New isolate of sweet potato virus 2 from Ipomoea nil: molecular characterization, codon usage bias, and phylogenetic analysis based on complete genome.

Autor: Wei KJ; Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China., Jiang AM; Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China., Jiang S; Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China., Huang YJ; Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China., Jiang SY; Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China., Su XL; Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China., Tettey CK; Department of Molecular Biology and Biotechnology, University of Cape Coast, PMB UCC, Cape Coast, Ghana., Wang XQ; Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China. wangxiaoqiang@caas.cn., Tang W; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Xuzhou, 221131, China. tangv0001@163.com., Cheng DJ; Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China. chengdejie@gxu.edu.cn.
Jazyk: angličtina
Zdroj: Virology journal [Virol J] 2024 Sep 19; Vol. 21 (1), pp. 222. Date of Electronic Publication: 2024 Sep 19.
DOI: 10.1186/s12985-024-02500-0
Abstrakt: Background: Viral diseases of sweet potatoes are causing severe crop losses worldwide. More than 30 viruses have been identified to infect sweet potatoes among which the sweet potato latent virus (SPLV), sweet potato mild speckling virus (SPMSV), sweet potato virus G (SPVG) and sweet potato virus 2 (SPV2) have been recognized as distinct species of the genus Potyvirus in the family Potyviridae. The sweet potato virus 2 (SPV2) is a primary pathogen affecting sweet potato crops.
Methods: In this study, we detected an SPV2 isolate (named SPV2-LN) in Ipomoea nil in China. The complete genomic sequence of SPV2-LN was obtained using sequencing of small RNAs, RT-PCR, and RACE amplification. The codon usage, phylogeny, recombination analysis and selective pressure analysis were assessed on the SPV2-LN genome.
Results: The complete genome of SPV2-LN consisted of 10,606 nt (GenBank No. OR842902), encoding 3425 amino acids. There were 28 codons in the SPV2-LN genome with a relative synonymous codon usage (RSCU) value greater than 1, of which 21 end in A/U. Among the 12 proteins of SPV2, P3 and P3N-PIPO exhibited the highest variability in their amino acid sequences, while P1 was the most conserved, with an amino acid sequence identity of 87-95.3%. The phylogenetic analysis showed that 21 SPV2 isolates were clustered into four groups, and SPV2-LN was clustered together with isolate yu-17-47 (MK778808) in group IV. Recombination analysis indicated no major recombination sites in SPV2-LN. Selective pressure analysis showed d N /d S of the 12 proteins of SPV2 were less than 1, indicating that all were undergoing negative selection, except for P1N-PISPO.
Conclusion: This study identified a sweet potato virus, SPV2-LN, in Ipomoea nil. Sequence identities and genome analysis showed high similarity between our isolate and a Chinese isolate, yu-17-47, isolated from sweet potato. These results will provide a theoretical basis for understanding the genetic evolution and viral spread of SPV2.
(© 2024. The Author(s).)
Databáze: MEDLINE
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