Comparative sequence analysis of nitrogen fixation-related genes in six legumes

Kim, D H and Parupalli, S and Azam, S and Lee, S H and Varshney, R K (2013) Comparative sequence analysis of nitrogen fixation-related genes in six legumes. Frontiers in Plant Science, 4 (300). pp. 1-8.

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Abstract

Legumes play an important role as food and forage crops in international agriculture especially in developing countries. Legumes have a unique biological process called nitrogen fixation (NF) by which they convert atmospheric nitrogen to ammonia. Although legume genomes have undergone polyploidization, duplication and divergence, NF-related genes, because of their essential functional role for legumes, might have remained conserved. To understand the relationship of divergence and evolutionary processes in legumes, this study analyzes orthologs and paralogs for selected 20 NF-related genes by using comparative genomic approaches in six legumes i.e., Medicago truncatula (Mt), Cicer arietinum, Lotus japonicus, Cajanus cajan (Cc), Phaseolus vulgaris (Pv), and Glycine max (Gm). Subsequently, sequence distances, numbers of synonymous substitutions per synonymous site (Ks) and non-synonymous substitutions per non-synonymous site (Ka) between orthologs and paralogs were calculated and compared across legumes. These analyses suggest the closest relationship between Gm and Cc and the highest distance between Mt and Pv in six legumes. Ks proportional plots clearly showed ancient genome duplication in all legumes, whole genome duplication event in Gm and also speciation pattern in different legumes. This study also reports some interesting observations e.g., no peak at Ks 0.4 in Gm-Gm, location of two independent genes next to each other in Mt and low Ks values for outparalogs for three genes as compared to other 12 genes. In summary, this study underlines the importance of NF-related genes and provides important insights in genome organization and evolutionary aspects of six legume species analyzed.

Item Type: Article
Divisions: UNSPECIFIED
CRPS: UNSPECIFIED
Uncontrolled Keywords: nitrogen fixation, legume, comparative analysis, Ks, evolution
Subjects: Mandate crops > Chickpea
Mandate crops > Pigeonpea
Mandate crops > Groundnut
Depositing User: Mr Siva Shankar
Date Deposited: 22 Aug 2013 10:56
Last Modified: 22 Aug 2013 10:58
URI: http://oar.icrisat.org/id/eprint/7061
Official URL: http://dx.doi.org/10.3389/fpls.2013.00300
Projects: Overcoming the Domestication Bottle neck for Symbiotic Nitrogen Fixation in Legumes, CGIAR Research Program on Grain Legumes
Funders: National Science Foundation (NSF), USA
Acknowledgement: UNSPECIFIED
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