A global assembly of cotton ESTs

Approximately 185,000 Gossypium EST sequences comprising >94,800,000 nucleotides were amassed from 30 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including drought stress and pathogen challenges. These libraries were derived from allopolyploid cott...

Full description

Saved in:

Bibliographic Details
Published in:	Genome Research Vol. 16; no. 3; pp. 441 - 450
Main Authors:	Udall, Joshua A, Swanson, Jordan M, Haller, Karl, Rapp, Ryan A, Sparks, Michael E, Hatfield, Jamie, Yu, Yeisoo, Wu, Yingru, Dowd, Caitriona, Arpat, Aladdin B, Sickler, Brad A, Wilkins, Thea A, Guo, Jin Ying, Chen, Xiao Ya, Scheffler, Jodi, Taliercio, Earl, Turley, Ricky, McFadden, Helen, Payton, Paxton, Klueva, Natalya, Allen, Randell, Zhang, Deshui, Haigler, Candace, Wilkerson, Curtis, Suo, Jinfeng, Schulze, Stefan R, Pierce, Margaret L, Essenberg, Margaret, Kim, Hyeran, Llewellyn, Danny J, Dennis, Elizabeth S, Kudrna, David, Wing, Rod, Paterson, Andrew H, Soderlund, Cari, Wendel, Jonathan F
Format:	Journal Article
Language:	English
Published:	United States Cold Spring Harbor Laboratory Press 01-03-2006
Subjects:	Diploidy DNA, Complementary - genetics Expressed Sequence Tags Gene Expression Profiling - methods Genome, Plant Gossypium - genetics Gossypium arboreum Gossypium hirsutum Gossypium raimondii Molecular Sequence Data Polyploidy Resources Sequence Analysis, DNA
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	Approximately 185,000 Gossypium EST sequences comprising >94,800,000 nucleotides were amassed from 30 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including drought stress and pathogen challenges. These libraries were derived from allopolyploid cotton (Gossypium hirsutum; A(T) and D(T) genomes) as well as its two diploid progenitors, Gossypium arboreum (A genome) and Gossypium raimondii (D genome). ESTs were assembled using the Program for Assembling and Viewing ESTs (PAVE), resulting in 22,030 contigs and 29,077 singletons (51,107 unigenes). Further comparisons among the singletons and contigs led to recognition of 33,665 exemplar sequences that represent a nonredundant set of putative Gossypium genes containing partial or full-length coding regions and usually one or two UTRs. The assembly, along with their UniProt BLASTX hits, GO annotation, and Pfam analysis results, are freely accessible as a public resource for cotton genomics. Because ESTs from diploid and allotetraploid Gossypium were combined in a single assembly, we were in many cases able to bioinformatically distinguish duplicated genes in allotetraploid cotton and assign them to either the A or D genome. The assembly and associated information provide a framework for future investigation of cotton functional and evolutionary genomics.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Corresponding author.E-mail jfw@iastate.edu; fax (515) 294-1337. Article published online ahead of print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.4602906. Supplemental material is available online at www.genome.org. The ESTs from GR_Ea and GR_Eb were deposited in GenBank under accession nos. CO069431–CO100583 and CO100584–CO132899.
ISSN:	1088-9051 1549-5469 1549-5477
DOI:	10.1101/gr.4602906