# Reexamining a Host-Associated Genomic Diversity of Bean Golden Mosaic Virus (BGMV) Isolates from Phaseolus Species and Other Fabaceae Hosts

## TL;DR

This study finds that Bean Golden Mosaic Virus isolates from different bean species are genetically distinct, suggesting some may belong to a new virus species.

## Contribution

The study reveals genomic and host-based diversity in BGMV isolates, indicating misclassification and the need for revised taxonomic criteria.

## Key findings

- BGMV isolates from Phaseolus vulgaris and P. lunatus form distinct genomic groups with 96–97% and 89–91% identity to a reference isolate.
- Genomic differences in iterons and Rep-associated protein motifs were observed between the two groups.
- Isolates from P. lunatus are likely misclassified as BGMV and may represent a new Begomovirus species.

## Abstract

Beans (Phaseolus vulgaris and P. lunatus) are the major hosts of bean golden mosaic begomovirus (BGMV). Robust taxonomic criteria were established for Begomovirus species demarcation. However, DNA–A identities among BGMV isolates display a continuous variation (89–100%), which conflicts with the current concept of a single viral species. The diversity of 146 Brazilian isolates designated in the GenBank as BGMV was assessed by comparing their complete DNA–A sequences. The isolates were clustered into four groups, being discriminated mainly by their original Fabaceae hosts. Additional Sequence Demarcation Tool analyses indicated that BGMV-related viruses comprise two clear-cut groups: isolates reported infecting mainly P. vulgaris (identities of 96–97% to the reference NC_004042 isolate) and a group associated with P. lunatus (identities of 89–91%). Moreover, we recognized a distinct set of genomic features in the iterons and Rep-associated protein motifs across these two diversity groups. The host prevalence and genomic differences suggest that most P. lunatus isolates are currently misclassified as BGMV strains, being more likely samples of a closely related (but distinct) Begomovirus species. Hence, the implications of this BGMV diversity should be taken into consideration by classical and biotech breeding programs aiming for large-spectrum viral resistance in Phaseolus species.