Ensamblaje del genoma de Leuconostoc mesenteroides IBUN 91.2.98. por medio de herramientas bioinformáticas
ilustraciones
- Autores:
-
Núñez Campos, César Augusto
- Tipo de recurso:
- Fecha de publicación:
- 2022
- Institución:
- Universidad Nacional de Colombia
- Repositorio:
- Universidad Nacional de Colombia
- Idioma:
- spa
- OAI Identifier:
- oai:repositorio.unal.edu.co:unal/83760
- Palabra clave:
- 000 - Ciencias de la computación, información y obras generales
500 - Ciencias naturales y matemáticas
520 - Astronomía y ciencias afines
Genoma
Tecnología de bajo costo
Genome
Low Cost Technology
reads
contigs
ensamblaje
tecnologías de secuenciación
traducción
- Rights
- openAccess
- License
- Reconocimiento 4.0 Internacional
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Ensamblaje del genoma de Leuconostoc mesenteroides IBUN 91.2.98. por medio de herramientas bioinformáticas |
| dc.title.translated.eng.fl_str_mv |
Assembly of the genome of Leuconostoc mesenteroides IBUN 91.2.98. through bioinformatics tools |
| title |
Ensamblaje del genoma de Leuconostoc mesenteroides IBUN 91.2.98. por medio de herramientas bioinformáticas |
| spellingShingle |
Ensamblaje del genoma de Leuconostoc mesenteroides IBUN 91.2.98. por medio de herramientas bioinformáticas 000 - Ciencias de la computación, información y obras generales 500 - Ciencias naturales y matemáticas 520 - Astronomía y ciencias afines Genoma Tecnología de bajo costo Genome Low Cost Technology reads contigs ensamblaje tecnologías de secuenciación traducción |
| title_short |
Ensamblaje del genoma de Leuconostoc mesenteroides IBUN 91.2.98. por medio de herramientas bioinformáticas |
| title_full |
Ensamblaje del genoma de Leuconostoc mesenteroides IBUN 91.2.98. por medio de herramientas bioinformáticas |
| title_fullStr |
Ensamblaje del genoma de Leuconostoc mesenteroides IBUN 91.2.98. por medio de herramientas bioinformáticas |
| title_full_unstemmed |
Ensamblaje del genoma de Leuconostoc mesenteroides IBUN 91.2.98. por medio de herramientas bioinformáticas |
| title_sort |
Ensamblaje del genoma de Leuconostoc mesenteroides IBUN 91.2.98. por medio de herramientas bioinformáticas |
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Núñez Campos, César Augusto |
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Ospina Sánchez, Sonia Amparo |
| dc.contributor.author.none.fl_str_mv |
Núñez Campos, César Augusto |
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Biopolímeros y Biofuncionales |
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César Augusto Núñez Campos [0000000152190836] |
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Núñez Campos, César Augusto |
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000 - Ciencias de la computación, información y obras generales 500 - Ciencias naturales y matemáticas 520 - Astronomía y ciencias afines |
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000 - Ciencias de la computación, información y obras generales 500 - Ciencias naturales y matemáticas 520 - Astronomía y ciencias afines Genoma Tecnología de bajo costo Genome Low Cost Technology reads contigs ensamblaje tecnologías de secuenciación traducción |
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Genoma Tecnología de bajo costo |
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Genome Low Cost Technology |
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reads contigs |
| dc.subject.proposal.spa.fl_str_mv |
ensamblaje tecnologías de secuenciación traducción |
| description |
ilustraciones |
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2022 |
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2022-10-07 |
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2023-04-24T13:54:41Z |
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2023-04-24T13:54:41Z |
