A global assembly of cotton ESTs
- Joshua A. Udall1,
- Jordan M. Swanson1,
- Karl Haller2,
- Ryan A. Rapp1,
- Michael E. Sparks1,
- Jamie Hatfield2,
- Yeisoo Yu3,
- Yingru Wu4,
- Caitriona Dowd4,
- Aladdin B. Arpat5,
- Brad A. Sickler5,
- Thea A. Wilkins5,
- Jin Ying Guo6,
- Xiao Ya Chen6,
- Jodi Scheffler7,
- Earl Taliercio7,
- Ricky Turley7,
- Helen McFadden4,
- Paxton Payton8,
- Natalya Klueva9,
- Randell Allen9,
- Deshui Zhang10,
- Candace Haigler10,
- Curtis Wilkerson11,
- Jinfeng Suo12,
- Stefan R. Schulze13,
- Margaret L. Pierce14,
- Margaret Essenberg14,
- HyeRan Kim3,
- Danny J. Llewellyn4,
- Elizabeth S. Dennis4,
- David Kudrna3,
- Rod Wing3,
- Andrew H. Paterson13,
- Cari Soderlund2, and
- Jonathan F. Wendel1,15
- 1 Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
- 2 Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
- 3 Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
- 4 CSIRO Plant Industry, Canberra City ACT 2601, Australia
- 5 Department of Plant Sciences, University of California–Davis, Davis, California 95616, USA
- 6 Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, 200032, China
- 7 United States Department of Agriculture–Agricultural Research Service, Stoneville, Mississippi 38776, USA
- 8 United States Department of Agriculture–Agricultural Research Service, Lubbock, Texas 79415, USA
- 9 Department of Biology, Texas Tech University, Lubbock, Texas 79409, USA
- 10 Department of Crop Science and Department of Botany, North Carolina State University, Raleigh, North Carolina 27695, USA
- 11 Bioinformatics Core Facility, Michigan State University, East Lansing, Michigan 48824, USA
- 12 Institute of Genetics and Developmental Biology, Beijing, 100101, China
- 13 Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
- 14 Oklahoma Agricultural Experiment Station, Oklahoma State University, Stillwater, Oklahoma 74078, USA
Abstract
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; AT and DT 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.
Footnotes
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[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.]
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Article published online ahead of print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.4602906.
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↵15 Corresponding author. E-mail jfw{at}iastate.edu; fax (515) 294-1337.
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- Accepted November 14, 2005.
- Received August 25, 2005.
- Cold Spring Harbor Laboratory Press
