Abstract
A total of 28,432 unique contigs (25,371 in consensus contigs and 3,061 as singletons) were assembled from all 268,786 cotton ESTs currently available. Several in silico approaches [comparative genomics, Blast, Gene Ontology (GO) analysis, and pathway enrichment by Kyoto Encyclopedia of Genes and Genomes (KEGG)] were employed to investigate global functions of the cotton transcriptome. Cotton EST contigs were clustered into 5,461 groups with a maximum cluster size of 196 members. A total of 27,956 indel mutants and 149,616 single nucleotide polymorphisms (SNPs) were identified from consensus contigs. Interestingly, many contigs with significantly high frequencies of indels or SNPs encode transcription factors and protein kinases. In a comparison with six model plant species, cotton ESTs show the highest overall similarity to grape. A total of 87 cotton miRNAs were identified; 59 of these have not been reported previously from experimental or bioinformatics investigations. We also predicted 3,260 genes as miRNAs targets, which are associated with multiple biological functions, including stress response, metabolism, hormone signal transduction and fiber development. We identified 151 and 4,214 EST-simple sequence repeats (SSRs) from contigs and raw ESTs respectively. To make these data widely available, and to facilitate access to EST-related genetic information, we integrated our results into a comprehensive, fully downloadable web-based cotton EST database (www.leonxie.com).
Highlights
Cotton is among most important crops for natural textile fiber oilseed and is planted widely in 70 developed and developing countries, including the U.S, China, India, and Australia [1,2]
There are more than 50 species in the genus Gossypium, only four of them are cultivated; these are upland cotton (Gossypium hirsutum L.), sea-island cotton (Gossypium barbadense), Asian cotton (Gossypium arboreum), and Arabian cotton (Gossypium herbaceum)
EST assembly A total of 268,786 cotton ESTs were collected from NCBI; they have been obtained from different tissues, including fiber, ovule, anther, boll, callus, cotyledon, embryo, leaf, root, stem, seedling, and cultured cells (Table 1)
Summary
Cotton is among most important crops for natural textile fiber oilseed and is planted widely in 70 developed and developing countries, including the U.S, China, India, and Australia [1,2]. By far, the most widely planted, accounting for more than 95% of the annual cotton crop worldwide. Upland cotton has a complex allotetraploid genome (AADD, 2n = 4x = 52) [3], with a haploid genome size estimated to be around 2.5 Gb [4]. Decoding the cotton genome is a crucial foundation for enhancing research on fiber development, quality, yield, and other important agronomic traits. Some progress has been made on cotton genetics and agronomic improvement, sequencing of the complete cotton genome is still ongoing, largely because of its overall genetic and structural complexity [3]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