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Trabajo de grado - Maestría |
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info:eu-repo/semantics/masterThesis |
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info:eu-repo/semantics/acceptedVersion |
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Text |
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http://purl.org/redcol/resource_type/TM |
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https://repositorio.unal.edu.co/handle/unal/83760 |
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Universidad Nacional de Colombia |
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Repositorio Institucional Universidad Nacional de Colombia |
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https://repositorio.unal.edu.co/ |
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spa |
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M. N. Ruiz, “Bioinformática: Conceptos y alcances en las fronteras de la ciencia,” p. 88, 2004. J. A. Valverde, “Anotación de genoma,” Conogasi, Conoc. para la vida, 2016. L. Brenes-Guillén, “Ensamblaje de genomas y anotación,” vol. 22, no. 3, p. 2013, 2013. S. González de la Fuente, “Ensamblaje de novo y anotación génica del genoma de Leishmania major mediante secuenciación masiva,” Uoc Univ. Oberta Catalunya, 2018, [Online]. Available: http://hdl.handle.net/10609/81889 M. Naessens, A. Cerdobbel, and W. Soetaert, “Leuconostoc dextransucrasa y dextrano : producción , propiedades y aplicaciones,” vol. 860, pp. 845–860, 2005. H. Neubauer, A. Bauché, and B. Mollet, “Molecular characterization and expression analysis of the dextransucrase DsrD of Leuconostoc mesenteroides Lcc4 in homologous and heterologous Lactococcus lactis cultures,” Microbiology, vol. 149, no. 4, pp. 973–982, 2003, doi: 10.1099/mic.0.26029-0. E. Díaz-Montes, J. Yáñez-Fernández, and R. Castro-Muñoz, “Microfiltration-mediated extraction of dextran produced by Leuconostoc mesenteroides SF3,” Food Bioprod. Process., vol. 119, pp. 317–328, 2020, doi: 10.1016/j.fbp.2019.11.017. G. S. Park, S. J. Hong, B. K. Jung, C. Lee, C. K. Park, and J. H. Shin, “The complete genome sequence of a lactic acid bacterium Leuconostoc mesenteroides ssp. dextranicum strain DSM 20484T,” J. Biotechnol., vol. 219, pp. 3–4, 2016, doi: 10.1016/j.jbiotec.2015.12.009. F. Chen, G. Huang, and H. Huang, “Preparation and application of dextran and its derivatives as carriers,” Int. J. Biol. Macromol., vol. 145, pp. 827–834, 2020, doi: 10.1016/j.ijbiomac.2019.11.151. V. Monchois, R. Willemot, and P. Monsan, “Glucansucrasas : mecanismo de acción y estructura ^ función relaciones,” vol. 23, 1999. M. Naessens, A. Cerdobbel, W. Soetaert, and E. J. Vandamme, “Leuconostoc dextransucrase and dextran: Production, properties and applications,” J. Chem. Technol. Biotechnol., vol. 80, no. 8, pp. 845–860, 2005, doi: 10.1002/jctb.1322. F. G. G. Yhon., “Estudio de la enzima dextransacarasa (DS) producida por Leuconostoc mesenteroides cepa IBUN 91.2.98.” Bogotá, p. 46, 2014. “Universidad de San Carlos de Guatemala Facultad de Ingeniería Escuela de Ingeniería Química EMMETT ECHEVERRÍA VALENZUELA ASESORADO POR M . Sc . ZENÓN MUCH SANTOS,” 2006. L. Alejandra and G. Galindo, “Caracterización molecular y funcional del gen codificante para la dextransacarasa de,” pp. 1–36, 2018. G. S. Park, S. J. Hong, B. K. Jung, C. Lee, C. K. Park, and J. H. Shin, “The complete genome sequence of a lactic acid bacterium Leuconostoc mesenteroides ssp. dextranicum strain DSM 20484T,” J. Biotechnol., vol. 219, pp. 3–4, 2016, doi: 10.1016/j.jbiotec.2015.12.009. B. H. Chun, K. H. Kim, H. H. Jeon, S. H. Lee, and C. O. Jeon, “Pan-genomic and transcriptomic analyses of Leuconostoc mesenteroides provide insights into its genomic and metabolic features and roles in kimchi fermentation,” Sci. Rep., vol. 7, no. 1, pp. 1–16, 