Molecular criteria for genus and species discrimination within the family Potyviridae

Abstract

A phylogenetic analysis of the optimised nucleotide (nt) alignment of the entire ORFs of a representative of each fully-sequenced species in the family Potyviridae provided strong support for several subgroups within the genus Potyvirus. A complete set of two-way comparisons was done between the sequences for the entire ORF and for each gene amongst all the 187 complete sequences from the family. Most species had 50-55% nt identity to other members of their genus in their ORFs but there were significant groups of more closely related species and species demarcation criteria were <76% nt identity and <82% amino acid identity. The corresponding thresholds for species demaracation using nt identity values for the individual genes ranged from 58% (P1 gene) to 74-78% (other genes) although a few comparisons between different species exceeded these values. For the entire ORF, genus demarcation criteria were <46% nt identity but this did not separate rymoviruses from potyviruses. Comparisons in the CI gene most accurately reflected those for the complete ORF and this region would therefore be the best for diagnostic and taxonomic studies if only a sub-portion of the genome is to be sequenced. Further comparisons were then made using all the 1220 complete capsid protein (CP) genes. These studies suggest that 76-77% nt identity is the optimal species demarcation criterion for the CP. The study has also helped to allocate the correct virus name to some sequences from the international databases that currently have incorrect or redundant names. The taxonomic status of the current genus Rymovirus and of three unassigned species in the family is discussed. Significant discontinuities in the distributions within and between the currently defined species suggest that the continuum of variation that is theoretically available is constrained or disrupted by molecular barriers that must have some biological significance.

New Record of Association of Bean yellow mosaic virus with Mosaic Disease of Vicia faba in India

“…The 86-87 % sequence identities of isolates under study with other BYMV strains reported all over the world and in accordance with the species demarcation criteria and identification guidelines for potyviruses [1] suggested the virus isolates of V. faba under study as two isolates of BYMV.…”

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

“…Our observations strengthen the view point of Adams et al [1] regarding the utility of CP gene in virus strain identification. Analysis of CP and CI (Cylindrical inclusion) region of potyvirus genome suggested that CI region provides better insight as it represents the reflection of complete ORF in the absence of full genome and has been regarded as the most accurate region for species identification [1]. However, to establish the identity of the newly designated strains, NL-1n and NL-7n needs confirmation by complete genome characterization.…”

Detecção e análise filogenética de vírus em melancia e construção de novos vetores virais para expressão de proteínas em células de inseto

“…As proteases P1 e HC-Pro autoclivam-se e a NIa está envolvida em seu próprio processo de clivagem em cis e em seis clivagens adicionais em trans, no total de oito a dez peptídeos maduros (Adams et al, 2005; Chung et al, 2008;Azad et al, 2014) (Tabela 2).…”

“…partir de estudos anteriores (Adams et al 2005;2015) foram preditas dez proteínas maduras (P1, HC-Pro, P3, 6k1, CI, 6k2, NIa-VPg, NIa-pro, NIb e CP) produzidas a partir da poliproteína. A análise da poliproteína, na junção entre as proteínas, estão previstas na Tabela 7.…”

“…Foram identificados 1.658.169 reads correspondendo ao genoma do vírus ZYMV espécie do gênero Potyvirus (Adams et al, 2005). O genoma predito de ZYMV obtido no presente estudo foi denominado ZYMV-TO e uma sequência completa de 9.666 nts, codificando para uma poliproteína.…”