Tomato yellow vein streak virus and Tomato golden vein virus : a reappraisal of the classification status of two South A
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Tomato yellow vein streak virus and Tomato golden vein virus: a reappraisal of the classification status of two South American Begomovirus species based upon genome–wide pairwise identity of multiple isolates Luciane de Nazaré Almeida dos Reis1 · Leonardo S. Boiteux1,2 · Maria Esther N. Fonseca2 · Rita de Cássia Pereira–Carvalho1 Received: 28 July 2020 / Accepted: 6 November 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Tomato yellow vein streak virus (ToYVSV) and tomato golden vein virus (TGVV) are begomoviruses reported infecting tomatoes and other hosts across South America. However, their close phylogenetic relationship has generated uncertainties about their taxonomic status and nomenclature. In fact, genomic DNA–A identity levels of isolates reported with an identical virus name may range from 89–100%. In view of the potential inaccuracy regarding the classification status of these viruses (strains vs. distinct species), we carried out a comprehensive set of analyses employing all 45 available isolates with complete DNA–A sequences with either ToYVSV or TGVV designation. Two clear–cut clusters were identified and they were consistent with the current criteria for Begomovirus species demarcation. Moreover, our reappraisal confirmed a large array of misnamed isolates and recognized a distinctive set of virus species–specific genomic, biological, and ecological features. Hence, the present work gives support to the notion that these viruses are closely–related, but they are distinct and valid Begomovirus species. From the breeding standpoint, this information will be useful in guiding germplasm screening strategies searching for sources of large–spectrum resistance to isolates of both viruses. Keywords TGVV · ToYVSV · Sequence demarcation tool · Begomovirus · Tomato · Diversity Begomovirus species (family Geminiviridae) infect many dicot plants and are efficiently transmitted by members of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) cryptic species complex [1]. Due to the crescent number of novel begomovirus descriptions worldwide, a new set of standardized criteria was established based upon MUSCLE alignment and Sequence Demarcation Tool (SDT) analyses Edited by Karel Petrzik. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11262-020-01810-z) contains supplementary material, which is available to authorized users. * Rita de Cássia Pereira–Carvalho [email protected] 1
Departamento de Fitopatologia, Universidade de Brasília (UnB), Brasília–DF, Brazil
National Center for Vegetable Crops Research (CNPH), Embrapa Vegetable Crops (Hortaliças), Brasília–DF, Brazil
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[2]. In the current classification system, a novel species is defined when the full DNA–A component displays less than 91% identity with all previously known begomoviruses [2]. In Brazil, field surveys conducted after the invasion of B. tabaci Middle East–Asia Minor 1 (MEAM1 = biotype B) in the early 1990s, revealed an array of over
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