Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton

Publication Overview
TitleDeep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton
AuthorsLacape JM, Claverie M, Vidal RO, Carazzolle MF, Guimarães Pereira GA, Ruiz M, Pré M, Llewellyn D, Al-Ghazi Y, Jacobs J, Dereeper A, Huguet S, Giband M, Lanaud C
TypeJournal Article
Journal NamePloS one
Volume7
Issue11
Year2012
Page(s)e48855
CitationLacape JM, Claverie M, Vidal RO, Carazzolle MF, Guimarães Pereira GA, Ruiz M, Pré M, Llewellyn D, Al-Ghazi Y, Jacobs J, Dereeper A, Huguet S, Giband M, Lanaud C. Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. PloS one. 2012; 7(11):e48855.
Publication CodePLO-7-e48855

Abstract

Cotton (Gossypium) fiber is the most prevalent natural product used in the textile industry. The two major cultivated species, G. hirsutum (Gh) and G. barbadense (Gb), are allotetraploids with contrasting fiber quality properties. To better understand the molecular basis for their fiber differences, EST pyrosequencing was used to document the fiber transcriptomes at two key development stages, 10 days post anthesis (dpa), representing the peak of fiber elongation, and 22 dpa, representing the transition to secondary cell wall synthesis. The 617,000 high quality reads (89% of the total 692,000 reads) from 4 libraries were assembled into 46,072 unigenes, comprising 38,297 contigs and 7,775 singletons. Functional annotation of the unigenes together with comparative digital gene expression (DGE) revealed a diverse set of functions and processes that were partly linked to specific fiber stages. Globally, 2,770 contigs (7%) showed differential expression (>2-fold) between 10 and 22 dpa (irrespective of genotype), with 70% more highly expressed at 10 dpa, while 2,248 (6%) were differentially expressed between the genotypes (irrespective of stage). The most significant genes with differential DGE at 10 dpa included expansins and lipid transfer proteins (higher in Gb), while at 22 dpa tubulins, cellulose, and sucrose synthases showed higher expression in Gb. DGE was compared with expression data of 10 dpa-old fibers from Affymetrix microarrays. Among 543 contigs showing differential expression on both platforms, 74% were consistent in being either over-expressed in Gh (242 genes) or in Gb (161 genes). Furthermore, the unigene set served to identify 339 new SSRs and close to 21,000 inter-genotypic SNPs. Subsets of 88 SSRs and 48 SNPs were validated through mapping and added 65 new loci to a RIL genetic map. The new set of fiber ESTs and the gene-based markers complement existing available resources useful in basic and applied research for crop improvement in cotton.

Features
This publication contains information about 35,600 features:
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mGhCIR0438mGhCIR0438genetic_marker
mGhCIR0439mGhCIR0439genetic_marker
mGhCIR0440mGhCIR0440genetic_marker
mGhCIR0441mGhCIR0441genetic_marker
mGhCIR0442mGhCIR0442genetic_marker
mGhCIR0443mGhCIR0443genetic_marker

Pages

Properties
Additional details for this publication include:
Property NameValue
Publication TypeJournal Article
Publication TypeResearch Support, Non-U.S. Gov't
Published Locatione48855
URLhttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048855
DOI10.1371/journal.pone.0048855
eISSN1932-6203
Elocation10.1371/journal.pone.0048855
ISSN1932-6203
Journal AbbreviationPLoS ONE
LanguageEnglish
Language Abbreng
Publication CodePLO-7-e48855
Publication Date2012
Publication ModelPrint-Electronic
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DatabaseAccession
PMID: PubMedPMID:23166598