Sequencing of plant genomes - a review

The scientific revolution that started with the human-genome sequencing project, carried out with first-generation sequencing technology, has initiated other sequencing projects, including those for plant species. Different technologies have been developed together with the second- and third-generat...

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Autores: Turktas, Mine, Yucebilgili Kurtoglu, Kuaybe, Dorado, Gabriel, Zhang, Baohong, Hernández Molina, Pilar, Unver, Turgay
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2015
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/158816
Acceso en línea:http://hdl.handle.net/10261/158816
Access Level:acceso abierto
Palabra clave:ChIP-Seq
Deep sequencing
High-throughput sequencing technologies
RNA-Seq
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spelling Sequencing of plant genomes - a reviewTurktas, MineYucebilgili Kurtoglu, KuaybeDorado, GabrielZhang, BaohongHernández Molina, PilarUnver, TurgayChIP-SeqDeep sequencingHigh-throughput sequencing technologiesRNA-SeqThe scientific revolution that started with the human-genome sequencing project, carried out with first-generation sequencing technology, has initiated other sequencing projects, including those for plant species. Different technologies have been developed together with the second- and third-generation sequencing platforms called “next-generation” sequencing. This review deals with the most relevant second-generation sequencing platforms, advanced analysis tools, and sequenced plant genomes. To date, a number of plant genomes have been sequenced, with many more projected for the near future. Using the new techniques and developed advanced bioinformatics tools, several studies including both plant genomics and transcriptomics were carried out. Likewise, completion of reference genome sequences and high-throughput resequencing projects presented opportunities to better understand the genomic nature of plants and accelerated the process of crop improvement. Modern sequencing and bioinformatics approaches have led to overcome the challenges that arose mainly in plant genomes with large size, high CG content, heterozygosity, transposable elements, repetitive DNA, and homopolymers or polyploidy, as may be the case with the most important crops. There is no doubt that the rest of the species will also benefit from such breakthroughs, which also include direct RNA sequencing without requiring cDNA synthesis. In fact, we are not in a postgenomic era as is sometimes stated, but rather in the beginning of a genomic revolution.MT and TÜ were funded by the Scientific and Technological Research Council of Turkey (TÜBİTAK) with grant numbers 111O036, 112O502, and, 113O016. PH and GD were funded by the Ministerio de Economía y Competitividad (MINECO grants AGL2010-17316 and BIO2011-15237-E) and the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (MINECO and INIA RF2012-00002-C02-02); Consejería de Agricultura y Pesca (041/C/2007, 75/C/2009 and 56/C/2010), Consejería de Economía, Innovación y Ciencia (P11-AGR-7322 and P12-AGR-0482), and Grupo PAI (AGR-248) of Junta de Andalucía; and Universidad de Córdoba (Ayuda a Grupos), Spain.Peer reviewedScientific and Technological Research Council of TurkeyThe Scientific and Technological Research Council of TürkiyeMinisterio de Economía y Competitividad (España)CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Junta de AndalucíaUniversidad de Córdoba (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]201820182015info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/158816reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://doi.org/10.3906/tar-1409-93Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1588162026-05-22T06:33:51Z
dc.title.none.fl_str_mv Sequencing of plant genomes - a review
title Sequencing of plant genomes - a review
spellingShingle Sequencing of plant genomes - a review
Turktas, Mine
ChIP-Seq
Deep sequencing
High-throughput sequencing technologies
RNA-Seq
title_short Sequencing of plant genomes - a review
title_full Sequencing of plant genomes - a review
title_fullStr Sequencing of plant genomes - a review
title_full_unstemmed Sequencing of plant genomes - a review
title_sort Sequencing of plant genomes - a review
dc.creator.none.fl_str_mv Turktas, Mine
Yucebilgili Kurtoglu, Kuaybe
Dorado, Gabriel
Zhang, Baohong
Hernández Molina, Pilar
Unver, Turgay
author Turktas, Mine
author_facet Turktas, Mine
Yucebilgili Kurtoglu, Kuaybe
Dorado, Gabriel
Zhang, Baohong
Hernández Molina, Pilar
Unver, Turgay
author_role author
author2 Yucebilgili Kurtoglu, Kuaybe
Dorado, Gabriel
Zhang, Baohong
Hernández Molina, Pilar
Unver, Turgay
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv The Scientific and Technological Research Council of Türkiye
Ministerio de Economía y Competitividad (España)
CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)
Junta de Andalucía
Universidad de Córdoba (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv ChIP-Seq
Deep sequencing
High-throughput sequencing technologies
RNA-Seq
topic ChIP-Seq
Deep sequencing
High-throughput sequencing technologies
RNA-Seq
description The scientific revolution that started with the human-genome sequencing project, carried out with first-generation sequencing technology, has initiated other sequencing projects, including those for plant species. Different technologies have been developed together with the second- and third-generation sequencing platforms called “next-generation” sequencing. This review deals with the most relevant second-generation sequencing platforms, advanced analysis tools, and sequenced plant genomes. To date, a number of plant genomes have been sequenced, with many more projected for the near future. Using the new techniques and developed advanced bioinformatics tools, several studies including both plant genomics and transcriptomics were carried out. Likewise, completion of reference genome sequences and high-throughput resequencing projects presented opportunities to better understand the genomic nature of plants and accelerated the process of crop improvement. Modern sequencing and bioinformatics approaches have led to overcome the challenges that arose mainly in plant genomes with large size, high CG content, heterozygosity, transposable elements, repetitive DNA, and homopolymers or polyploidy, as may be the case with the most important crops. There is no doubt that the rest of the species will also benefit from such breakthroughs, which also include direct RNA sequencing without requiring cDNA synthesis. In fact, we are not in a postgenomic era as is sometimes stated, but rather in the beginning of a genomic revolution.
publishDate 2015
dc.date.none.fl_str_mv 2015
2018
2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/158816
url http://hdl.handle.net/10261/158816
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://doi.org/10.3906/tar-1409-93
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Scientific and Technological Research Council of Turkey
publisher.none.fl_str_mv Scientific and Technological Research Council of Turkey
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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