Abstract
High-throughput sequencing from symptomatic tomato and pepper plants collected in Panama rendered the complete genome of the southern tomato virus (isolate STV_Panama) and bell pepper endornavirus (isolate BPEV_Panama), and almost-complete genomes of three other BPEV isolates. Tomato chlorosis virus, tomato mosaic virus, and impatiens necrotic spot virus were also detected. Analysis of the complete genome of STV and BPEV worldwide isolates revealed nucleotide diversities of 0.004246 and 0.070523, respectively. Bayesian phylogenetic analysis showed two main groups for each virus (I and II), and several subgroups for BPEV (IA, IB, IC, IIA and IIB). Isolate STV_Panama clustered with NC_12-03-08 from USA and Tom3-T from France (99.97% nucleotide identity) in Group I and BPEV_Panama was close to the Canadian isolate BPEV_Ontario (99.66% nucleotide identity) in Subgroup IB. No correlation was observed between geographic and genetic distances for both viruses. Panamanian BPEV isolates were divergent, belonging to Groups I and II (nucleotide identities > 87.33%). Evolutionary analysis showed purifying selection in all encoding regions of both viruses, being stronger in the overlapping region of both STV genes. Finally, recombination was detected in BPEV but not in STV. This is the first report of STV and BPEV in Panama.
Highlights
Some viruses exhibit persistent lifestyle in their host plants through vertical seed transmission
Recent studies have shown that southern tomato virus (STV), a persistent virus infecting tomato (Solanum lycopersicum), interacts with cucumber mosaic virus (CMV) and pepino mosaic virus (PepMV) in mixed infections by increasing the pathogenic effect of these viruses [4]
bell pepper endornavirus (BPEV) has a double stranded RNA (dsRNA) genome of approximately 14.7 kb containing a single open reading frame (ORF), which is translated into a large polyprotein of 4815–4884 aa
Summary
Some viruses exhibit persistent lifestyle in their host plants through vertical seed transmission. BPEV has a dsRNA genome of approximately 14.7 kb containing a single open reading frame (ORF), which is translated into a large polyprotein of 4815–4884 aa This polyprotein contains several conserved functional domains, such as putative viral methyltransferase (MTR), helicase 1 (Hel-1), UDP-glycosyltransferase (UDG) and RNA-dependent RNA polymerase (RdRp). We have detected STV and BPEV by HTS of small RNAs (sRNAs) from symptomatic tomato and pepper samples, respectively, collected in Panama The presence of both viruses was confirmed by real-time PCR (RTqPCR) using specific primer sets. In Panama, tomato production has been increasing over the recent years, due to the interest of the food processing industry, to reach around 15,000 T [14] Pepper is another important horticultural crop in the region, with a production of around 7000 T [14], being used mainly as a condiment or fresh food. Analyses of the genetic diversity and evolution of STV and BPEV are crucial to understanding their epidemiology, and to developing accurate detection methods [15]
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