A global assembly of cotton ESTs

Joshua A. Udall, Jordan M. Swanson, Karl Haller, Ryan A. Rapp, Michael E. Sparks, Jamie Hatfield, Yeisoo Yu, Yingru Wu, Caitriona Dowd, Aladdin B. Arpat, Brad A. Sickler, Thea A. Wilkins, Ying Guo Jin, Ya Chen Xiao, Jodi Scheffler, Earl Taliercio, Ricky Turley, Helen McFadden, Paxton Payton, Natalya KluevaRandell Allen, Deshui Zhang, Candace Haigler, Curtis Wilkerson, Jinfeng Suo, Stefan R. Schulze, Margaret L. Pierce, Margaret Essenberg, Hye Ran Kim, Danny J. Llewellyn, Elizabeth S. Dennis, David Kudrna, Rod Wing, Andrew H. Paterson, Cari Soderlund, Jonathan F. Wendel

Research output: Contribution to journalArticle

118 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)441-450
Number of pages10
JournalGenome Research
Volume16
Issue number3
DOIs
StatePublished - Mar 1 2006

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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    Udall, J. A., Swanson, J. M., Haller, K., Rapp, R. A., Sparks, M. E., Hatfield, J., Yu, Y., Wu, Y., Dowd, C., Arpat, A. B., Sickler, B. A., Wilkins, T. A., Jin, Y. G., Xiao, Y. C., Scheffler, J., Taliercio, E., Turley, R., McFadden, H., Payton, P., ... Wendel, J. F. (2006). A global assembly of cotton ESTs. Genome Research, 16(3), 441-450. https://doi.org/10.1101/gr.4602906