Secuenciación de Próxima Generación: nuevas tecnologías para acceso a las comunidades microbianas
DOI:
https://doi.org/10.35642/rm.v8i1.1248Palabras clave:
Microorganismos, Diversidad, Conservação genética, Datos, AnálisisResumen
Los secuenciadores de próxima generación, del inglés Next-Generation Sequencing (NGS), son plataformas capaces de generar millones de datos de secuencias de DNA o RNA en un solo circuito a través de la clonación in vitro, técnica utilizada para incrementar el número de moléculas y permitir el análisis. Pero hay que agrupar informaciones que ofrezcan al investigador condiciones de decidir cual mejor metodología a adoptarse. Luego, el objetivo de ese artículo fue realizar un estudio de revisión de literatura abordando tecnologías de NGS, compararlas entre si y a métodos más comunes, mostrando su importancia en microbiología agrícola y ambiental. El método de Sanger es el principal método de obtención de secuencias conocido actualmente. Sin embargo, la metodología adoptada por las plataformas NGS utilizan abordajes que dinamizan la secuenciación; y el avance de las técnicas vienen reduciendo considerablemente los costos de la secuenciación. Para realizar los estudios fueron utilizados datos de artículos y de las plataformas de las empresas detentoras de las tecnologías, realizándose comparaciones y análisis sobre el tema. Por eso, la investigación es de carácter bibliográfico y este artículo se caracteriza como artículo de revisión de literatura. Varias plataformas de secuenciación de próxima generación están disponibles en el mercado, pero son de alto costo y están restringidas a algunos países. Aún hay dificultad de encontrar algoritmos adecuados para analizar la cantidad de datos (secuencias) generados, pero, a pesar de eso, los métodos de NGS han creado buenas expectativas y prometen avances importantes en estudios con la finalidad de acceso e identificación de los grupos que componen la estructura de la comunidad microbiana en investigaciones ambientales.
Descargas
Citas
ALDERBORN, A.; KRISTOFFERSON, A.; HAMMERLING, U. Determination of Single-Nucleotide Polymorphisms by Real-time Pyrophosphate DNA Sequencing. Genome research, v.10, p.1249–1258, 2000. DOI: https://doi.org/10.1101/gr.10.8.1249.
ALLEN, R. A.; WILLIAMS, C. L.; PENROD, Y.; MCCLOSKEY, C.; CARPENTER‐AZEVEDO, K.; HUARD, R. C.; KING, E.; DUNN, S. T. A pyrosequencing protocol for rapid identification of SARS‐CoV‐2 variants. Journal of Medical Virology, v. 94, n. 8, p. 3661-3668, 2022. DOI: https://doi.org/10.1002/jmv.27770.
ANDREOTO, F.D. Análise genômica e transcriptômica de Methylobacterium mesophilicum SR1.6/6 em interação com a planta hospedeira. 2011. 80f. Dissertação (Mestrado) - Escola Superior de Agricultura "Luiz de Queiroz", Piracicaba-SP, 2011.
ANJOS, L. M. Diversidade genética de Plasmopara viticola e mapeamento de QTLs de resistência ao míldio em videira (Vitis spp.). Brasília, Novembro 2013.277p. : il. Tese (Doutorado). Programa de Pós-graduação em Fitopatologia, Universidade de Brasília, Brasília. 227p. 2013.
ANSORGE, Wilhelm J. Next-generation DNA sequencing techniques. New biotechnology, v. 25, n. 4, p. 195-203, 2009. DOI: https://doi.org/10.1016/j.nbt.2008.12.009
ATHANASOPOULOU, K.; BOTI, M. A.; ADAMOPOULOS, P. G.; SKOUROU, P. C.; SCORILAS, A. Third-generation sequencing: the spearhead towards the radical transformation of modern genomics. Life, v. 12, n. 1, p. 30, 2021. DOI: https://doi.org/10.3390/life12010030.
