Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L.

<h4>Background</h4>Cotton fiber is the world's leading natural fiber used in the manufacture of textiles. Gossypium is also the model plant in the study of polyploidization, evolution, cell elongation, cell wall development, and cellulose biosynthesis. G. barbadense L. is an ideal c...

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Autores principales:	Daojun Yuan, Lili Tu, Xianlong Zhang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a65addcc085644b191ed49358d3eade6
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spelling	oai:doaj.org-article:a65addcc085644b191ed49358d3eade62021-11-18T06:49:08ZGeneration, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L.1932-620310.1371/journal.pone.0022758https://doaj.org/article/a65addcc085644b191ed49358d3eade62011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21829504/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Cotton fiber is the world's leading natural fiber used in the manufacture of textiles. Gossypium is also the model plant in the study of polyploidization, evolution, cell elongation, cell wall development, and cellulose biosynthesis. G. barbadense L. is an ideal candidate for providing new genetic variations useful to improve fiber quality for its superior properties. However, little is known about fiber development mechanisms of G. barbadense and only a few molecular resources are available in GenBank.<h4>Methodology and principal findings</h4>In total, 10,979 high-quality expressed sequence tags (ESTs) were generated from a normalized fiber cDNA library of G. barbadense. The ESTs were clustered and assembled into 5852 unigenes, consisting of 1492 contigs and 4360 singletons. The blastx result showed 2165 unigenes with significant similarity to known genes and 2687 unigenes with significant similarity to genes of predicted proteins. Functional classification revealed that unigenes were abundant in the functions of binding, catalytic activity, and metabolic pathways of carbohydrate, amino acid, energy, and lipids. The function motif/domain-related cytoskeleton and redox homeostasis were enriched. Among the 5852 unigenes, 282 and 736 unigenes were identified as potential cell wall biosynthesis and transcription factors, respectively. Furthermore, the relationships among cotton species or between cotton and other model plant systems were analyzed. Some putative species-specific unigenes of G. barbadense were highlighted.<h4>Conclusions/significance</h4>The ESTs generated in this study are from the first large-scale EST project for G. barbadense and significantly enhance the number of G. barbadense ESTs in public databases. This knowledge will contribute to cotton improvements by studying fiber development mechanisms of G. barbadense, establishing a breeding program using marker-assisted selection, and discovering candidate genes related to important agronomic traits of cotton through oligonucleotide array. Our work will also provide important resources for comparative genomics, polyploidization, and genome evolution among Gossypium species.Daojun YuanLili TuXianlong ZhangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 7, p e22758 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Daojun Yuan Lili Tu Xianlong Zhang Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L.
description	<h4>Background</h4>Cotton fiber is the world's leading natural fiber used in the manufacture of textiles. Gossypium is also the model plant in the study of polyploidization, evolution, cell elongation, cell wall development, and cellulose biosynthesis. G. barbadense L. is an ideal candidate for providing new genetic variations useful to improve fiber quality for its superior properties. However, little is known about fiber development mechanisms of G. barbadense and only a few molecular resources are available in GenBank.<h4>Methodology and principal findings</h4>In total, 10,979 high-quality expressed sequence tags (ESTs) were generated from a normalized fiber cDNA library of G. barbadense. The ESTs were clustered and assembled into 5852 unigenes, consisting of 1492 contigs and 4360 singletons. The blastx result showed 2165 unigenes with significant similarity to known genes and 2687 unigenes with significant similarity to genes of predicted proteins. Functional classification revealed that unigenes were abundant in the functions of binding, catalytic activity, and metabolic pathways of carbohydrate, amino acid, energy, and lipids. The function motif/domain-related cytoskeleton and redox homeostasis were enriched. Among the 5852 unigenes, 282 and 736 unigenes were identified as potential cell wall biosynthesis and transcription factors, respectively. Furthermore, the relationships among cotton species or between cotton and other model plant systems were analyzed. Some putative species-specific unigenes of G. barbadense were highlighted.<h4>Conclusions/significance</h4>The ESTs generated in this study are from the first large-scale EST project for G. barbadense and significantly enhance the number of G. barbadense ESTs in public databases. This knowledge will contribute to cotton improvements by studying fiber development mechanisms of G. barbadense, establishing a breeding program using marker-assisted selection, and discovering candidate genes related to important agronomic traits of cotton through oligonucleotide array. Our work will also provide important resources for comparative genomics, polyploidization, and genome evolution among Gossypium species.
format	article
author	Daojun Yuan Lili Tu Xianlong Zhang
author_facet	Daojun Yuan Lili Tu Xianlong Zhang
author_sort	Daojun Yuan
title	Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L.
title_short	Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L.
title_full	Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L.
title_fullStr	Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L.
title_full_unstemmed	Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L.
title_sort	generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of gossypium barbadense l.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/a65addcc085644b191ed49358d3eade6
work_keys_str_mv	AT daojunyuan generationannotationandanalysisoffirstlargescaleexpressedsequencetagsfromdevelopingfiberofgossypiumbarbadensel AT lilitu generationannotationandanalysisoffirstlargescaleexpressedsequencetagsfromdevelopingfiberofgossypiumbarbadensel AT xianlongzhang generationannotationandanalysisoffirstlargescaleexpressedsequencetagsfromdevelopingfiberofgossypiumbarbadensel
_version_	1718424372218167296

Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L.

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