Статья

A global assembly of cotton ESTs

Joshua A. UdallDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USAJordan M SwansonDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA;Karl HallerArizona Genomics Computational Laboratory, BIO5 Institute,Ryan A. RappDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA;Michael E. SparksDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA;Jamie HatfieldArizona Genomics Computational Laboratory, BIO5 Institute,Yeisoo YuArizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA;Yingru WuCSIRO Plant Industry, Canberra City ACT 2601, Australia;Caitriona DowdCSIRO Plant Industry, Canberra City ACT 2601, Australia;Alaaddin Bulak ArpatDepartment of Plant Sciences, University of California-Davis, Davis, California 95616, USA;Brad SicklerDepartment of Plant Sciences, University of California-Davis, Davis, California 95616, USA;Thea A. WilkinsDepartment of Plant Sciences, University of California-Davis, Davis, California 95616, USA;Jin Ying GuoInstitute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, 200032, China;Xiao Ya ChenInstitute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai, 200032, China;Jodi SchefflerUnited States Department of Agriculture-Agricultural Research Service, Stoneville, Mississippi 38776, USA;Earl TaliercioUnited States Department of Agriculture-Agricultural Research Service, Stoneville, Mississippi 38776, USA;Rickie B. TurleyIowa State UniversityHelen McFaddenCSIRO Plant Industry, Canberra City ACT 2601, Australia;Paxton PaytonUnited States Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415, USA;Natalya KluevaDepartment of Biology, Texas Tech University, Lubbock, Texas 79409, USA;Randell AllenDepartment of Biology, Texas Tech University, Lubbock, Texas 79409, USA;Deshui ZhangDepartment of Crop Science and Department of Botany, North Carolina State University, Raleigh, North Carolina 27695, USA;Candace H. HaiglerDepartment of Crop Science and Department of Botany, North Carolina State University, Raleigh, North Carolina 27695, USA;Curtis G. WilkersonBioinformatics Core Facility, Michigan State University, East Lansing, Michigan 48824, USA;Jinfeng SuoInstitute of Genetics and Developmental Biology, Beijing, 100101, China;Stefan SchulzePlant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA;Margaret L. PierceOklahoma Agricultural Experiment Station, Oklahoma State University, Stillwater, Oklahoma 74078, USAMargaret EssenbergOklahoma Agricultural Experiment Station, Oklahoma State University, Stillwater, Oklahoma 74078, USAHye‐Ran KimArizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA;Danny LlewellynCSIRO Plant Industry, Canberra City ACT 2601, Australia;Elizabeth S. DennisCSIRO Plant Industry, Canberra City ACT 2601, Australia;David KudrnaArizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA;Rod A. WingArizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA;Andrew H. PatersonPlant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA;Cari SoderlundArizona Genomics Computational Laboratory, BIO5 Institute,Jonathan F. WendelDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA;

2006en

ABI

Аннотация

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.

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Идентификаторы

DOI: 10.1101/gr.4602906

Цитирования и источники

Цитирований: 2Использованных источников: 0

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