2017, doi: 10.1038/s41598-017-12016-z. W. Ruppitsch et al., “Genetic diversity of leuconostoc mesenteroides isolates from traditional montenegrin brine cheese,” Microorganisms, vol. 9, no. 8, pp. 1–16, 2021, doi: 10.3390/microorganisms9081612. P. Zhang, P. Zhang, J. Wu, D. Tao, and R. Wu, “Effects of Leuconostoc mesenteroides on physicochemical and microbial succession characterization of soybean paste, Da-jiang,” Lwt, vol. 115, 2019, doi: 10.1016/j.lwt.2019.04.029. L. H. Deegan, P. D. Cotter, C. Hill, and P. Ross, “Bacteriocins: Biological tools for bio-preservation and shelf-life extension,” Int. Dairy J., vol. 16, no. 9, pp. 1058–1071, 2006, doi: 10.1016/j.idairyj.2005.10.026. N. A. Vega Castro and E. A. Reyes Montaño, “Introducción al análisis estructural de proteínas y glicoproteínas,” Introd. al análisis estructural proteínas y glicoproteínas, 2020, doi: 10.36385/fcbog-3-0. L. Liu et al., “Comparison of next-generation sequencing systems,” J. Biomed. Biotechnol., vol. 2012, 2012, doi: 10.1155/2012/251364. J. M. Heather and B. Chain, “The sequence of sequencers: The history of sequencing DNA,” Genomics, vol. 107, no. 1, pp. 1–8, 2016, doi: 10.1016/j.ygeno.2015.11.003. T. J. Treangen and S. L. Salzberg, “Repetitive DNA and next-generation sequencing: Computational challenges and solutions,” Nat. Rev. Genet., vol. 13, no. 1, pp. 36–46, 2012, doi: 10.1038/nrg3117. N. B. Larson, A. L. Oberg, A. A. Adjei, and L. Wang, “A Clinician’s Guide to Bioinformatics for Next-Generation Sequencing,” J. Thorac. Oncol., vol. 18, no. 2, pp. 143–157, 2023, doi: 10.1016/j.jtho.2022.11.006. L. J. Fennell et al., “Comparative analysis of Illumina Mouse Methylation BeadChip and reduced-representation bisulfite sequencing for routine DNA methylation analysis,” Cell Reports Methods, vol. 2, no. 11, p. 100323, 2022, doi: 10.1016/j.crmeth.2022.100323. Y. Guo et al., “Metagenomic next-generation sequencing to identify pathogens and cancer in lung biopsy tissue,” EBioMedicine, vol. 73, p. 103639, 2021, doi: 10.1016/j.ebiom.2021.103639. M. Yermagambetova, S. Abugalieva, Y. Turuspekov, and S. Almerekova, “Illumina sequencing data of the complete chloroplast genome of rare species Juniperus seravschanica (Cupressaceae) from Kazakhstan,” Data Br., vol. 46, p. 108866, 2023, doi: 10.1016/j.dib.2022.108866. T. Soni, R. Pandit, D. Blake, C. Joshi, and M. Joshi, “Comparative analysis of two next-generation sequencing platforms for analysis of antimicrobial resistance genes,” J. Glob. Antimicrob. Resist., vol. 31, pp. 167–174, 2022, doi: 10.1016/j.jgar.2022.08.017. Z. Liang et al., “Combined Illumina and Pacbio sequencing technology on transcriptome analysis reveals several key regulations during the early development of American shad (Alosa sapidissima),” Aquac. Reports, vol. 25, no. July, p. 101264, 2022, doi: 10.1016/j.aqrep.2022.101264. L. Aguilar-Bultet and L. Falquet, “Secuenciación y ensamblaje de novo de genomas bacterianos: una alternativa para el estudio de nuevos patógenos,” Rev. Salud Anim, vol. 37, no. 2, pp. 125–132, 2015. H. E. L. Lischer and K. K. Shimizu, “Reference-guided de novo assembly approach improves genome reconstruction for related species,” BMC Bioinformatics, vol. 18, no. 1, pp. 1–12, 2017, doi: 10.1186/s12859-017-1911-6. B. Wajid and E. Serpedin, “Review of General Algorithmic Features for Genome Assemblers for Next Generation Sequencers,” Genomics, Proteomics Bioinforma., vol. 10, no. 2, pp. 58–73, 2012, doi: 10.1016/j.gpb.2012.05.006. S. Andrews, “Index of projects fastqc help 3 - Analysis Modules,” 2010. M. J. Chaisson and G. Tesler, “Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): Application and theory,” BMC Bioinformatics, vol. 13, no. 1, 2012, doi: 10.1186/1471-2105-13-238. L. T. G. Navarrete, “Garcia Navarrete (2018) Estrategia computacional,” Universidad Nacional de Colombia. 