A global assembly of cotton ESTs
| Autor: | Jodi A. Scheffler, Earl Taliercio, Candace H. Haigler, Jonathan F. Wendel, Andrew H. Paterson, Karl Haller, Yeisoo Yu, Jin Ying Guo, Jinfeng Suo, Margaret L. Pierce, Randell Allen, Curtis G. Wilkerson, Michael E. Sparks, Ricky Turley, Jamie Hatfield, Natalya Klueva, Xiao-Ya Chen, Stefan R. Schulze, Aladdin B. Arpat, Deshui Zhang, Hyeran Kim, Rod A. Wing, Jordan M. Swanson, Margaret Essenberg, David Kudrna, Danny J. Llewellyn, Helen G. McFadden, Thea A. Wilkins, Joshua A. Udall, Caitriona Dowd, Elizabeth S. Dennis, Yingru Wu, Cari Soderlund, Brad Sickler, Ryan A. Rapp, Paxton Payton |
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| Rok vydání: | 2006 |
| Předmět: |
Expressed Sequence Tags
Genetics Gossypium DNA Complementary Contig biology cDNA library Gene Expression Profiling Molecular Sequence Data food and beverages Genomics Sequence Analysis DNA Gossypium raimondii biology.organism_classification Diploidy Genome Resources Polyploidy UniProt Gene Genome Plant Genetics (clinical) |
| Zdroj: | Genome Research. 16:441-450 |
| ISSN: | 1088-9051 |
| Popis: | Approximately 185,000GossypiumEST 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; ATand DTgenomes) as well as its two diploid progenitors,Gossypium arboreum(A genome) andGossypium 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 putativeGossypiumgenes 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 allotetraploidGossypiumwere 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. |
| Databáze: | OpenAIRE |
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