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.
Udall
Joshua A
JA
Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA.
Swanson
Jordan M
JM
Haller
Karl
K
Rapp
Ryan A
RA
Sparks
Michael E
ME
Hatfield
Jamie
J
Yu
Yeisoo
Y
Wu
Yingru
Y
Dowd
Caitriona
C
Arpat
Aladdin B
AB
Sickler
Brad A
BA
Wilkins
Thea A
TA
Guo
Jin Ying
JY
Chen
Xiao Ya
XY
Scheffler
Jodi
J
Taliercio
Earl
E
Turley
Ricky
R
McFadden
Helen
H
Payton
Paxton
P
Klueva
Natalya
N
Allen
Randell
R
Zhang
Deshui
D
Haigler
Candace
C
Wilkerson
Curtis
C
Suo
Jinfeng
J
Schulze
Stefan R
SR
Pierce
Margaret L
ML
Essenberg
Margaret
M
Kim
Hyeran
H
Llewellyn
Danny J
DJ
Dennis
Elizabeth S
ES
Kudrna
David
D
Wing
Rod
R
Paterson
Andrew H
AH
Soderlund
Cari
C
Wendel
Jonathan F
JF
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