2018. K. J. McKernan et al., “Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding,” Genome Res., vol. 19, no. 9, pp. 1527–1541, 2009, doi: 10.1101/gr.091868.109. M. Hernández, N. M. Quijada, D. Rodríguez-Lázaro, and J. M. Eiros, “Bioinformatics of next generation sequencing in clinical microbiology diagnosis,” Rev. Argent. Microbiol., vol. 52, no. 2, pp. 150–161, 2020, doi: 10.1016/j.ram.2019.06.003. N. Nagarajan and M. Pop, “Sequence assembly demystified,” Nat. Rev. Genet., vol. 14, no. 3, pp. 157–167, 2013, doi: 10.1038/nrg3367. S. Meader, L. D. W. Hillier, D. 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Reconocimiento 4.0 Internacionalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Ospina Sánchez, Sonia Amparo116924f4f0abca4647115a08c2e62940Núñez Campos, César Augusto7bf699b12602adaa313790f5aac21ba4Biopolímeros y BiofuncionalesCésar Augusto Núñez Campos [0000000152190836]Núñez Campos, César Augusto2023-04-24T13:54:41Z2023-04-24T13:54:41Z2022-10-07https://repositorio.unal.edu.co/handle/unal/83760Universidad Nacional de ColombiaRepositorio Institucional Universidad Nacional de Colombiahttps://repositorio.unal.edu.co/ilustracionesA pesar de la importancia del dextrano en varias aplicaciones industriales y la necesidad de masificar su producción, no se tiene muy documentado el mecanismo de expresión y regulación de las dextransacarasas en cepas productoras como el Leuconostoc mesenteroides cepa IBUN 91.2.98. El desarrollo de métodos de secuenciación de segunda generación y el uso de herramientas bioinformáticas permitirán secuenciar, ensamblar y evaluar genomas completos a un costo relativamente bajo guiados por un genoma de referencia de L. mesenteroides subsp. mesenteroides ATCC 8293, para ayudar al proceso de ensamblaje. La secuenciación produjo un total de 1.47 Gb de datos crudos, que después del trimming y control de calidad generaron 1,40 Gb (7.78 X de profundidad) que se usaron para el ensamblaje. Se obtuvo un ensamblaje para el Leuconostoc mesenteroides cepa IBUN 91.2.98 de una longitud de 2,064 Mpb. La longitud del ensamblaje represento el 85% del tamaño estimado del genoma de referencia de L. mesenteroides subsp. mesenteroides ATCC 8293. (Texto tomado de la fuente)Despite the importance of dextran in various industrial applications and the need to massify your production, the mechanism of expression and regulation of dextransucrases in producer strains such as Leuconostoc mesenteroides strain IBUN 91.2.98 has not been well documented. The development of second-generation sequencing methods and the use of bioinformatic tools will make it possible to sequence, assemble, and evaluate complete of genomes at relatively low cost guided by a reference genome of L. mesenteroides subsp. mesenteroides ATCC 8293, to help the assembly process. Sequencing produced a total of 1.47 Gb of raw data, which after trimming and quality control were generated 1.40 Gb (7.78 X deep) which was used for assembly. An assembly for Leuconostoc mesenteroides strain IBUN 91.2.98 with a length of 2,064 Mpb was obtained. The assembly length represented 85% of the estimated size of the reference genome of L. mesenteroides subsp. mesenteroides ATCC 8293.MaestríaMagíster en Ciencias - Química59 páginasapplication/pdfspaUniversidad Nacional de ColombiaBogotá - Ciencias - Maestría en Ciencias - QuímicaFacultad de CienciasBogotá,ColombiaUniversidad Nacional de Colombia - Sede Bogotá000 - Ciencias de la computación, información y obras generales500 - Ciencias naturales y matemáticas520 - Astronomía y ciencias afinesGenomaTecnología de bajo costoGenomeLow Cost Technologyreadscontigsensamblajetecnologías de secuenciacióntraducciónEnsamblaje del genoma de Leuconostoc mesenteroides IBUN 91.2.98. por medio de herramientas bioinformáticasAssembly of the genome of Leuconostoc mesenteroides IBUN 91.2.98. through bioinformatics