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 Sickler,Thea A. Wilkins,Jin Ying Guo,Xiao-Ya Chen,Jodi A. Scheffler,Earl Taliercio,Ricky Turley,Helen G. McFadden,Paxton Payton,Natalya Klueva,Randell Allen,Deshui Zhang,Candace H. Haigler,Curtis G. Wilkerson,Jinfeng Suo,Stefan R. Schulze,Margaret L. Pierce,Margaret Essenberg,Hyeran Kim,Danny J. Llewellyn,Elizabeth S. Dennis,David Kudrna,Rod A. Wing,Andrew H. Paterson,Cari Soderlund,Jonathan F. Wendel +35 more
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TLDR
Because ESTs from diploid and allotetraploid Gossypium were combined in a single assembly, the assembly and associated information provide a framework for future investigation of cotton functional and evolutionary genomics.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; A and D 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.read more
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Journal ArticleDOI
Toward Sequencing Cotton ( Gossypium ) Genomes
Z. Jeffrey Chen,Brian E. Scheffler,Elizabeth S. Dennis,Barbara A. Triplett,Tianzhen Zhang,Wangzhen Guo,Xiao-Ya Chen,David M. Stelly,Pablo D. Rabinowicz,Christopher D. Town,Tony Arioli,Curt L. Brubaker,Roy G. Cantrell,Jean Marc Lacape,Mauricio Ulloa,Peng W. Chee,Alan R. Gingle,Candace H. Haigler,Richard G. Percy,Sukumar Saha,Thea A. Wilkins,Robert J. Wright,Allen Van Deynze,Yu-Xian Zhu,Shuxun Yu,Ibrokhim Y. Abdurakhmonov,Ishwarappa S. Katageri,P. Ananda Kumar,Mehboob-ur-Rahman,Yusuf Zafar,John Z. Yu,Russell J. Kohel,Jonathan F. Wendel,Andrew H. Paterson +33 more
TL;DR: Despite rapidly decreasing costs and innovative technologies, sequencing of angiosperm genomes is not yet undertaken lightly and the difficulties of sequencing and assembling complex genomes de novo are not yet addressed.
Journal ArticleDOI
A Microsatellite-Based, Gene-Rich Linkage Map Reveals Genome Structure, Function and Evolution in Gossypium
Wangzhen Guo,Caiping Cai,Changbiao Wang,Zhiguo Han,Xianliang Song,Kai Wang,Xiaowei Niu,Cheng Wang,Keyu Lu,Ben Shi,Tianzhen Zhang +10 more
TL;DR: No relationship was observed between the level of polymorphism, motif type, and tissue origin, but the polymorphism appeared to be correlated with repeat type.
Journal ArticleDOI
Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development.
Junkang Rong,F. Alex Feltus,V. N. Waghmare,Gary J. Pierce,Peng W. Chee,Xavier Draye,Yehoshua Saranga,Robert J. Wright,Thea A. Wilkins,O. Lloyd May,C. Wayne Smith,John R. Gannaway,Jonathan F. Wendel,Andrew H. Paterson +13 more
TL;DR: Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks, suggesting that fiber variation involves a complex network of interacting genes.
Journal ArticleDOI
CottonGen: a genomics, genetics and breeding database for cotton research
Jing Yu,Sook Jung,Chun-Huai Cheng,Stephen P. Ficklin,Taein Lee,Ping Zheng,Don C. Jones,Richard G. Percy,Dorrie Main +8 more
TL;DR: CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data.
Journal ArticleDOI
Genomic expression dominance in allopolyploids
TL;DR: Global patterns of gene expression accompanying genomic merger and doubling in inter-specific crosses in the cotton genus are described to provide novel insights into the architecture of gene Expression in the allopolyploid nucleus and raise questions regarding the responsible underlying mechanisms of genome dominance.
References
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