De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.

The common bean (Phaseolus vulgaris L.) is one of the most important food legumes, far ahead of other legumes. The average grain yield of the common bean worldwide is much lower than its potential yields, primarily due to drought in the field. However, the gene network that mediates plant responses...

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Autores principales:	Jing Wu, Lanfen Wang, Long Li, Shumin Wang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7587cb9572ba4fe0a011f45e533a8a10
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spelling	oai:doaj.org-article:7587cb9572ba4fe0a011f45e533a8a102021-11-25T05:58:13ZDe novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.1932-620310.1371/journal.pone.0109262https://doaj.org/article/7587cb9572ba4fe0a011f45e533a8a102014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0109262https://doaj.org/toc/1932-6203The common bean (Phaseolus vulgaris L.) is one of the most important food legumes, far ahead of other legumes. The average grain yield of the common bean worldwide is much lower than its potential yields, primarily due to drought in the field. However, the gene network that mediates plant responses to drought stress remains largely unknown in this species. The major goals of our study are to identify a large scale of genes involved in drought stress using RNA-seq. First, we assembled 270 million high-quality trimmed reads into a non-redundant set of 62,828 unigenes, representing approximately 49 Mb of unique transcriptome sequences. Of these unigenes, 26,501 (42.2%) common bean unigenes had significant similarity with unigenes/predicted proteins from other legumes or sequenced plants. All unigenes were functionally annotated within the GO, COG and KEGG pathways. The strategy for de novo assembly of transcriptome data generated here will be useful in other legume plant transcriptome studies. Second, we identified 10,482 SSRs and 4,099 SNPs in transcripts. The large number of genetic markers provides a resource for gene discovery and development of functional molecular markers. Finally, we found differential expression genes (DEGs) between terminal drought and optimal irrigation treatments and between the two different genotypes Long 22-0579 (drought tolerant) and Naihua (drought sensitive). DEGs were confirmed by quantitative real-time PCR assays, which indicated that these genes are functionally associated with the drought-stress response. These resources will be helpful for basic and applied research for genome analysis and crop drought resistance improvement in the common bean.Jing WuLanfen WangLong LiShumin WangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 10, p e109262 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jing Wu Lanfen Wang Long Li Shumin Wang De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.
description	The common bean (Phaseolus vulgaris L.) is one of the most important food legumes, far ahead of other legumes. The average grain yield of the common bean worldwide is much lower than its potential yields, primarily due to drought in the field. However, the gene network that mediates plant responses to drought stress remains largely unknown in this species. The major goals of our study are to identify a large scale of genes involved in drought stress using RNA-seq. First, we assembled 270 million high-quality trimmed reads into a non-redundant set of 62,828 unigenes, representing approximately 49 Mb of unique transcriptome sequences. Of these unigenes, 26,501 (42.2%) common bean unigenes had significant similarity with unigenes/predicted proteins from other legumes or sequenced plants. All unigenes were functionally annotated within the GO, COG and KEGG pathways. The strategy for de novo assembly of transcriptome data generated here will be useful in other legume plant transcriptome studies. Second, we identified 10,482 SSRs and 4,099 SNPs in transcripts. The large number of genetic markers provides a resource for gene discovery and development of functional molecular markers. Finally, we found differential expression genes (DEGs) between terminal drought and optimal irrigation treatments and between the two different genotypes Long 22-0579 (drought tolerant) and Naihua (drought sensitive). DEGs were confirmed by quantitative real-time PCR assays, which indicated that these genes are functionally associated with the drought-stress response. These resources will be helpful for basic and applied research for genome analysis and crop drought resistance improvement in the common bean.
format	article
author	Jing Wu Lanfen Wang Long Li Shumin Wang
author_facet	Jing Wu Lanfen Wang Long Li Shumin Wang
author_sort	Jing Wu
title	De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.
title_short	De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.
title_full	De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.
title_fullStr	De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.
title_full_unstemmed	De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.
title_sort	de novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/7587cb9572ba4fe0a011f45e533a8a10
work_keys_str_mv	AT jingwu denovoassemblyofthecommonbeantranscriptomeusingshortreadsforthediscoveryofdroughtresponsivegenes AT lanfenwang denovoassemblyofthecommonbeantranscriptomeusingshortreadsforthediscoveryofdroughtresponsivegenes AT longli denovoassemblyofthecommonbeantranscriptomeusingshortreadsforthediscoveryofdroughtresponsivegenes AT shuminwang denovoassemblyofthecommonbeantranscriptomeusingshortreadsforthediscoveryofdroughtresponsivegenes
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De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes.

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