BARBA, M.; CZOSNEK, H.; HADIDI, A. Historical perspective, development and applications of next-generation sequencing in plant virology. Virus, v.6, p.106-136, 2014. DOI: https://doi.org/10.3390/v6010106
BOISVERT, S.; LAVIOLETTE, F.; CORBEIL, J. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. Journal of computational biology, v.17, p.1519–1533, 2010. DOI: https://doi.org/10.1089/cmb.2009.0238
BOKULICH, N. A. et al. Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine. Plos one, v.8, n. 10, p.1-10, 2012. DOI: https://doi.org/10.1371/journal.pone.0036357
BROWN, S. P.; CALLAHAM JR, M. C.; OLIVER, A. K.; JUMPPONEN, A. Deep Ion Torrent sequencing identifies soil fungal community shifts after frequent prescribed fires in a southeastern US forest ecosystem. FEMS Microbiology Ecology, v. 86, p.557–566, 2013. DOI: https://doi.org/10.1111/1574-6941.12181.
BUTLER, J.; MACCALLUM, I.; KLEBER, M.; SHLYAKHTER, I. A.; BELMONTE, M. K.; LANDER,E. S.; NUSBAUM, C. ; JAFFE, D. B. Allpaths: de novo assembly of wholegenome shotgun microreads. Genome Research, v.18, p. 810–820, 2008. DOI: https://doi.org/10.1101/gr.7337908
CAPORASO, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME journal, v.6, n. 8, p.1621–1624, 2012. DOI: https://doi.org/10.1038/ismej.2012.8.
CHEVREUX, B. MIRA: an automated genome and EST assembler. 2007. Disponível em: https://archiv.ub.uni-heidelberg.de/volltextserver/7871/1/thesis_zusammenfassung.pdf. Acesso em: 01 jul. 2016.
CHEVREUX, B.; WETTER, T.; SUHAI, S. Genome sequence assembly using trace signals and additional sequence information. Journal of Computer Science & Systems Biology, v.99, p. 45–56, 1999. Disponível em: https://xueshu.baidu.com/usercenter/paper/show?paperid=871ec78542a2b2c43b1a3ce337066be1. Acesso em: 01 jul. 2016.
COLLINS, M. D.; HUTSON, R. A.; FALSEN. E.; SJÖDÉN, B. Facklamia tabacinasalis sp. nov., from powdered tobacco. International journal of systematic bacteriology, v.49, p.1247-1250, 1999. DOI: https://doi.org/10.1099/00207713-49-3-1247.
CONWAY, T. C.; BROMAGE, A. J. Succinct data structures for assembling large genomes. Bioinformatics, v.27, p.479–486, 2011. DOI: https://doi.org/10.1093/bioinformatics/btq697
COUTO, A. D.; CERQUEIRA, F. R.; GUERRA, R. L.; GONÇALVES, L. B.; GOULART, C. C.; SIQUEIRA-BATISTA, R.; FERREIRA, R. S.; OLIVEIRA, A. P. Theoretical basis of a new method for dna fragment assembly in k-mer graphs. 31st International Conference of the Chilean Computer Science Society, 2012. DOI: https://doi.org/10.1109/SCCC.2012.16
DI MAIUTA, N. et al. Microbial population dynamics in the faeces of wood-eating loricariid catfishes. Letters in applied microbiology, v.56, n. 6, p.401-407, 2013. DOI: https://doi.org/10.1111/lam.12061.
DURBIN, R. M. et al. A map of human genome variation from population-scale sequencing. Nature, v. 467, p.1061-1073, 2010. DOI: https://doi.org/10.1038/nature09534.
