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Parampreet Kaur wins Poster Award at Genomics & Proteomics Research 2014
Parampreet Kaur wins Poster Award at Genomics & Proteomics Research 2014

Bread wheat is one of the most widely cultivated and consumed food crops in the world. It is a complex polyploid with genome size of 17Gb and large amount of repetitive elements. To reduce the complexity of genome, individual wheat chromosome arms were flow-sorted using double ditelosomic stocks, followed by sequencing using both shotgun and BAC-by-BAC approach.
Poster
In Silico Functional Analysis of Genes Corresponding to FlcDNAs using NGS DATA of chromosome 2A of Hexaploid Wheat
In Silico Functional Analysis of Genes Corresponding to FlcDNAs using NGS DATA of chromosome 2A of Hexaploid Wheat
Parampreet Kaur
P Kaur1, Yadav1, S Jindal1, B Yadav1, A Kaur1, P Sharma1, K Neelam1, P Malik1, P Chhuneja1, OP Gupta1, Y Vikal1, S Kaur1, NS Bains1, AK Mahato2, V Dogra2, K Gaikwad2, A Mithra2, TR Sharma2, N Sharma3, C Chaudhary3, S Mathur3, P Khurana3
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Poster Abstract
Wheat is an important cereal crop having genome size of 17Gb. Whole wheat genome is being sequenced using flow sorted chromosome arms, adopting both shotgun sequencing as well as BAC-by-BAC approach. Whole genome shotgun sequences were generated using GAII and HiSeq2000 platforms of Illumina and Roche 454. A de novo hybrid assembly of 2A was generated. The present study identified and annotated genes using flcDNAs specific to 2A BLAST searched against whole genome shotgun assembly. The contigs so identified were used for gene prediction using FGENESH 2.1 and 478 putative genes were identified. To characterize these genes, BLAST search was performed against NR database to identify putative homologs.

Functional annotation was done using blast2go and interpro scan. Putative functions were assigned based on signatures obtained by Pfam, Gene3D, Panther, Superfamily, Phobius, TMHMM, SignalP, Prints, Prosite, TIGRfam, SMART, PIRSF, Coils and BLASTProDom. GO analysis revealed that among biological processes, majority of genes were involved in metabolism (33%) followed by cellular processes (27%). The class of proteins ‘catalytic and binding activities’ comprised about 88% of the total number of molecular functions. 48 genes were identified to be involved in various metabolic pathways, of which starch and sucrose metabolism was the most predominant pathway.

Three genes were found to contain NB-ARC /Disease resistance domain, six genes were found to possess transmembrane helices. Genes possessing stress and stimulus response, Cupin, Cupredoxin, ABC-2 transporters, Gliadin, SWEET sugar transporter, signal transduction, pollen allergen domains were identified. In silico analysis revealed presence of gene families on 2A ranging from disease resistance/stress response to signaling and transportation.