In silico annotation of 458 genes identified from comparative analysis of Full length cDNAs and NextGen Sequence of chromosome 2A of hexaploid wheat

Abstract

Bread wheat (2n = 6x = 42) is one among the most important staple food crops in the world and plays a crucial role in food security. Owing to its large size of 17 Gb and > 80% repetitive DNA content, the approach used to obtain gold standard rice reference sequence could not be used in wheat. However, flow sorted chromosome arms from specialized cytogenetic stocks were used for shotgun sequencing by International Wheat Genome Sequencing Consortium to obtain a draft sequence. The arm specific genome sequence approach reduced the complexity in several ways. Utilizing a de novo hybrid assembly, generated from shotgun sequence data of chromosome 2AS and 2AL, the present study identified, characterized and annotated genes corresponding to full length cDNAs (FLcDNA) specific to 2A. In the present study, 458 genes corresponding to FLcDNAs were predicted on chromosome 2A. The coding sequences of these genes were characterized using BLASTX search against the NCBI non-redundant database at E-value of 1e-15. Among the 429 genes, putative 413 homologues were identified and their functions were assigned, based on signatures obtained from 13 different databases. GO enrichment annotated these genes to represent diverse molecular functions, cellular localization and biological processes. Forty-five genes could be identified with EC number and assigned to 25 metabolic pathways, of which starch and sucrose metabolism was the most predominant pathway. In silico analysis revealed the presence of gene families on 2A ranging from disease resistance/stress response to signaling and transportation. The results represented annotation for 458 genes of chromosome 2A at nucleotide-, protein-, and process-level. Annotation of genes corresponding to FLcDNAs provides a valuable evidence based resource for characterizing specific pathways, processes and functions for chromosome 2A of wheat.