FELSKE, A.; AKKERMANS, A. D. L.; VOS, W. M. In situ detection of an uncultured predominant bacillus in Dutch grassland soils. Applied and environmental microbiology, v.64, p.4588–4590, 1998. DOI: https://doi.org/10.1128/AEM.64.11.4588-4590.1998
HALL, N. Advantages sequencing technologies and their wider impact in microbiology. The journal of experimental biology, v. 209, p.1518-1525, 2007. DOI: https://doi.org/10.1242/jeb.001370
HU, T.; CHITNIS, N.; MONOS, D.; DINH, A. Next-generation sequencing technologies: An overview. Human Immunology, v. 82, n. 11, p. 801-811, 2021. DOI: https://doi.org/10.1016/j.humimm.2021.02.012.
HUSE, S. M.; HUBER, J. A.; MORRISON, H. G.; SOGIN, M. L.; WELCH, D. M. Accuracy and quality of massively parallel DNA pyrossequencing. Genome biology, v.8, p.1-9, 2007. DOI: https://doi.org/10.1186/gb-2007-8-7-r143
KOCHE, J. C. Fundamentos de metodologia científica: teoria da ciência e iniciação à pesquisa. 34. ed. Petrópolis, RJ: Vozes, 2015.
LANDER, E.S. et al. Initial sequencing and analysing of the human genome. Nature, v. 409, p.860-921, 2001. DOI: https://doi.org/10.1038/35057062.
LEMOS, L. N.; FULTHORPE, R. R.; TRIPLETT, E. W.; ROESCH, L. F.. Rethinking microbial diversity analysis in the high throughput sequencing era. Journal of microbiological methods, v.86, p.42–51, 2011. DOI: https://doi.org/10.1016/j.mimet.2011.03.014
LI, R.; ZHU, H.; RUAN, J.; QIAN, W.; FANG, X.; SHI, Z.; LI, Y.; LI, S. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome research, v.20, p.265–272, 2010. DOI: https://doi.org/10.1101/gr.097261.109
LIFE TECHNOLOGIES CORPORATION. Longer read lengths improve bacterial identification using 16s rRNA Gene Sequencing on Theion PGM™ System. Your Innovative Research, p.1-6, 2013. Disponível em: https://assets.thermofisher.com/TFS-Assets/LSG/brochures/16S-rRNA-Gene-Sequencing-App-Note.pdf. Acesso em: 20 mar. 2016.
LIMA, Milena Tavares. Análise funcional de um consórcio microbiano de solo e prospecção de genes envolvidos na desconstrução da biomassa. 2014. iii, 45 p. Dissertação (mestrado) - Universidade Estadual Paulista Júlio de Mesquita Filho, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, 2014. Disponível em: http://hdl.handle.net/11449/121846. Acesso em: 20 mar. 2016.
LIU, L.; LI, Y.; LI, S.; HU, N.; HE, Y.; PONG, R.; LIN, D.; LU, L.; LAW, M. Comparison of Next-Generation Sequencing Systems. Journal of biomedicine and biotechnology, p.1-12, 2012. DOI: https://doi.org/10.1155/2012/251364.
LOMAN, N. J.; MISRA, R. V.; DALLMAN, T. J.; CONSTANTINIDOU, C.; GHARBIA, S. E.; WAIN, J.; PALLEN, M. J. Performance comparison of benchtop high-throughput sequencing platforms. Nature biotechnology, v.30, n.5, p.434-562, 2012. DOI: https://doi.org/10.1038/nbt.2198.
MA, J.; WANG, Z.; ZOU, X.; FENG, J.; WU, Z.Microbial communities in an anaerobic dynamic membrane bioreactor (AnDMBR) for municipal wastewater treatment: Comparison of bulk sludge and cake layer. Process biochemistry, v.48, n. 3, p.510–516, 2013. DOI: https://doi.org/10.1016/j.procbio.2013.02.003
MADROÑERO, L. J. Análise trancriptômica da interação mamoeiro-Papaya Meleira Virus. 2014. 76 f. : il. Dissertação (Mestrado em Biotecnologia) – Universidade Federal do Espírito Santo, Centro de Ciências da Saúde.
