Geographically distant isolates of the persistent southern tomato virus (STV) show very low genetic diversity in the put
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SHORT REPORT
Geographically distant isolates of the persistent southern tomato virus (STV) show very low genetic diversity in the putative coat protein gene L. Elvira‑González1,2 · L. Rubio1 · L. Galipienso1 Received: 27 April 2020 / Accepted: 20 July 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract Southern tomato virus (STV) from genus Amalgavirus (Family Amalgaviridae) is a persistent virus infecting tomato crops worldwide. Information on genetic diversity and evolutionary mechanisms for plant persistent viruses are very scarce in comparison with plant acute viruses. In this work, the putative coat protein gene of worldwide STV isolates was analyzed showing very low nucleotide diversity ( 0.100). Regarding the acute viruses, the nucleotide diversity was variable ranging from 0.0090 ± 0.0019 to 0.2846 ± 0.0402. The two members of the genus Tenuivirus infecting rice plants showed a nucleotide diversity of 0.0202 ± 0.0030 and 0.0338 ± 0.0038. The phylogenetic tree of STV showed two clades or groups of STV isolates: Group A with isolates from Spain, Mexico, UK, Dominican Republic, USA, South Korea Bangladesh and China; and Group B with isolates from Switzerland and China (Fig. 1 and Supplementary Table S3). The mean nucleotide distance between both groups was 0.0112 ± 0.0028 whereas within Group A and Group B were 0.0012 ± 0.0004 and 0.0018 ± 0.0010, respectively. No correlation between the geographic and nucleotide distance was found and some isolates from different countries had identical nucleotide sequences such
Virus Genes Table 1 Nucleotide diversity of the coat protein gene of several persistent and acute viruses Virus Persistent STV BBLV VCV WCCV1 CSpV1 PCV1 PCV2 GaRV LRV1 TVV1 Acute RGST RST CGMMV PMMoV ToMV PepMV PVX CMV TSWV PVY BBWV-2
Genus
Family
Host
No. of isolates
Model
Nucleotide diversity
Amalgavirus Amalgavirus Alphapartitivirus Alphapartitivirus Cryspovirus Deltapartitivirus Deltapartitivirus Gammapartitivirus Leishmaniavirus Trichomonasvirus
Amalgaviridae Amalgaviridae Partitiviridae Partitiviridae Partitiviridae Partitiviridae Partitiviridae Partitiviridae Totiviridae Totiviridae
Plant Plant Plant Plant Protozoa Plant Plant Fungi Protozoa Protozoa
28 38 7 10 14 6 14 44 20 10
TN93 JC TN93 + G + I T92 T92 + G TN93 T92 + G K2 + G TN93 + G TN93 + G + I
0.0031 ± 0.0008 0.0012 ± 0.0003 0.0238 ± 0.0024 0.0058 ± 0.0033 0.0103 ± 0.0017 0.0053 ± 0.0017 0.0247 ± 0.0028 0.0339 ± 0.0058 0.1244 ± 0.0067 0.2268 ± 0.0086
Tenuivirus Tenuivirus Tobamovirus Tobamovirus Tobamovirus Potexvirus Potexvirus Cucumovirus Tospovirus Potyvirus Fabavirus
Phenuiviridae Phenuiviridae Virgaviridae Virgaviridae Virgaviridae Alphaflexiviridae Alphaflexiviridae Bromoviridae Bunyaviridae Potyviridae Secoviridae
Plant Plant Plant Plant Plant Plant Plant Plant Plant Plant Plant
7 20 10 10 11 15 14 23 10 12 10
T92 T92 + G K2 + G K2 T92 K2 + I K2 + G K2 + G T92 + G TN93 + G T93 + I
0.0202 ± 0.0030 0.0338 ± 0.0038 0.0542 ± 0.0071 0.0274 ± 0.0039 0.0088 ± 0.
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