MEGHA SIHAG, SURESH KUMAR GAHLAWAT AND PRIYANKA SIWACH
Department of Biotechnology, Chaudhary Devi Lal University, Sirsa-125 055 (Haryana), India
*(e-mail : Psiwach20@gmail.com; Mobile : 01666247143)
(Received : March 1, 2019; Accepted : May 8, 2019)
Expressed Sequence Tags (ESTs) analysis from different tissues and organs provides the basis for functional genomics research. In the present work, a total of 33,387 unigenes (7,530 in consensus contigs and 25,857 as singletons) were assembled from all 64,903 cotton ESTs currently available. After systematic assembly of unigenes, these were subjected to annotation, comparative genomics, Blast, Gene Ontology (GO) analysis, and pathway enrichment by KEGG to investigate global functions of the cotton transcriptome. Over 29,658 (88.83%) unigenes were found to show similarities with publicly available proteins. KEEG annotations from GO proteins, results showed enrichment for the category ‘metabolism’ (79.76%), followed by– for the categories organismal systems (11.23%) and cellular processes (9%). Further, 73.47% unigenes showed 100% similarity to coding sequences (CDS) of G. arboreum. In a comparison with six model plant species, cotton ESTs showed the highest overall similarity to Vitis vinifera. 739 and 1346 simple sequence repeats (SSRs) were identified using two different softwares, SSRIT and WebSat, respectively, of which 628 SSRs were common. The latter were subjected to designing of viable primer pairs for future applications.
Key words :Expressed sequence tags (ESTs), coding sequences (CDS), genome sequence, simple sequence repeats (SSRs), gene ontology (GO)