MADSEN, A.M.; ZERVAS, A.; TENDAL, K.; NIELSEN, J. L. Microbial diversity in bioaerosol samples causing ODTS compared to reference bioaerosol samples as measured using Illuminas equencing and MALDI TOF. Environmental research, v.140, p.255–267, 2015. DOI: https://doi.org/10.1016/j.envres.2015.03.027
MARGULIES, M. et al. Genome Sequencing in Open Microfabricated High Density Picoliter Reactors. Nature, v. 437, p. 376–380. 2005. DOI: https://doi.org/10.1038/nature03959.
MILLER, J. R.; KOREN, S.; SUTTON, G. Assembly algorithms for next-generation sequencing data. Genomics, v.95, p. 315-327, 2010. DOI: https://doi.org/10.1016/j.ygeno.2010.03.001.
MYERS, E. W. et al. A whole-genome assembly of drosophila. Science, v.287, p.2196–2204, 2000. DOI: https://doi.org/10.1126/science.287.5461.2196
NAGARAJAN, N.; POP, M. Sequence assembly demystified. Nature Review Genetics, v.14, p.157–167, 2013. DOI: https://doi.org/10.1038/nrg3367
NIKOLAKI, S.; TSIAMIS, G. Microbial diversity in the era of omic technologies. BioMed Research International, v.2013, p.1-15, 2013. DOI: http://dx.doi.org/10.1155/2013/958719
OLSON, M. V. The human genome project. Proceedings of the National Academy of Sciences, v. 90, n. 10, p. 4338-4344, 1993. DOI: https://doi.org/10.1073/pnas.90.10.4338.
ORLANDO, L. et al. True single-molecule DNA sequencing of a pleistocene horse bone. Genome Research, v. 21, p. 1705–1719. DOI: https://doi.org/10.1101/gr.122747.111
OXFORD NANOPORE TECHNOLOGIES. Disponível em: www.nanoporetech.com. Acesso em: 01 jul. 2016.
PETTERSSON, E.; LUNDEBERG, J.; AHMADIAN, A. Generations of sequencing technologies. Genomics, v. 93, n. 2, p. 105-111, 2009. DOI: https://doi.org/10.1016/j.ygeno.2008.10.003.
PYLRO, V. S.; ROESCH, L. F. W.; MORAIS, D. K.; CLARK, I. M.; HIRSCH, P. R.; TÓTOLA, M. R. Data analysis for 16S microbial profiling from different benchtop sequencing platforms. Journal of Microbiological Methods, v.107, p.30–37, 2014. DOI: https://doi.org/10.1016/j.mimet.2014.08.018
PEVZNER, P.A.; TANG, H., WATERMAN, M.S. An Eulerian path approach to DNA fragment assembly. Proceedings of the National Academy of Sciences, vol. 98, no. 17, 9748-9753, 2001. DOI: https://doi.org/10.1073/pnas.171285098.
QUICK, J.; QUINLAN, A.R.; LOMAN, N.J. A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer. GigaScience, v.3, n.22, p.1-6, 2014. DOI: https://doi.org/10.1186/2047-217X-3-22
RAMACHANDRAN, A.; LIU, Y.; ASQHAR, W.; IQBAL, S. M. Characterization of DNA-nanopore INteretions by Molecular Dynamics. American journal of biomedical sciences, v.1, p.344-351, 2009. DOI: https://doi.org/10.5099/aj090400344.
RAUEN, F. J. Roteiros de investigação científica. 2. ed. Tubarão: Unisul, 2018.
RAVIN, N. V. Modern Methods of Genome Sequencing and Their Application for Deciphering Genomes of Microorganisms. Applied Biochemistry and Microbiology, V.46, p.663–670, 2010. DOI: http://dx.doi.org/10.1134/S000368381007001X.
RHOADS, A.; AU, K. F. PacBio sequencing and its applications. Genomics proteomics bioinformatics, v.13, p.278–289, 2015. DOI: http://dx.doi.org/10.1016/j.gpb.2015.08.002.
