Genetic characterization of novel putative rhabdovirus and dsRNA virus from Japanese persimmon

Abstract

Deep-sequencing analysis of nucleic acids from leaf tissue of Japanese persimmon trees exhibiting fruit apex disorder in some fruits detected two molecules that were graft transmitted to healthy seedlings. One of the complete genomes consisted of 13 467 nt and encoded six genes similar to those of plant rhabdoviruses. The virus formed a distinct cluster in the genus Cytorhabdovirus with lettuce necrotic yellows virus, lettuce yellow mottle virus and strawberry crinkle virus in a phylogenetic tree based on the L protein (RNA-dependent RNA polymerase, RdRp). The other consisted of 7475 nt and shared a genome organization similar to those of some insect and fungal viruses having dsRNA genomes. In a phylogenetic tree using the RdRp sequence of several unassigned dsRNA viruses, the virus formed a possible new genus cluster with two insect viruses, Circulifer tenellus virus 1 and Spissistilus festinus virus 1, and one plant virus, cucurbit yellows-associated virus.

Complete genome sequence and integrated protein localization and interaction map for alfalfa dwarf virus, which combines properties of both cytoplasmic and nuclear plant rhabdoviruses

“…The degree of complementarity found between 3 0 leader and 5 0 trailer sequences for ADV (22/22) is the highest within the cytorhabdoviruses (17/20 for PeVA, 22/25 for LYMoV, 19/25 for LNYV and 13/20 for NCMV). Furthermore, no unmatched base overhangs were observed in the aligned leader sequence of ADV whereas overhangs in the leader sequences have been reported for cytorhabdovirus genomes PeVA (Ito et al, 2013), LYMoV (Heim et al, 2008), LNYV (Dietzgen et al, 2006) and NCMV (Tanno et al, 2000); nevertheless the significance of this finding regarding potential influence on the virus life cycle is unknown. As is the case for all plant rhabdoviruses, ADV genes are separated by intergenic "gene junction" regions that are highly conserved but slightly divergent from those reported for the other plant rhabdoviruses.…”

“…Although more than 75 plant rhabdoviruses have been detected in a variety of host species based on their large bacilliform virions, the complete genome sequences of only 6 cytorhabdoviruses (Dietzgen et al, 2006;Heim et al, 2008;Ito et al, 2013;Schoen et al, 2004;Tanno et al, 2000;Yan et al, 2015) and 8 nucleorhabdoviruses (Bandyopadhyay et al, 2010;Heaton et al, 1989;Huang et al, 2003;Massah et al, 2008;Pappi et al, 2013;Reed et al, 2005;Revill et al, 2005;Tsai et al, 2005) have been determined. Thus, the sequence determination of the complete genomes of additional plant rhabdoviruses is sorely needed to support and clarify the taxonomy of this important group of viruses and lead to a better understanding of their evolutionary trajectories.…”

Characterization of New Isolates of Apricot vein clearing-associated virus and of a New Prunus-Infecting Virus: Evidence for Recombination as a Driving Force in Betaflexiviridae Evolution

“…These results further illustrate the power of the NGS (Next Generation Sequencing) based approaches to identify and characterize known or novel fruit tree viruses [12,19–21,29,32,33]. …”

Merida virus, a putative novel rhabdovirus discovered in Culex and Ochlerotatus spp. mosquitoes in the Yucatan Peninsula of Mexico

“…The advent of UHTS has resulted in the discovery of many novel rhabdoviruses (Grard et al, 2012;Ito et al, 2013;Kading et al, 2013;Tokarz et al, 2014;Binger et al, 2015;Sakai et al, 2015;Stremlau et al, 2015), including several which were isolated from Anopheles, Culex, Ochlerotatus and Psorophora spp. mosquitoes (Quan et al, 2010;Coffey et al, 2014;Vasilakis et al, 2014).…”

“…Many novel rhadboviruses have been discovered in recent years due to the advent of unbiased high-throughput sequencing (UHTS) (Quan et al, 2010;Ito et al, 2013;Kading et al, 2013;Tokarz et al, 2014;Binger et al, 2015;Sakai et al, 2015;Stremlau et al, 2015), including Bas-Congo virus which was associated with an outbreak of acute haemorrhagic fever in humans in the Democratic Republic of Congo (Grard et al, 2012). Here, we report the genomic organization and prevalence of an apparently novel rhabdovirus tentatively named Merida virus (MERDV) that was discovered by UHTS in mosquitoes in the Yucatan Peninsula of Mexico.…”