Journal of Petroleum & Environmental Biotechnology

CGPSA- Comparative Genomics Methodology for Phylogenetic and Synteny Analysis of gene families in different species

Hukam C. Rawal, N.K. Singh and T.R. Sharma

: Agrotechnol

Abstract:

With the advancement in the scientific genomic research, there is an explosion in the number of completely sequenced genomes over the past decade, which brought us to the urgency of a well established computational strategy or methodology to analyse different genomes or different gene families in these genomes. We developed a computational strategy, to compare different gene families among various plant species. The analysis pipeline comprised of 5 main steps including identification of genes for the specific gene family, In-silico expression analysis and physical mapping of the identified genes. The phylogenetic analysis can be performed for gene families among different species and the synteny analysis can be done to identify the orthologous and non orthologous genes of a gene family among different species. A care was taken on how to represent the huge sequence data to draw meaningful conclusions. We used this strategy to perform the comparative analaysis of the seven defense response gene families such as Beta-glucanase and Chitinase in 23 plant species that not only represents two major classes- diocts and monocots but also belong to very diverse groups like legumes, fruits, vegetables, spices, flowers, medicinal and aromatic plants , grains, and trees. With this strategy a total of 6864 defense response genes were identified and analysed comparatively in the 23 plant species. The developed strategy for comparative genomics of any gene or gene family with computational methods can be used effectively across the genomes

Biography :

Hukam Chand Rawal has completed his M.Sc. in Bioinformatics from Jamia Millia Islamia, New Delhi, India and now working as Senior Research Fellow (on Bioinformatics and Comparative Genomics of crops) at National Research Centre on Plant Biotechnology under Dr. T. R. Sharma