Sida chlorotic leaf virus : a new recombinant begomovirus found in non-cultivated plants and Cucumis sativus L

• Published in: PeerJ (San Francisco, CA) Vol. 11; p. e15047
• Main Authors: García-Rodríguez, Daniel Alejandro, Partida-Palacios, Brenda Lizet, Regla-Márquez, Carlos Fernando, Centeno-Leija, Sara, Serrano-Posada, Hugo, Bañuelos-Hernández, Bernardo, Cárdenas-Conejo, Yair
• Format: Journal Article
• Language: English
• Published: United States PeerJ. Ltd 22-03-2023; PeerJ Inc
• Subjects: Agricultural efficiency; Agricultural Science; Analysis; Base Sequence; Begomovirus; Begomovirus - genetics; Biotechnology industry; Circular DNA; Cucumis sativus - genetics; DNA, Viral - genetics; Food security; Food, Water and Energy Nexus; Geminivirus; Genomics; High-Throughput Sequencing; Malvaceae - genetics; Molecular Biology; Phylogeny; Plant Science; Recombination; Reservoirs; Sida Plant; Virology; United States; Mexico; Agricultural efficiency; Recombination; Virome; Food security; Geminivirus; High-Throughput Sequencing; Begomovirus; Circomics; Weeds
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.15047

Begomoviruses are circular single-stranded DNA plant viruses that cause economic losses worldwide. Weeds have been pointed out as reservoirs for many begomoviruses species, especially from members of the
and
genera. These weeds have the ability to host multiple begomoviruses species simultaneously, which can lead to the emergence of new viral species that can spread to commercial crops. Additionally, begomoviruses have a natural tendency to recombine, resulting in the emergence of new variants and species.
To explore the begomoviruses biodiversity in weeds from genera
and
in Colima, México, we collected symptomatic plants from these genera throughout the state. To identify BGVs infecting weeds, we performed circular DNA genomics (circomics) using the Illumina platform. Contig annotation was conducted with the BLASTn tool using the GenBank nucleotide "nr" database. We corroborated by PCR the presence of begomoviruses in weeds samples and isolated and sequenced the complete genome of a probable new species of begomovirus using the Sanger method. The demarcation process for new species determination followed the International Committee on Taxonomy of Viruses criteria. Phylogenetic and recombination analyses were implemented to infer the evolutionary relationship of the new virus.
We identified a new begomovirus species from sida and malvastrum plants that has the ability to infect
L. According to our findings, the novel species
is the result of a recombination event between one member of the group known as the Squash leaf curl virus (SLCV) clade and another from the Abutilon mosaic virus (AbMV) clade. Additionally, we isolated three previously identified begomoviruses species, two of which infected commercial crops: okra (
) and cucumber (
).
These findings support the idea that weeds act as begomovirus reservoirs and play essential roles in begomovirus biodiversity. Therefore, controlling their populations near commercial crops must be considered in order to avoid the harmful effects of these phytopathogens and thus increase agricultural efficiency, ensuring food and nutritional security.