Phylogenetic analysis of divergent structural organization of nucleotide binding domain encoded by resistance genes and gene homologs in the family Fabaceae

Abstract

In higher plants, disease resistance (R) genes are present in abundance and majority of these encode proteins with a nucleotide-binding site (NBS). N-terminal end of the NBS is either endowed with TIR or by Non-TIR sequences. We have cloned and sequenced one yellow mosaic virus-resistance linked R gene homolog (RGH) from Vigna mungo, line VM-1, GenBank accession number AY297425. Later, two other RGHs from YMV resistant lines, V. mungo WBU 108 and V. radiata Pusa 9072 were selectively amplified using R gene targeted degenerate primers and were cloned subsequently (AY301991 and trIQ7XZT9, respectively). Characterization of these three RGHs and analysis of a total of 221 R genes and RGHs lead to the question of the evolution and distribution of the R genes/RGHs in the family Fabaceae, to which the primary hosts of the YMV belong. These 14 species mainly comprised grain legumes and the R gene phylogeny were reconstructed. The phylogenetic analyses indicate that two-third of the sequences are of the TIR-NBS type, while about one third represent the Non-TIR subfamily. Simultaneous presence of the TIR and the Non-TIR domains within the Fabaceae indicates divergent evolution and heterogeneity within the NBS domain. The plausible mechanism of continued diversification of the NBS sequences within the family Fabaceae has been substantiated by the supportive published evidences. It is presumed that such cases of divergent architectures of NB-domains of R genes within a single species or in the cultivars of the species has been influenced considerably through human interference during domestication, as against, evolution and random selection in nature. This finding reflects that the successful introgression of the functional R gene could be possible to the disease susceptible cultivars within the tribes Phaseoleae and Trifoleae.