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Background   Rice black-streaked dwarf virus  (RBSDV) and  Southern rice black-streaked dwarf virus  (SRBSDV) seriously interfered in the production of rice and maize in China. These two viruses are members of the genus  Fijivirus  in the family  Reoviridae  and can cause similar dwarf symptoms in rice. Although some studies have reported the phylogenetic analysis on RBSDV or SRBSDV, the evolutionary relationship between these viruses is scarce.    Methods  In this study, we analyzed the evolutionary relationships between RBSDV and SRBSDV based on the data from the analysis of codon usage, RNA recombination and phylogenetic relationship, selection pressure and genetic characteristics of the bicistronic RNAs (S5, S7 and S9).    Results  RBSDV and SRBSDV showed similar patterns of codon preference: open reading frames (ORFs) in S7 and S5 had with higher and lower codon usage bias, respectively. Some isolates from RBSDV and SRBSDV formed a clade in the phylogenetic tree of S7 and S9. In addition, some recombination events in S9 occurred between RBSDV and SRBSDV.    Conclusions  Our results suggest close evolutionary relationships between RBSDV and SRBSDV. Selection pressure, gene flow, and neutrality tests also supported the evolutionary relationships.    Electronic supplementary material  The online version of this article (10.1186/s12985-019-1163-3) contains supplementary material, which is available to authorized users.

virology journal

Close evolutionary relationship between rice black-streaked dwarf virus and southern rice black-streaked dwarf virus based on analysis of their bicistronic RNAs