Abstract
Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease or rice black-streaked dwarf disease and can lead to severe yield losses in maize and rice. To analyse RBSDV evolution, codon usage bias and genetic structure were investigated in 111 maize and rice RBSDV isolates from eight geographic locations in 2013 and 2014. The linear dsRNA S7 is A+U rich, with overall codon usage biased toward codons ending with A (A3s, S7-1: 32.64%, S7-2: 29.95%) or U (U3s, S7-1: 44.18%, S7-2: 46.06%). Effective number of codons (Nc) values of 45.63 in S7-1 (the first open reading frame of S7) and 39.96 in S7-2 (the second open reading frame of S7) indicate low degrees of RBSDV-S7 codon usage bias, likely driven by mutational bias regardless of year, host, or geographical origin. Twelve optimal codons were detected in S7. The nucleotide diversity (π) of S7 sequences in 2013 isolates (0.0307) was significantly higher than in 2014 isolates (0.0244, P = 0.0226). The nucleotide diversity (π) of S7 sequences in isolates from Jinan (0.0391) was higher than that from the other seven locations (P < 0.01). Only one S7 recombinant was detected in Baoding. RBSDV isolates could be phylogenetically classified into two groups according to S7 sequences, and further classified into two subgroups. S7-1 and S7-2 were under negative and purifying selection, with respective Ka/Ks ratios of 0.0179 and 0.0537. These RBSDV populations were expanding (P < 0.01) as indicated by negative values for Tajima's D, Fu and Li's D, and Fu and Li's F. Genetic differentiation was detected in six RBSDV subpopulations (P < 0.05). Absolute Fst (0.0790) and Nm (65.12) between 2013 and 2014, absolute Fst (0.1720) and Nm (38.49) between maize and rice, and absolute Fst values of 0.0085-0.3069 and Nm values of 0.56-29.61 among these eight geographic locations revealed frequent gene flow between subpopulations. Gene flow between 2013 and 2014 was the most frequent.
Highlights
Rice black-streaked dwarf virus (RBSDV), a member of the genus Fijivirus in the family Reoviridae, causes maize rough dwarf disease (MRDD) and rice black-streaked dwarf disease (RBSDD), which lead to severe yield losses in maize and rice in East Asia [1, 2]
No significant difference was found in codon usage bias among subpopulations, delineated as years, hosts, or geographic locations (P > 0.05)
The genetic diversity of the virus might be supported by its frequent transmission by the small brown planthopper (SBPH) vector in maize and rice hosts in these eight geographic locations in 2013 and 2014
Summary
Rice black-streaked dwarf virus (RBSDV), a member of the genus Fijivirus in the family Reoviridae, causes maize rough dwarf disease (MRDD) and rice black-streaked dwarf disease (RBSDD), which lead to severe yield losses in maize and rice in East Asia [1, 2]. We investigated the population codon usage bias and genetic structure of RBSDV in 111 MRDD and RBSDD isolates (S1 Table) sampled from eight geographic locations in 2013 and 2014. These locations were mainly in the Yellow and Huai River summer maize-growing regions of China, where the MRDD prevailed, including Henan, Shandong, Jiangsu, Hebei provinces and Beijing. P7-2 is a nonstructural protein comprised of 309 amino acids with a molecular mass of 36 kDa that interacts with SKP1, a core subunit of SCF ubiquitin ligase [13]. The interactions of host plants with RBSDV should be examined to gain insights into the evolution of the S7 dsRNA
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