Complete genome sequence of citrus yellow spot virus, a newly discovered member of the family Betaflexiviridae
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Complete genome sequence of citrus yellow spot virus, a newly discovered member of the family Betaflexiviridae Zhiyou Xuan1,2 · Shuai Li1,2 · Song Zhang1,2 · Wenyi Ran1,3 · Yan Zhou1,2 · Fangyun Yang1 · Changyong Zhou1,2 · Mengji Cao1,2 Received: 28 April 2020 / Accepted: 2 August 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract A novel plant virus with a positive single-stranded (+ss) RNA genome was detected in Taibei pomelo (Citrus grandis (L.) Osbeck cv. Taibeiyou) in China by high-throughput sequencing (HTS). Tentatively named “citrus yellow spot virus” (CiYSV), it has 8,061 nucleotides (nt) excluding the poly(A) tail and contains three open reading frames (ORFs). ORF1 is predicted to encode a replicase polyprotein (RP) with conserved domains typical of members of the family Betaflexiviridae. ORF2 encodes a protein sharing the highest sequence identity with the putative movement protein (MP) found in the negativestranded RNA virus Trifolium pratense virus B (TpVB, MH982249, genus Cytorhabdovirus). ORF3 overlaps ORF2 by 137 nt and encodes a predicted coat protein (CP) that is distantly related to those of betaflexiviruses. Phylogenetic analysis based on the MP amino acid sequence showed that the CiYSV clustered with cytorhabdoviruses rather than betaflexiviruses, whilst trees based on the whole genome, RP, and CP showed it to belong to the family Betaflexiviridae but to be distinct from any other known betaflexiviruses. These results suggest that the CiYSV should be considered the first member of a tentative new genus in the family Betaflexiviridae. Members of the virus family Betaflexiviridae have a monopartite positive single-stranded (+ss) polyadenylated RNA genome of 6.5–9.5 kb with flexuous, filamentous virions. There are two subfamilies, Trivirinae and Quinvirinae, distinguished by the type of cell-to-cell movement protein (MP), 30K-like, or triple gene block (TGB) [1]. All of the viruses have a short 5′ untranslated region (UTR) Handling Editor: Stephen John Wylie. Zhiyou Xuan and Shuai Li co-first author. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00705-020-04794-1) contains supplementary material, which is available to authorized users. * Mengji Cao [email protected] 1
National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
2
Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
3
Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
preceding an open reading frame (ORF) encoding a large (185–250 kDa) replication-associated polyprotein (RP) with several conserved domains for the methyltransferase (Met), helicase (Hel), and RNA-dependent RNA polymerase (RdRp) [1, 2]. The coat protein (CP) always follows the movement protein (MP) or combines with the RP, and some genera have an ORF near the 3′ terminus that encodes a nucleic acid binding protein (NB) [3, 4]. At present, ther
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