ROBERTS, R.J.; CARNEIRO, M.O.; SCHARTZ, M.C. The advantages of SMRT sequencing. Genome biology, v.14, n.405, p.1-4, 2013. DOI: http://doi.org/10.1186/gb-2013-14-7-405.
ROESCH, L.F.W. et al. Pyrosequencing enumerates and contrasts soil microbial diversity. The ISME journal, v.1, n. 4, p.283–290, 2007. DOI: http://doi.org/10.1038/ismej.2007.53
RONAGHI, M. Pyrosequencing Sheds Light on DNA Sequencing. Genome research, v.11, p.3-11, 2001. DOI: http://doi.org/10.1101/gr.11.1.3.
RONAGHI, M.; KARAMOHAMED, S.; PETTERSON, B.; UHLÉN, M.; NYRÉN, P. Real-Time DNA Sequencing Using Detection of Pyrophosphate Release. Analytical Biochemistry, v.242, p.84-89, 1996. DOI: http://dx.doi.org/10.1006/abio.1996.0432.
SANGER, F.; COULSON, A. R.; BARREL, B. G.; SMITH, A. J. H.; ROE, B. A. Cloning in Single-stranded Bacteriophage as an Aid to Rapid DNA Sequencing. J. Mol. Biol. v.143, p.161-178, 1980. DOI: https://doi.org/10.1016/0022-2836(80)90196-5.
SANGER, F.; COULSON, A. R.; FRIEDMANN, T.; AIR, G. M.; BARRELL, B. G.; BROWN, N. L.; FIDDES, J. C.; HUTCHISON, C. A.; SLOCOMBE, P. M.; SMITH, M. The Nucleotide Sequence of Bacteriophage ØX174. Journal of molecular biology, v.125, p.225-246, 1978. DOI: https://doi.org/10.1016/0022-2836(78)90346-7.
SANGER, F.; NICKLEN, S.; COULSON, A.R. DNA sequencing with chain-terminating inhibitors. Procedings of the national academy of sciences USA, v.74, p.5463-5467, 1977. DOI: https://doi.org/10.1073/pnas.74.12.5463.
SATAM, H.; JOSHI, K.; MANGROLIA, U.; WAGHOO, S.; ZAIDI, G.; RAWOOL, S.; TRAKARE, R. P.; BANDAY, S.; MISHRA, A. K.; DAS, G; MALONIA, S. K. Next-generation sequencing technology: current trends and advancements. Biology, v. 12, n. 7, p. 997, 2023. DOI: https://doi.org/10.3390/biology12070997.
SCHADT, E. E.; TURNER, S.; KASARSKIS, A. A window into third-generation sequencing. Human Molecular Genetics, v.19, p.227–240, 2010. DOI: https://doi.org/10.1093/hmg/ddq416.
SCHATZ, M. C.; DELCHER, A. L.; SALZBERG, S. L. Assembly of large genomes using second-generation sequencing. Genome research, v.20, pp.1165–1173, 2010. DOI: https://doi.org/10.1101/gr.101360.109
SEQUENCING PLATFORMS. Disponível em: http://www.illumina.com. Acesso em: 20 dez. 2014.
SHENDURE, J.; JI, H. Next-generation DNA sequencing. Nature Biotecnologie, v.26, p.1135-1145, 2008. DOI: https://doi.org/10.1038/nbt1486
SHOKRALLA, S.; SPALL,J. L.; GIBSON, J. F.; HAJIBABAEI, M. Next-generation sequencing technologies for environmental DNA research. Molecular Ecology, v.21, p.1794–1805, 2012. DOI: https://doi.org/10.1111/j.1365-294X.2012.05538.x.
SILVA, K. N. Caracterização molecular de Johnsongrass mosaic virus em plantas forrageiras dos gêneros Brachiaria, Panicum e Pennisetum. Brasília, 2015.p.111. Dissertação (Mestrado). Programa de Pós-graduação em Fitopatologia, Universidade de Brasília, Brasília.
