Genome sequence of a novel member of the order Picornavirales from the endoparasitoid wasp Diversinervus elegans
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ANNOTATED SEQUENCE RECORD
Genome sequence of a novel member of the order Picornavirales from the endoparasitoid wasp Diversinervus elegans Chao‑Yan Wu1 · You‑Jie Zhao1 · Jia‑Ying Zhu1 Received: 21 March 2020 / Accepted: 25 August 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract Here, we report a novel RNA virus from an encyrtid endoparasitoid wasp (Diversinervus elegans). This virus has a genome of 8845 nucleotides in length with a poly(A) tail. It contains one open reading frame (ORF) encoding a single polyprotein that shares the most significant similarity to the polyproteins of dicistroviruses. Phylogenetic analysis suggested that this virus belongs to the family Dicistroviridae from the order Picornavirales, but its genomic organization is distinct from that of the other known dicistroviruses, which have two ORFs. Consequently, we propose that this virus is a member of a new species in the order Picornavirales, and have named it “Diversinervus elegans virus” (DEV). The Picornavirales are a large order of viruses with a nonenveloped icosahedral particle approximately 30 nm in diameter. They are characterized by a monopartite or bipartite single-stranded positive-sense RNA genome. One major hallmark of Picornavirales genomes is the presence of HelPro-Pol domains consisting of a superfamily III helicase, a chymotrypsin-like proteinase, and a superfamily I RNAdependent RNA polymerase (RdRp) [1]. Currently, the order Picornavirales is divided into eight families: Caliciviridae, Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae, Polycipiviridae, Secoviridae, and Solinviviridae [2, 3]. Viruses assigned to this order have been found in a diverse range of hosts, including vertebrates, arthropods, plants, and unicellular organisms, which are known to cause a range of diseases such as paralysis, meningitis, and hepatitis [4]. Here, we report the genome sequence of a new member of the order Picornavirales, named “Diversinervus elegans virus” (DEV), which was identified in an encyrtid endoparasitoid wasp. Handling Editor: Tim Skern. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00705-020-04824-y) contains supplementary material, which is available to authorized users. * Jia‑Ying Zhu [email protected]; [email protected] 1
Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming 650224, China
The transcriptome of D. elegans (Hymenoptera: Encyrtidae) female adults has been sequenced on an Illumina Hiseq platform, as described earlier [5]. After de novo assembly with Trinity, the resulting unigenes were compared to the NCBI viral database using local BLASTx algorithm with an E-value less than 10−5. The consensus sequence identified as the sequence of DEV was used to design RACE (rapid amplification of cDNA ends) primers (5′RACE, 5′-CACATG AATAGCATTCCGTAACTCTGAT-3′; 3′RACE, 5′-CCG TGATTC AACCATCAAAATCAAAGAT-3′), which were used to amplify two overlapping cDNA fr
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