Analysis of 3′-Terminal Region of Bean common mosaic virus Strains Infecting Common Bean in India

Abstract

Four strains (NL-1, NL-1n, NL-7 and NL-7n) of Bean common mosaic virus (BCMV) prevalent on common bean (Phaseolus vulgaris) in Himachal Pradesh, a north-western Himalayan state of India were compared at the 3 0 terminal region of the viral genome to elucidate variation and relationship among these strains. 3 0 terminal region comprising of partial nuclear inclusion b (NIb) (171-233 bp), complete coat protein (CP) (860 bp) and 3 0 untranslated region (UTR) (208-244 bp) shared 96-98% nucleotide and 96-99% amino acids identity among various strains of BCMV. Multiple alignment as well as cluster dendrograms of the 3 0 terminal region placed the test isolates in BCMV species of genus Potyvirus. Phylogenetic analysis of complete CP as well as 3 0 UTR also showed Indian strains to be distinct strains. Sequence homology, multiple alignment and evolutionary divergence of 3 0 terminal region could not differentiate the pathogenic strain groups, thereby establishing least role of this region in strain characterization of the virus. Comparisons of CP and 3 0 UTR region of BCMV strains and other members of genus Potyvirus clearly indicated the little utility of 3 0 terminal region in distinction of virus strains. Implications of coat protein region in viral strain distinction are also discussed.

Bean Common Mosaic Virus and Bean Common Mosaic Necrosis Virus

“…Sequencing of BCMV strains DeMV, NL-1, NL-1n, NL-4, NL-7, and NL-7n, as well as some BCMV strains collected in Australia showed that the BCMV CP possess the DAG motif (Coutts et al, 2011;Hamid et al, 2013;Hu et al, 1995;Sharma et al, 2011). Hamid et al (2013) also identified a BCMV-specific conserved motif in the CP amino acid sequence (MVWCIDN) in strains NL-1, NL-4, and NL-7.…”

“…Currently, there are 22 complete BCMV genome sequences and 9 complete BCMNV genome sequences available through NCBI. Sequence data for CP genes and 3 0 -untranslated regions have been used extensively to place BCMV isolates taxonomically (Fang et al, 1995;Sharma et al, 2011). As a result, most partial or complete sequences of BCMV or BCMNV are for the CP gene.…”

A Novel Isolate of Bean Common Mosaic Virus Isolated from Crownvetch (Securigera varia L. Lassen)

“…Another source of emerging genetic variation are recombinations, which benefit viruses in overcoming host resistance and successful infection [10,11]. Many new strains or pathotypes do not behave like traditional BCMV strains and cannot be distinguished, even using the partial sequence of the CP and 3'-UTR of the virus genome [12,13]. Therefore, molecular characterization using whole-genome sequence analysis is currently used as a precise and reliable criterion for the differentiation of BCMV isolates and strains [14].…”

First Full Length Genome Sequence of Bean Common Mosaic Necrosis Virus (BCMNV) Isolated from Common Bean in Western Kenya

“…By 2015, there were 22 BCMV full length genome sequences and 9 BCMNV full length genome sequences available through NCBI currently [13]. 3 0 -UTR sequence data and CP genes have been used to group BCMV isolates [14]. BCMNV is transmitted by seeds up to 83% in Phaseolus vulgaris L and by several aphid species [15].…”