Sequence analysis and genome organization of a new marafivirus from Leptochloa chinensis

High-throughput sequencing was used to identify and characterize a novel marafivirus from the weed Leptochloa chinensis, which was tentatively named "Leptochloa chinensis marafivirus" (LcMV). The complete genome of the virus consists of 6,178 base pairs, and its nucleotide sequence is 73.82% identical to that of Sorghum almum marafivirus, which is a member of the genus Marafivirus within the family Tymoviridae. The LcMV genome contains a relatively large open reading frame (ORF) encoding a single polyprotein (220.6 kDa) with five functional domains (methyltransferase, papain-like protease, helicase, RNA-dependent RNA polymerase, and coat proteins), which is a characteristic of members of this genus. Furthermore, a 16-nucleotide conserved marafibox sequence was identified at nucleotide positions 5341–5356. The coat protein of LcMV is 68.02% identical to that of Sorghum almum marafivirus. Phylogenetic analysis based on nucleotide and polyprotein sequences showed that LcMV is closely related to members of the genus Marafivirus. Our findings support the classification of LcMV as a member of a new species within this genus. This is the first report of a marafivirus infecting Leptochloa chinensis, a very important weed of rice.