Revision of Begomovirus taxonomy based on pairwise sequence comparisons

Abstract

Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

Complexity of begomovirus and betasatellite populations associated with chilli leaf curl disease in India

“…Based on 91 % nucleotide sequence identity as the species demarcation threshold for DNA-A (Brown et al, 2015) and by pairwise sequence comparison, these DNA-A/DNA-Alike isolates were categorized into seven distinct species including one newly identified species (HM007119). When compared with the genomic sequences available in GenBank, the majority of these sequences had high similarity with previously reported begomoviruses associated with either chilli or tomato (Fig.…”

Phylogenetic and Genome-Wide Pairwise Distance Analysis of the Genus Luteovirus

“…However, for species demarcation, inference from the full length sequences is more meaningful, if considered, since they correspond to biological entities and may represent occurrence of genetic recombination. Pairwise sequence comparison carried out, in this study, using sequence demarcation tool (Muhire et al, 2014), has previously been used for Mastrevirus (Muhire et al, 2013), Curtovirus and more recently for Begomovirus (Brown et al, 2015) of the family Geminiviridae. Sequence based species cutoff alone is accurate and reflects biological differences between viruses belonging to different species (Brown et al, 2015) at least in the case of Begomovirus [Family Geminiviridae] -Bean golden mosaic virus (phloem restricted) and Bean golden yellow mosaic virus (invades mesophyll tissues).…”

“…Pairwise sequence comparison carried out, in this study, using sequence demarcation tool (Muhire et al, 2014), has previously been used for Mastrevirus (Muhire et al, 2013), Curtovirus and more recently for Begomovirus (Brown et al, 2015) of the family Geminiviridae. Sequence based species cutoff alone is accurate and reflects biological differences between viruses belonging to different species (Brown et al, 2015) at least in the case of Begomovirus [Family Geminiviridae] -Bean golden mosaic virus (phloem restricted) and Bean golden yellow mosaic virus (invades mesophyll tissues). In addition, phylogenetic trees that represent gene tree instead of a virus tree can create misconceptions about viral genome structure and can lead to incorrect evolutionary inferences.…”

Tomato Leaf Curl Sudan Virus (TLCSDV) causing leaf curl disease on a new host Amaranthus cruentus L.

“…Begomoviruses belongs to family Geminiviridae are serious problems for many crops globally. The family Geminiviridae has now been reported to have seven genera known as Mastrevirus, Curtovirus, Begomovirus, Topocuvirus, Eragrovirus, Turncurtovirus, Becurtovirus (Muhire et al, 2014;Brown et al, 2015;Varsani et al, 2014). Members of the genus begomovirus have circular single-stranded DNA (ssDNA) with either a mono-or bipartite genome.The bipartite begomovirus genome has two ssDNA molecules (~2.7 kb), known as DNA-A and DNA-B while mono-partite begomovirus has only DNA-A with satellite molecule known as betasatellites (Briddon et al, 2003).…”