Genome sequencing of two Bell pepper endornavirus (BPEV) variants infecting Capsicum annuum in Colombia

Abstract

Transcriptome analysis of chili and bell pepper samples from commercial plots in the municipalities of Santa Fe de Antioquia and El Peñol in the province of Antioquia revealed the presence of viral sequences with significant similarity to genomes of members of the genus Endornavirus. Assembly of the chili and bell pepper transcriptomes resulted in consensus sequences of 14,727 nt and 14,714 nt that were identified as Bell pepper endornavirus (BPEV). Both sequences were nearly identical by 99.9 % at both nucleotide and amino acid levels. The presence of BPEV was confirmed by RT-qPCR, RT-PCR and Sanger sequencing using RdRp-specific primers designed from the assembled sequences in ten independent random samples taken from the investigated bell pepper stands. The phylogenetic analysis of both BPEV variants and their affiliation within the genus Endornavirus is discussed. For our knowledge, this is the first study on this group of viruses in Colombia.

Development and application of a universal and simplified multiplex RT-PCR assay to detect five potato viruses

“…In spite of their low abundance, this finding suggests the circulation of this PVX type of strains in Antioquia. Endornaviridae-like sequences were only found in the dsRNA dataset and were 100% identical to segments of bell pepper alphaendornavirus isolates identified in Capsicum annuum from el Peñol and Marinilla (Muñoz-Baena et al 2017a). Potyvirus-like sequences were 100% identical to either the PVV isolate La Union varA (KT985458) infecting S. phureja (Alvarez-Yepes et al 2016) or to isolate NTN_diacol_capira (MF176827) infecting S. tuberosum (Figure 3C).…”

Next generation sequencing and proteomics in plant virology: how is Colombia doing?

“…Several studies (Table 2) involving the use of NGS for genome sequencing (complete or partial), detection, and characterization of RNA viruses infecting potato (S. tuberosum and S. phureja) (Gutiérrez-Sánchez et al, 2014;Villamil-Garzón et al, 2014;Muñoz et al, 2016;Vallejo C et al, 2016), peanut (Gutiérrez Sánchez et al, 2016), rice (Jimenez et al, 2018), cassava (Carvajal-Yepes et al, 2014), exotic fruits, such as Solanum quitoense (Gallo et al, 2018), Solanum betaceum , Physalis peruviana (Gutiérrez et al, 2015), Passiflora edulis (Jaramillo Mesa et al, 2018;Jaramillo Mesa et al, 2019), and horticultural products (Gutiérrez et al, 2017;Muñoz Baena et al, 2017) have been included. The above studies have been conducted using mainly total RNA isolated from symptomatic virus infected plants followed by depletion of rRNA and whole RNA sequencing.…”

Coinfección natural de virus de ARN en cultivos de papa (<i>Solanum tuberosum</i> subsp. Andigena) en Antioquia (Colombia)

“…Diacol Capiro en el oriente de Antioquia. Los análisis bioinformáticos realizados confirmaron la presencia en el transcriptoma bajo análisis de secuencias de los genomas de los virus PVX, PVY, PVS, PYVV y PLRV y adicionalmente se detectaron secuencias asociadas a miembros del género Endornavirus, que corresponde a virus de ARN de doble cadena que carecen de cápside, con genomas de 9,8 -17,6 kb y un solo ORF que codifica para una poliproteína de 3000 -6000 aminoácidos con dominios funcionales para metil-transferasa, helicasa viral, glucosil-transferasa y una polimerasa de ARN dependiente de ARN (RDRP) (Muñoz-Baena et al, 2017). También se hallaron dos contigs asociados a genomas de caulimovirus y cavemovirus, dos grupos de virus con genomas de ADN que posiblemente correspondan a transcritos derivados de virus defectuosos integrados en el genoma de la papa.…”