Identification and complete genomic sequence of a novel sadwavirus discovered in pineapple ( Ananas comosus )
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ANNOTATED SEQUENCE RECORD
Identification and complete genomic sequence of a novel sadwavirus discovered in pineapple (Ananas comosus) Adriana Larrea‑Sarmiento1 · Alejandro Olmedo‑Velarde1 · James C. Green1 · Maher Al Rwahnih2 · Xupeng Wang1 · Yun‑He Li3 · Weihuai Wu4 · Jingxin Zhang5 · Tracie K. Matsumoto6 · Jon Y. Suzuki6 · Marisa M. Wall6 · Wayne Borth1 · Michael J. Melzer1 · John S. Hu1 Received: 19 December 2019 / Accepted: 15 February 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract The complete genomic sequence of a putative novel member of the family Secoviridae was determined by high-throughput sequencing of a pineapple accession obtained from the National Plant Germplasm Repository in Hilo, Hawaii. The predicted genome of the putative virus was composed of two RNA molecules of 6,128 and 4,161 nucleotides in length, excluding the poly-A tails. Each genome segment contained one large open reading frame (ORF) that shares homology and phylogenetic identity with members of the family Secoviridae. The presence of this new virus in pineapple was confirmed using RT-PCR and Sanger sequencing from six samples collected in Oahu, Hawaii. The name “pineapple secovirus A” (PSVA) is proposed for this putative new sadwavirus. Members of the family Secoviridae are non-enveloped viruses containing linear positive-sense single-stranded RNA [(+)-ssRNA] genomes that are monopartite or bipartite. Each genome segment encodes a large polyprotein, is covalently linked to a viral protein (VPg) at its 5’- end, and Communicated by Jesús Navas-Castillo. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00705-020-04592-9) contains supplementary material, which is available to authorized users. * John S. Hu [email protected] 1
Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, USA
2
Department of Plant Pathology, University of California, Davis, CA, USA
3
South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang, China
4
Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
5
Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
6
United States Department of Agriculture, Agricultural Research Service, Pacific Basin Agricultural Research Center, Hilo, HI, USA
has a poly-A tract at its 3’- end. Secovirids form isometric viral particles and are classified within eight genera: Nepovirus, Comovirus, Fabavirus, Sadwavirus, Cheravirus, Torradovirus, Sequivirus, and Waikavirus [1]. Recently, some unassigned secoviruses were classified within the genus Sadwavirus. It has been proposed that this genus should be further divided into three subgenera: “Stramovirus”, “Satsumavirus”, and “Cholivirus” [2]. An additional ninth genus, “Stralarivirus”, was recently proposed based on sequencing of several isolate
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