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Cotton EST database
Cotton is one of the most important economic and fiber crops in the world. There are more than 50 species in the Gossypium genus. Of them, four species (Gossypium hirsutum L., G. barbadense, G. arboreum, G. herbaceum) are widely planted in 70 developed and developing countries, including the U.S., China, and India. It is estimated that more than 180 million people are associated with the cotton fiber industry that annually produces 20 to 30 billion dollars worth of raw cotton. Trade in cotton-related products represents almost 50% of the total $115 billion trade in textiles and the $133 billion trade in clothing. Upland cotton is allotetraploid with complicated genome (2n=4x=52). Currently, the complete gnome of upland cotton is still unclear. Therefore, Expressed sequence tags (ESTs) of cotton provide rich molecular data for cotton research. We used TGICL to assemble a total of 268,786 cotton ESTs from NCBI and obtained 2,8432 contigs (25,371 for consensus and 3,061 for singletons). A great deal of EST redundancy was reduced. BLASTX, BLASTX, and BLASTP were performed to annotate these contigs. Analysis of GO and KEGG were done to classify contigs function and related biological pathway. Based on assembling result, sequence polymorphism including SNP and indel mutant was investigated. Comparative genomic approach was employed to predict miRNAs and their targets in the generated contigs using all known plant miRNAs from miRBase (Release 15: April 2010) as reference set. SSR were predicted based on both original ESTs and contigs. Furthermore, SSR information from cotton marker database (CMD, www.cottonmarker.org/) was collected and was incorporated into our current cotton EST database. In conclusion, we presented an integrated database platform for cotton EST-related information, which covered assembled contigs, function annotation, analysis of GO and KEGG, SNP, miRNA, SSR-related marker information.

References
  1. Xie F, Sun G, Stiller JW, Zhang B. Genome-Wide Functional Analysis of the Cotton Transcriptome by Creating an Integrated EST Database. PLoS One. 2011;6(11):e26980.(If you use the database, please cite it, thank you!)
  2. Zhang B, Wang Q, Wang K, Pan X, Liu F, Guo T, Cobb GP, Anderson TA. Identification of cotton microRNAs and their targets. Gene(2007). 397: 26-37.
  3. Floyd and Bowman, 2004 S.K. Floyd and J.L. Bowman, Gene regulation: ancient microRNA target sequences in plants, Nature 428 (2004), pp.485-486. Full Text via CrossRef | View Record in Scopus | Cited By in Scopus (148)
  4. Heijbroek and Husken, 1996 A. Heijbroek and H. Husken, The International Cotton Complex, Rabobank, Utrecht, Netherlands (1996).