toolsTrabajo de grado - Maestríainfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/acceptedVersionTexthttp://purl.org/redcol/resource_type/TMM. N. Ruiz, “Bioinformática: Conceptos y alcances en las fronteras de la ciencia,” p. 88, 2004.J. A. Valverde, “Anotación de genoma,” Conogasi, Conoc. para la vida, 2016.L. Brenes-Guillén, “Ensamblaje de genomas y anotación,” vol. 22, no. 3, p. 2013, 2013.S. González de la Fuente, “Ensamblaje de novo y anotación génica del genoma de Leishmania major mediante secuenciación masiva,” Uoc Univ. Oberta Catalunya, 2018, [Online]. Available: http://hdl.handle.net/10609/81889M. Naessens, A. Cerdobbel, and W. Soetaert, “Leuconostoc dextransucrasa y dextrano : producción , propiedades y aplicaciones,” vol. 860, pp. 845–860, 2005.H. Neubauer, A. Bauché, and B. Mollet, “Molecular characterization and expression analysis of the dextransucrase DsrD of Leuconostoc mesenteroides Lcc4 in homologous and heterologous Lactococcus lactis cultures,” Microbiology, vol. 149, no. 4, pp. 973–982, 2003, doi: 10.1099/mic.0.26029-0.E. Díaz-Montes, J. Yáñez-Fernández, and R. Castro-Muñoz, “Microfiltration-mediated extraction of dextran produced by Leuconostoc mesenteroides SF3,” Food Bioprod. Process., vol. 119, pp. 317–328, 2020, doi: 10.1016/j.fbp.2019.11.017.G. S. Park, S. J. Hong, B. K. Jung, C. Lee, C. K. Park, and J. H. Shin, “The complete genome sequence of a lactic acid bacterium Leuconostoc mesenteroides ssp. dextranicum strain DSM 20484T,” J. Biotechnol., vol. 219, pp. 3–4, 2016, doi: 10.1016/j.jbiotec.2015.12.009.F. Chen, G. Huang, and H. Huang, “Preparation and application of dextran and its derivatives as carriers,” Int. J. Biol. Macromol., vol. 145, pp. 827–834, 2020, doi: 10.1016/j.ijbiomac.2019.11.151.V. Monchois, R. Willemot, and P. Monsan, “Glucansucrasas : mecanismo de acción y estructura ^ función relaciones,” vol. 23, 1999.M. Naessens, A. Cerdobbel, W. Soetaert, and E. J. Vandamme, “Leuconostoc dextransucrase and dextran: Production, properties and applications,” J. Chem. Technol. Biotechnol., vol. 80, no. 8, pp. 845–860, 2005, doi: 10.1002/jctb.1322.F. G. G. Yhon., “Estudio de la enzima dextransacarasa (DS) producida por Leuconostoc mesenteroides cepa IBUN 91.2.98.” Bogotá, p. 46, 2014.“Universidad de San Carlos de Guatemala Facultad de Ingeniería Escuela de Ingeniería Química EMMETT ECHEVERRÍA VALENZUELA ASESORADO POR M . Sc . ZENÓN MUCH SANTOS,” 2006.L. Alejandra and G. Galindo, “Caracterización molecular y funcional del gen codificante para la dextransacarasa de,” pp. 1–36, 2018.G. S. Park, S. J. Hong, B. K. Jung, C. Lee, C. K. Park, and J. H. Shin, “The complete genome sequence of a lactic acid bacterium Leuconostoc mesenteroides ssp. dextranicum strain DSM 20484T,” J. Biotechnol., vol. 219, pp. 3–4, 2016, doi: 10.1016/j.jbiotec.2015.12.009.B. H. Chun, K. H. Kim, H. H. Jeon, S. H. Lee, and C. O. Jeon, “Pan-genomic and transcriptomic analyses of Leuconostoc mesenteroides provide insights into its genomic and metabolic features and roles in kimchi fermentation,” Sci. Rep., vol. 7, no. 1, pp. 1–16, 2017, doi: 10.1038/s41598-017-12016-z.W. Ruppitsch et al., “Genetic diversity of leuconostoc mesenteroides isolates from traditional montenegrin brine cheese,” Microorganisms, vol. 9, no. 8, pp. 1–16, 2021, doi: 10.3390/microorganisms9081612.P. Zhang, P. Zhang, J. Wu, D. Tao, and R. Wu, “Effects of Leuconostoc mesenteroides on physicochemical and microbial succession characterization of soybean paste, Da-jiang,” Lwt, vol. 115, 2019, doi: 10.1016/j.lwt.2019.04.029.L. H. Deegan, P. D. Cotter, C. Hill, and P. Ross, “Bacteriocins: Biological tools for bio-preservation and shelf-life extension,” Int. Dairy J., vol. 16, no. 9, pp. 1058–1071, 2006, doi: 10.1016/j.idairyj.2005.10.026.N. A. Vega Castro and E. A. 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