Molecular characterization of the largest and smallest genome segments, S1 and S12, of Rice gall dwarf virus

Abstract

The nucleotide sequences of segments S1 and S12 of a Chinese isolate of Rice gall dwarf virus (RGDV) were determined. This provides the first complete sequences of these segments. The complete sequence of S1, the largest genome segment of RGDV, was 4,505 nucleotides in length and was predicted to encode a large protein of 1,458 amino acids with a calculated molecular mass of nearly 166.2 kDa. The protein was related to that encoded by S1 of Rice dwarf virus (RDV; 50% identity and 67% similarity) and (to a lesser extent) to some large proteins of other reoviruses. It appears to be an RNA-dependent RNA polymerase (RdRp) and is probably present in particles as a minor core protein. S12, the smallest genome segment of RGDV, was 853 nucleotides in length, encoding a single major protein of 206 amino acids with a calculated molecular mass of nearly 23.6 kDa. This protein, though a little larger than those of RDV S11 and Wound tumor virus (WTV) S12 in size, showed some similarity to them, especially in the conserved N-terminal region and may have RNA-binding properties. Despite having a common host plant, RDV and RGDV were not more closely related to one another than either of them was to WTV. Phylogenetic analysis of the RdRp showed that members of the genus Phytoreovirus were more closely related to those of the genus Rotavirus than to any other genus within the family Reoviridae.

The Additional 15 nt of 5′ UTR in a Novel Recombinant Isolate of Chilli Veinal Mottle Virus in Solanum nigrum L. Is Crucial for Infection

“…For 5′ RACE, the first strand cDNA was synthesized with a gene-specific reverse primer 5’-RACE-ChiVMV-YunN-R and the adapter primer ZHM1 was ligated to cDNA/RNA duplexes using T4 RNA ligase (Takara) ( Figure S1A ). The PCR product of 5′ RACE was amplified with ZHM2 and 5’-RACE-R, and then cloned and sequenced [ 19 ]. To ensure the integrity and authenticity of full-length sequences, two overlapping sequence fragments were amplified with the primer pairs ChiVMV-2L-1 and ChiVMV-2L-2 ( Figure S1B ).…”

Identification and Genome Characterization of a Novel Nege-like Virus Isolated from Aphids (Aphis gossypii) in Yunnan Province

“…For 5 ′ RACE, first strand cDNA synthesis utilized a gene-specific reverse primer (5 ′ RACE-AGNLV-1 R) and an adapter primer (ZHM1) which were ligated to the cDNA/RNA duplexes using T4 RNA ligase (TaKaRa, Dalian, China) [31]. The first-round PCR product of 5 ′ RACE was amplified using ZHM2 and 5 ′ RACE-AGNLV-1 R primers, and the secondround PCR used ZHM2 and 5 ′ RACE-AGNLV-2 R, with the subsequent cloning and sequencing of the segments.…”

Complete Genomic Sequence of Maize Rough Dwarf Virus, a Fijivirus Transmitted by the Small Brown Planthopper

“…The 13 ORFs share the highest homologies (81 to 97%) with those of the corresponding segments of RBSDV. S1 contained the major motifs characteristic of an RNA-dependent RNA polymerase (RdRp) (10), which can be aligned with those from the RdRp proteins of other reoviruses and which is thought to be a minor component of the core particle. RBSDV, MRDV, RBSDV-2, and MRCV were always closely clustered together in phylogenetic analyses of their segments, and the new sequences of MRDV will be important for determining the appropriate taxonomic positions of these viruses, which sometimes have been considered isolates of a single species (11).…”