First report of Potato spindle tuber viroid infecting tree tomato in Kenya in mixed infection with Potato virus Y

Abstract

Next generation sequencing, RT-PCRPotato spindle tuber viroid (PSTVd) is composed of a single stranded circular RNA and was first described causing disease in potato in 1922.PSTVd is also known to cause disease in pepper and tomato but it can be symptomless in other species (CABI, 2021). In Kenya it has been detected in Solanum coagulons (Skelton et al., 2019).Leaf samples of tree tomato (Solanum betaceum) showing virusassociated symptoms, including leaf malformation and mottling, and veinal necrosis (Fig. 1), were collected from 14 farms during a survey in four counties in Kenya: Embu, Machakos, Meru and Tharaka-Nithi.Sequencing was done on a pooled sample, formed by selecting one sample from those collected from each of the farms. A single representative leaf sample from each farm was selected, and pooled into the single sample for high throughput sequencing (HTS) analysis. RNA was extracted using a CTAB method (Gambino et al., 2008) then taken for cDNA synthesis. Sequencing was done on the Ion Torrent S5 XL (Thermo Fisher Scientific, USA) platform resulting in nine million reads with an average read length of 146 bp. The CLC Genomics workbench (QIAGEN, Germany) was used to trim 15 nucleotides from the 3′ end of all raw sequence reads and those less than 20 bp in length were discarded. A query of a local download GenBank virus database, revealed 26 reads aligning to PSTVd, and 1440 aligning to members of the Potato virus Y (PVY) complex. Reference-guided genome assembly for PSTVd was conducted using the exemplar strain (GenBank Accession No. NC002030) and resulted in a 359 bp consensus genome sequence, which was added to GenBank (MZ054164). BLAST results showed a 97.78% nucleotide alignment to a PSTVd isolate from the USA (JX280944).This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Xanthohumol and echinocystic acid induces PSTVd tolerance in tomato

“…Dwarf and thin stems, reduced height, low fruit yield, and root biomass, as well as shrunken leaves, were seen on PSTVd‐infected SC‐96 plants, but not on the other genotypes. Similar results were reported for viroids inoculated on tomatoes by Mackie et al ( 2019 ) and Kinoga et al ( 2021 ). Infection usually causes malformed leaves, leaf chlorosis, reduced size, stunting, aborted flowers, necrosis of petioles, midribs, and stems, and decreases in fruit quality and yield.…”

“…Dwarf and thin stems, reduced height, low fruit yield, and root biomass, as well as shrunken leaves, were seen on PSTVd-infected SC-96 plants, but not on the other genotypes. Similar results were reported for viroids inoculated on tomatoes by Mackie et al (2019) and Kinoga et al (2021).…”

First report of potato spindle tuber viroid isolated from pepper seeds produced in Vietnam

“…Although PSTVd was originally reported in North America, it has spread to Africa, Asia, Europe, and South America (Smith et al 1997). In recent years, PSTVd has been identi ed in several countries, and new viroids are being continuously discovered (Kinoga et al 2021;Matsushita et al 2021;Sial and Khan 2018).…”

“…The genus Pospiviroid in the family Pospiviroidae consists of nine species, of which one is the potato spindle tuber viroid (PSTVd) (Full ICTV Report on the Genus Pospiviroid; https://ictv.global/report/chapter/pospiviroidae/pospiviroidae/pospiviroid).Although PSTVd was originally reported in North America, it has spread to Africa, Asia, Europe, and South America (Smith et al 1997). In recent years, PSTVd has been identi ed in several countries, and new viroids are being continuously discovered (Kinoga et al 2021;Matsushita et al 2021;Sial and Khan 2018).PSTVd infects various host plants and causes stunting, leaf chlorosis, leaf epinasty, fruit distortion, and stem and leaf necrosis in tomatoes (Solanum lycopersicum) and potatoes (S. tuberosum) (Hadidi et al 2003;Singh et al 2003). Viroids spread mechanically through plant sap, grafting, and transmission through seeds and pollen (Matsushita et al 2018).…”