Use of deep sequencing to profile small RNAs derived from tomato spotted wilt orthotospovirus and hippeastrum chlorotic ringspot orthotospovirus in infected Capsicum annuum.

Virus-derived small RNAs are one of the key factors of RNA silencing in plant defence against viruses. We obtained virus-derived small interfering RNA profiles from Tomato spotted wilt orthotospovirus and Hippeastrum chlorotic ringspot orthotospovirus infected Capsicum annuum XX19 and XY11 by deep sequencing one day after inoculation. The vsiRNAs data were mapped to the TSWV and HCRV genomes, and the results showed that the vsiRNAs measured 19-24 nucleotides in length. Most of the vsiRNAs were mapped to the S segment of the viral genome. For XX19 and XY11 infected with HCRV, the distribution range of vsiRNAs in S RNA was 52.06-55.20%, while for XX19 and XY11 infected with TSWV, the distribution range of vsiRNAs in S RNA was 87.76-89.07%. The first base at the 5' end of the siRNA from TSWV and HCRV was primarily biased towards A, U, or C. Compared with mock-inoculated XX19 and XY11, the expression level of CaRDR1 was upregulated in TSWV- and HCRV-inoculated XX19 and XY11. CaAGO2 and CaAGO5 were upregulated in XY11 against HCRV infection, and CaRDR2 was downregulated in TSWV-infected XY11 and XX19. The profile of HCRV and TSWV vsiRNA verified in this study could be useful for selecting key vsiRNA such as those in disease-resistant varieties by artificially synthesizing amiRNA.

Complete genome sequence of a distinct calla lily chlorotic spot virus isolated in mainland China.

The first complete genome sequence of calla lily chlorotic spot virus (CCSV) from Lijiang in northwestern Yunnan Province was obtained using RT-PCR with designed primers. The genome of CCSV isolate LJ-1-Yunnan is tripartite. The small (S) RNA is 3182 nucleotides (nt) in length and encodes a nonstructural protein (NSs, 1383 nt) and a nuclear nucleocapsid (N, 834 nt), separated by an 836-nt intergenic region (IGR). The medium (M) RNA is 4749 nt in length and encodes a nonstructural movement protein (NSm, 930 nt) and a glycoprotein (GnGc, 3,372 nt), also separated by a 349-nt IGR. The large (L) RNA is 8912 nt in length and encodes a predicted RNA-dependent RNA polymerase (RdRp, 8652 nt). The nucleotide sequences of the three viral RNA segments are 92-94 % identical to the published CCSV genome sequence, and the amino acid sequences of the encoded proteins are 96-98 % identical. However, the IGRs of the S and M RNAs are less similar, with 86 and 72 % identity, respectively. Genome sequence comparisons and phylogenetic analysis indicate that the Lijiang CCSV isolate is a unique tospovirus isolate that differs from CCSV isolates in other geographic regions.