De Novo Assembly of the Common Bean Transcriptome Using Short Reads for the Discovery of Drought-Responsive Genes

doi:10.1371/journal.pone.0109262

CORC > 中国农业科学院 > 作物科学研究所

	De Novo Assembly of the Common Bean Transcriptome Using Short Reads for the Discovery of Drought-Responsive Genes
	Wu, Jing ; Wang, Lanfen ; Li, Long ; Wang, Shumin 1
刊名	PLOS ONE
	2014
卷号	9 期号:10 页码:-
ISSN号	1932-6203
DOI	10.1371/journal.pone.0109262
通讯作者	Wu, Jing
英文摘要	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.
学科主题	Multidisciplinary Sciences
语种	英语
出版者	PUBLIC LIBRARY SCIENCE
WOS记录号	WOS:000342591500089
内容类型	期刊论文
源URL	[http://111.203.20.206/handle/2HMLN22E/4823]
专题	作物科学研究所
作者单位	1.Minist Agr, Key Lab Crop Germplasm Resources & Utilizat, Beijing, Peoples R China 2.Chinese Acad Agr Sci, Inst Crop Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Beijing 100193, Peoples R China
推荐引用方式 GB/T 7714	Wu, Jing,Wang, Lanfen,Li, Long,et al. De Novo Assembly of the Common Bean Transcriptome Using Short Reads for the Discovery of Drought-Responsive Genes[J]. PLOS ONE,2014,9(10):-.
APA	Wu, Jing,Wang, Lanfen,Li, Long,&Wang, Shumin.(2014).De Novo Assembly of the Common Bean Transcriptome Using Short Reads for the Discovery of Drought-Responsive Genes.PLOS ONE,9(10),-.
MLA	Wu, Jing,et al."De Novo Assembly of the Common Bean Transcriptome Using Short Reads for the Discovery of Drought-Responsive Genes".PLOS ONE 9.10(2014):-.