SIMPSON, J. T.; WONG, K.; JACKMAN, S. D.; SCHEIN, J. E.; JONES, S. J.; BIROL,N. Abyss: A parallel assembler for short read sequence data. Genome research, v.19, p. 1117–1123, 2009. DOI: https://doi.org/10.1101/gr.089532.108
SOMMER, D.; DELCHER, A.; SALZBERG, S. ; POP, M. Minimus: a fast, lightweight genome assembler. BMC bioinformatics, v.8, p.1-11, 2007. DOI: https://doi.org/10.1186/1471-2105-8-64
STADEN, R. A Strategy of DNA sequencing employing computer programs. Nucelic Acids Research, v.6, n.7, p.1-10, 1979. DOI: https://doi.org/10.1093/nar/6.7.2601
SUMINDA, G. G. D.; GHOSH, M.; SON, Y. The innovative informatics approaches of high-throughput technologies in livestock: spearheading the sustainability and resiliency of agrigenomics research. Life, v. 12, n. 11, p. 1893, 2022. DOI: https://doi.org/10.3390/life12111893.
TREFFER, R.; DECKER, V. Recent advances in single-molecule sequencing. Current Opinion in Biotechnology, v.21, n. 1, p.4–11, 2010. DOI: https://doi.org/10.1016/j.copbio.2010.02.009
WANG, Y.; ZHAO, Y.; BOLLAS, A.; WANG, Y.; AU, K. F. Nanopore sequencing technology, bioinformatics and applications. Nature biotechnology, v. 39, n. 11, p. 1348-1365, 2021. DOI: https://doi.org/10.1038/s41587-021-01108-x.
YERGEAU, E.; LAWRENCE, J. R.; SANSCHAGRIN, S.; WAISER, M. J.; KORBER, D. R.; GREER, C. W. Next-Generation Sequencing of Microbial Communities in the Athabasca River and Its Tributaries in Relation to Oil Sands Mining Activities. Applied and environmental microbiology, v.78, n.21, p.7626–7637, 2012. DOI: https://doi.org/10.1128/AEM.02036-12
ZERBINO, D. R.; BIRNEY, E. Velvet: Algorithms for de novo short read assembly using de bruijin graphs. Genome Research, v.18, p. 821–829, 2008. DOI: https://doi.org/10.1101/gr.074492.107
ZHANG, J.; CHIODINI, R.; BADR, A.; ZHANG, G. The impact of next-generation sequencing on genomics. Journal of genetics and genômics, v. 38, n. 3, p.96-109, 2011. DOI: https://doi.org/10.1016/j.jgg.2011.02.003.
ZHANG, L. et al. Advances in metagenomics and its application in environmental microorganisms. Frontiers in microbiology, v. 12, p. 766364, 2021. DOI: https://doi.org/10.3389/fmicb.2021.766364.
ZHANG,H.; SUN, Z.; LIU, B.; XUAN, Y.; JIANG, M.; PAN, Y.; ZHANG, Y.; GONG, Y.; LU, X.; YU, D.; KUMAR, D.; HU, X.; CAO, G.; XUE, R.; GONG, C. Dynamic changes of microbial communities in Litopenaeus vannamei cultures and the effects of environmental factors. Aquaculture, v.455, p.97-108, 2016. DOI: https://doi.org/10.1016/j.aquaculture.2016.01.011.
ZIMMER, A.; DURAND, C.; LOIRA, N.; DURRENS, P.; SHERMAN, D. J.; MARULLO, P. QTL. Dissection of Lag Phase in Wine Fermentation Reveals a New Translocation Responsible for Saccharomyces cerevisiae adaptation to sulfite. Plos One, v.9, 2014. DOI: https://doi.org/10.1371/journal.pone.0086298
Descargas
Publicado
Cómo citar
Número
Sección
Licencia
Derechos de autor 2024 Revista Macambira
Esta obra está bajo una licencia internacional Creative Commons Atribución-NoComercial-CompartirIgual 4.0.
