Complete genome sequence and genome organization of achyranthes virus A, a novel member of the genus Potyvirus
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Complete genome sequence and genome organization of achyranthes virus A, a novel member of the genus Potyvirus Davaajargal Igori1 · Seungmo Lim2 · Suk‑Yoon Kwon3 · Hye Sun Cho3 · Jeong Mee Park3 · Hyun‑Soon Kim3 · Hyo‑Jun Lee3 · Su‑Heon Lee4 · Jae Sun Moon3 Received: 15 June 2020 / Accepted: 17 July 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract The complete genomic sequence of achyranthes virus A (AcVA), from an Achyranthes bidentata Blume plant in South Korea, was determined. The genomic RNA has 9491 nucleotides (nt), excluding the 3′-terminal poly(A) tail and contains an open reading frame typical of members of the genus Potyvirus, family Potyviridae, encoding a large putative polyprotein of 3103 amino acids (aa). Pairwise comparisons showed that the AcVA sequence shares 47.81–57.78% nt sequence identity at the complete genome level, 41.89–56.41% aa sequence identity at the polyprotein level, and 50–63.8% aa sequence identity at the coat protein level with other members of genus Potyvirus. These pairwise comparison values are below the species demarcation cutoff for the family Potyviridae. Our results therefore suggest that this virus should be regarded as a novel member of the genus Potyvirus, tentatively named “achyranthes virus A”. Potyviridae is the largest family of RNA plant viruses, and its members cause a vast amount of crop damage throughout the world [1]. Currently, this family comprises 228 plantinfecting viruses distributed in 12 genera, with the genus Potyvirus containing the most species [2]. The potyvirus genome consists of a single molecule of linear positive-sense Handling Editor: Ralf Georg Dietzgen. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00705-020-04778-1) contains supplementary material, which is available to authorized users. * Su‑Heon Lee [email protected] * Jae Sun Moon [email protected] 1
Department of Biology, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, Mongolia
2
Department of Plant Quarantine, Animal and Plant Quarantine Agency, Plant Quarantine Research Center, Gimcheon 39660, Republic of Korea
3
Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
4
School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
ssRNA, approximately 10 kb in length, containing a single long open reading frame (ORF), associated with a genomelinked protein (VPg), and containing a 3′ poly(A) tail. The polyprotein is processed by three virally encoded proteases (P1, HC-Pro, and NIa) into 10 smaller functional proteins (P1, HC-pro, P3, 6K1, CI, 6K2, VPg, NIa-pro, NIb, and CP) and a small frameshift-derived peptide (PIPO) [1, 3, 4]. Achyranthes bidentata Blume is a perennial herb of the family Amaranthaceae with a wide distribution all over Asia. It has historically
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