Reexamination of the sida micrantha mosaic virus and sida mottle virus complexes: classification status, diversity, cognate DNA–B components, and host spectrum.
2024
QUEIROZ-FERREIRA, M. S. DE | REIS, L. DE N. A. DOS | FONSECA, M. E. N. | MELO, F. F. S. | REIS, A. | BOITEUX, L. S. | PEREIRA-CARVALHO, R. DE C. | MARCOS SILVA DE QUEIROZ-FERREIRA, UNIVERSIDADE DE BRASÍLIA; LUCIANE DE NAZARÉ ALMEIDA DOS REIS, UNIVERSIDADE DE BRASÍLIA; MARIA ESTHER DE N FONSECA BOITEUX, CNPH; FELIPE FOCHAT SILVA MELO, UNIVERSIDADE DE BRASÍLIA; AILTON REIS, CNPH; LEONARDO SILVA BOITEUX, CNPH; RITA DE CÁSSIA PEREIRA-CARVALHO, UNIVERSIDADE DE BRASÍLIA.
Sida mottle virus (SiMoV) and Sida micrantha mosaic virus (SiMMV) are major Brazilian begomoviruses (Geminiviridae). However, the range of DNA–A identity of isolates of these viruses (81–100%) is not in agreement with the current criteria for Begomovirus species demarcation (<91%). To clarify this putative classification problem, we performed a comprehensive set of molecular analyses with all 53 publicly available isolates (with complete DNA–A genomes) designated as either SiMoV or SiMMV (including novel isolates obtained herein from nationwide metagenomics-based studies). Two well-defined phylogenetic clusters were identified. The SiMMV complex (n = 47) comprises a wide range of strains (with a continuum variation of 88.8–100% identity) infecting members of five botanical families (Malvaceae, Solanaceae, Fabaceae, Oxalidaceae, and Passifloraceae). The SiMoV group now comprises eight isolates (90–100% identity) restricted to Malvaceae hosts, including one former reference SiMMV isolate (gb|NC_077711) and SP77 (gb|FN557522; erroneously named as “true SiMMV”). Iteron analyses of metagenomics-derived information allowed for the discovery of the missing DNA–B cognate of SiMoV (93.5% intergenic region identity), confirming its bipartite nature. Henceforth, the correct identification of SiMoV and SiMMV isolates will be a crucial element for effective classical and biotech resistance breeding of the viral host species.
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