Complete genome sequences and recombination analysis of three divergent Satsuma dwarf virus isolates

Abstract

Citrus mosaic virus (CiMV) and navel orange infectious mottling virus (NIMV) are considered strains of satsuma dwarf virus (SDV). To understand the distribution of different isolates of SDV in China, a field survey was conducted, which allowed for the detection of CiMV and NIMV in citrus plants in Zhejiang and Sichuan provinces, respectively. In the present work, two CiMV isolates, including one named CiMV-GTC1 from Goutoucheng sour orange and one named CiMV-SE1 from Setoka tangor, as well as one NIMV isolate named NIMV-EH1 from Ehime-ken No. 38 tangor were, for the first time, fully sequenced. Among the isolates, CiMV-SE1 and CiMV-GTC1 were closely associated with the partial genomes of known CiMV isolates, while NIMV-EH1 was markedly different from known NIMV isolate. Sequence analysis demonstrated that CiMV, NIMV, and SDV shared similar genome organization and high nucleotide identities at the genome level. In addition, phylogenetic reconstruction of the three viruses also suggested a close relationship. Furthermore, recombination analysis provided evidence for their common cooccurrence in nature. These findings contribute significantly to our understanding of the natural evolution of SDV populations and can provide a basis for preventing the spread of different SDV isolates in the main citrus production regions.

Major Citrus Viruses in Japan

“…ex Tanaka), respectively (Ito et al 2004, Miyakawa & Yamaguchi 1981). These viruses have properties in common with SDV (Tanaka & Yamada 1972, Iwanami 2010, Hyun et al 2020, Usugi et al 1986) and they have been classified as SDV strains; however, NIMV and HV are apparently distinct from SDV (Iwanami 2010, Iwanami et al 2001, Ito et al 2004, Yan et al 2020. i) Properties of CiMV CiMV typically induces the development of green blotches and ring-shaped spots on the fruit rind during coloration as well as delayed coloring of the affected areas (Miyakawa & Yamaguchi 1981, Yamada & Tanaka 1968).…”

“…The type isolate Ci-968 (Iwanami et al 1993a) was collected from a satsuma mandarin tree in Wakayama Prefecture. CiMV is often found in other parts of Japan (Iwanami et al 1991a(Iwanami et al , 1993aMiyoshi S. et al 2020) as well as in Korea and China (Hyun et al 2017, Yan et al 2020. To date, CiMV has not been detected in Turkey.…”

Plant viruses and viroids in Japan

“…SDV and SMoV commonly occur in Japan, whereas other viruses that belong to the genus Sadwavirus have not been reported. A few distinct SDV strains were recognized, and their taxonomic status deserves reconsideration (Ito et al 2004;Iwanami 2010;Iwanami et al 2001;Yan et al 2021).…”

Exotic and Emergent Citrus Viruses Relevant to the Mediterranean Region

“…Satsuma dwarf virus (SDV) is a small isometric virus (26 nm in diameter) of two + ssRNAs (6790 and 5345 nt, genomic molecules). Complete genome sequences of three Satsuma dwarf virus isolates have been recently obtained by HTS [66] (Table 2). The virus is graft and mechanically transmitted, without a reported vector present in the EPPO region countries (Supplementary Figure S3).…”