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 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.
Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA.
Joshua A
JA
Udall
Jordan M
JM
Swanson
Karl
K
Haller
Ryan A
RA
Rapp
Michael E
ME
Sparks
Jamie
J
Hatfield
Yeisoo
Y
Yu
Yingru
Y
Wu
Caitriona
C
Dowd
Aladdin B
AB
Arpat
Brad A
BA
Sickler
Thea A
TA
Wilkins
Jin Ying
JY
Guo
Xiao Ya
XY
Chen
Jodi
J
Scheffler
Earl
E
Taliercio
Ricky
R
Turley
Helen
H
McFadden
Paxton
P
Payton
Natalya
N
Klueva
Randell
R
Allen
Deshui
D
Zhang
Candace
C
Haigler
Curtis
C
Wilkerson
Jinfeng
J
Suo
Stefan R
SR
Schulze
Margaret L
ML
Pierce
Margaret
M
Essenberg
Hyeran
H
Kim
Danny J
DJ
Llewellyn
Elizabeth S
ES
Dennis
David
D
Kudrna
Rod
R
Wing
Andrew H
AH
Paterson
Cari
C
Soderlund
Jonathan F
JF
Wendel
D018076:DNA, Complementary / Q000235:genetics; D004171:Diploidy; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D008969:Molecular Sequence Data; D011123:Polyploidy; D017422:Sequence Analysis, DNA
D018076:DNA, Complementary