, R. E. W., Haney, E. F. & Gill, E. E. The immunology of host defence peptides: beyond antimicrobial activity. Nat Rev Immunol 16, 321–334 (2016).Rollins-Smith, L. A. The importance of antimicrobial peptides (AMPs) in amphibian skin defense. Developmental & Comparative Immunology 142, 104657 (2023).Hao, X. et al. Amphibian cathelicidin fills the evolutionary gap of cathelicidin in vertebrate. Amino Acids 43, 677–685 (2012).Nguyen, L. T., Haney, E. F. & Vogel, H. J. The expanding scope of antimicrobial peptide structures and their modes of action. Trends in Biotechnology 29, 464–472 (2011).Soltaninejad, H. et al. Antimicrobial Peptides from Amphibian Innate Immune System as Potent Antidiabetic Agents: A Literature Review and Bioinformatics Analysis. Journal of Diabetes Research 2021, e2894722 (2021).Mu, L. et al. The first identified cathelicidin from tree frogs possesses anti-inflammatory and partial LPS neutralization activities. Amino Acids 49, 1571–1585 (2017).Huang, N. et al. Pyramiding of bacterial blight resistance genes in rice: marker-assisted selection using RFLP and PCR. Theor Appl Genet 95, 313–320 (1997).Nell, M. J. et al. Development of novel LL-37 derived antimicrobial peptides with LPS and LTA neutralizing and antimicrobial activities for therapeutic application. Peptides 27, 649–660 (2006).Koczulla, R. et al. An angiogenic role for the human peptide antibiotic LL-37/hCAP-18. J Clin Invest 111, 1665–1672 (2003).Steinstraesser, L. et al. Host Defense Peptides in Wound Healing. Mol Med 14, 528–537 (2008).Sang, Y. et al. Canine cathelicidin (K9CATH): Gene cloning, expression, and biochemical activity of a novel pro-myeloid antimicrobial peptide. Developmental & Comparative Immunology 31, 1278–1296 (2007).Yu, H. et al. Identification and polymorphism discovery of the cathelicidins, Lf-CATHs in ranid amphibian (Limnonectes fragilis). The FEBS Journal 280, 6022–6032 (2013).Zanetti, M. Cathelicidins, multifunctional peptides of the innate immunity. Journal of Leukocyte Biology 75, 39–48 (2004).Lewin, H. A. et al. Earth BioGenome Project: Sequencing life for the future of life. Proceedings of the National Academy of Sciences 115, 4325–4333 (2018).Paez, S. et al. Reference genomes for conservation. Science 377, 364–366 (2022).Portik, D. M., Streicher, J. W. & Wiens, J. J. Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species. Molecular Phylogenetics and Evolution 188, 107907 (2023).Womack, M. C. & Bell, R. C. Two-hundred million years of anuran body-size evolution in relation to geography, ecology and life history. Journal of Evolutionary Biology 33, 1417–1432 (2020).Blackburn, D. C. & Wake, D. B. Class Amphibia Gray, 1825. In: Zhang, Z.-Q. (Ed.) Animal biodiversity: An outline of higher-level classi­fication and survey of taxonomic richness. Zootaxa 3148, (2011).de Queiroz, K. & Gauthier, J. Phylogeny as a Central Principle in Taxonomy: Phylogenetic Definitions of Taxon Names. Systematic Biology 39, 307–322 (1990).Duellman, W. E. & Trueb, L. Biology of Amphibians. (McGraw-Hill, New York, 670 pp, 1986).Faivovitch, J. et al. Systematic review of the frog family Hylidae, with special reference to Hylinae: phylogenetic analysis and taxonomic revision. Bull Amer Mus Nat Hist 294, 1–240 (2005).Amphibian Species of the World. A Taxonomic and Geographical Reference. Allen Press and Association of Systematics Collections, Lawrence, Kansas 732 pp, (1985).Frost, D. R. et al. The Amphibian Tree of Life. Bull Amer Mus Nat Hist 297, 1–370 (2006).Pyron, A. & Wiens, J. J. A large-scale phylogeny of Amphibia with over 2,800 species, and a revised classification of extant frogs, salamanders, and caecilians. Mol Phy Evol 61, 543–583 (2011).Bickham, J. et al. Turtle taxonomy: methodology, recommendations, and guidelines. in Defining turtle diversity: Proceedings of a workshop on genetics, ethics, and taxonomy of freshwater turtles and tortoises. Chelonian Research Monographs, 4. Lunenburg (eds. Shaffer, H. B., FitzSimmons, N. N., Georges, A. & Agj, R.) 73–84 (Chelonian Research Foundation, MA), 2007).Qi, R.-H. et al. Identification and characterization of two novel cathelicidins from the frog Odorrana livida. Zool Res 40, 94–101 (2019).Emms, D. M. & Kelly, S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology 16, 157 (2015).Emms, D. davidemms/OrthoFinder. (2024).Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20, 238 (2019).Madeira, F. et al. The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024. Nucleic Acids Research gkae241 (2024) doi:10.1093/nar/gkae241.Wang, X., Duan, H., Li, M., Xu, W. & Wei, L. Characterization and mechanism of action of amphibian-derived wound-healing-promoting peptides. Front. Cell Dev. Biol. 11, (2023).Lu, S. et al. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res 48, D265–D268 (2020).Marchler-Bauer, A. et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res 45, D200–D203 (2017).Zanetti, M. The Role of Cathelicidins in the Innate Host Defenses of Mammals. Current Issues in Molecular Biology 7, 179–196 (2005).Hughes, A. L. & Friedman, R. Gene Duplication and the Properties of Biological Networks. J Mol Evol 61, 758–764 (2005).Zelezetsky, I. et al. Evolution of the primate cathelicidin. Correlation between structural variations and antimicrobial activity. J Biol Chem 281, 19861–19871 (2006).Efron, B., Halloran, E. & Holmes, S. Bootstrap confidence levels for phylogenetic trees. Proceedings of the National Academy of Sciences 93, 13429–13429 (1996).Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Molecular Biology and Evolution 32, 268–274 (2015).Pamilo, P. & Nei, M. Relationships between gene trees and species trees. Molecular Biology and Evolution 5, 568–583 (1988).Swenson, K. M. & El-Mabrouk, N. Gene trees and species trees: irreconcilable differences. BMC Bioinformatics 13, S15 (2012).Wei, L. et al. Structure and function of a potent lipopolysaccharide-binding antimicrobial and anti-inflammatory peptide. J Med Chem 56, 3546–3556 (2013).Roelants, K. et al. Global patterns of diversification in the history of modern amphibians. Proceedings of the National Academy of Sciences 104, 887–892 (2007).Lu, B. Evolutionary Insights into the Relationship of Frogs, Salamanders, and Caecilians and Their Adaptive Traits, with an Emphasis on Salamander Regeneration and Longevity. Animals (Basel) 13, 3449 (2023).Tennessen, J. A. Molecular evolution of animal antimicrobial peptides: widespread moderate positive selection. J Evol Biol 18, 1387–1394 (2005).Koonin, E. V. & Novozhilov, A. S. Origin and evolution of the genetic code: the universal enigma. IUBMB Life 61, 99–111 (2009).Ohno, S. Duplication for the Sake of Producing More of the Same. in Evolution by Gene Duplication (ed. 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