Metagenomics of Neotropical Single-Stranded DNA Viruses in Tomato Cultivars with and without the Ty-1 Gene

Abstract

A complex of begomoviruses (Geminiviridae) can cause severe tomato yield losses in the neotropics. Here, next-generation sequencing was employed for large-scale assessment of single-stranded (ss)DNA virus diversity in tomatoes either harboring or lacking the large-spectrum begomovirus tolerance Ty-1 gene. Individual leaf samples exhibiting begomovirus-like symptoms (n = 107) were field-collected, circular DNA-enriched, subdivided into pools (with and without Ty-1), and Illumina-sequenced. Virus-specific PCR and Sanger dideoxy sequencing validations confirmed 15 distinct ssDNA virus/subviral agents (occurring mainly in mixed infections), which highlight the potential drawbacks of employing virus-specific resistance in tomato breeding. More viruses (14 versus 6 species) were observed in tomatoes without the Ty-1 gene. A gemycircularvirus (Genomoviridae), a new alpha-satellite, and two novel Begomovirus species were identified exclusively in samples without the Ty-1 gene. A novel begomovirus was found only in the Ty-1 pool, being the only species associated with severe symptoms in Ty-1 plants in our survey. Our work is the first step towards the elucidation of the potential begomovirus adaptation to Ty-1 and its specific filtering effects on a subset of ssDNA viral/subviral agents.

Special Issue: “Plant Virus Pathogenesis and Disease Control”

“…This practical application of this relatively inexpensive and portable technology provides a new platform for rapid, accurate identification of specific virus genotypes. Illumina HiSeq and bioinformatics were used to identify a complex of ssDNA viruses in field-grown tomatoes having and lacking the Ty-1 resistance gene, from different growing regions in Brazil [4]. New ssDNA viruses and an alpha satellite were discovered and as expected, more were found from tomatoes lacking the Ty-1 gene.…”

“…Della Bartola and colleagues [3], and de Nazare Almeida Dos Reis and colleagues [4] used contemporary sequence and bioinformatics approaches to look at etiology and diversity of viruses in potatoes and tomatoes, respectively. Nanopore sequencing was used to identify complete genomes for four different viruses infecting potatoes, and even proved to be an effective approach for identification of potato virus Y variants and recombinants in mixed infections [3].…”

Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing

“…Out of this set, 14 were discovered using HTS, and in 2020 alone, seven novel species were discovered just by three HTS-based studies (Ciuffo et al, 2020;de Nazaré Almeida dos Reis et al, 2020;Ma et al, 2020). In this period, also four viral families were associated with tomato for the first time, in four HTS-based studies, i.e., Iflaviridae (Saqib et al, 2015), Phenuiviridae (Lecoq et al, 2019), Kitaviridae (Ciuffo et al, 2020), and Genomoviridae (de Nazaré Almeida dos Reis et al, 2020). Specifically, more than half of the RNA viruses were discovered using HTS (7/13), while most of the DNA viruses (including satellite virus species) were discovered using a non-HTS approach (24/32).…”

“…In France, a novel ilarvirus was found in tomatoes and Solanum nigrum, named Solanum nigrum ilarvirus 1 (SnIV1) (Ma et al, 2020). Three begomoviruses, a gemycircularvirus, and a new alpha satellite were discovered by HTS in tomatoes in Brazil (de Nazaré Almeida dos Reis et al, 2020). A novel begomovirus named tomato-associated geminivirus 1 (TaGV1) was discovered using HTS in Brazil and was suggested as a member of a putative new genus closely related to Capulavirus (Fontenele et al, 2017).…”

“…Currently, HTS is used for discovery of many novel viruses and is now establishing its position as one of the classical approaches in plant virology research and diagnostics laboratories (Massart et al, 2019). HTS is often employed with one of the possible nucleic acid preparation approaches, such as sequencing of double-stranded (ds)RNA, small (s)RNAs, total (tot)DNA after rolling circle amplification, virion-associated RNA (VANA), and total (tot)RNA after ribosomal (r)RNA depletion (Pecman et al, 2017;Ma et al, 2019;de Nazaré Almeida dos Reis et al, 2020;Gaafar and Ziebell, 2020). Each method has its pros and cons (Roossinck, 2017) and should be selected according to the aims of the study; e.g., sequencing rRNA depleted totRNA or sRNA might be the most straightforward and generic approaches for detection of a wide range of viruses in single samples or relatively small sample pools (Pecman et al, 2017).…”