中国农业科学Issue(2)：270-279,10.DOI:10.3864/j.issn.0578-1752.2015.02.07
PVYNTN-NW榆林分离物的全基因组序列测定与分析
Complete Genome Analysis of a PVYNTN-NW Recombinant Isolate from Yulin of China
摘要
Abstract
[Objective] Potato virus Y (PVY) is a typical member of the genus Potyvirus in the family Potyviridae. It is one of the most destructive pathogens affecting potato and tobacco and causes significant economic losses worldwide. The objective of this study is to determine the genomic structure of an isolate of PVY from Yulin of China and its phylogenetic relationship with reported PVY strains.[Method]The complete genome of the ShX14 was amplified and sequenced from overlapping fragments using 11 pairs of primers designed from the conserved regions of the known PVY isolates. Genomic structure and recombination events of the isolate were evaluated by various bioinformatics approaches. Phylogenetic tree was reconstructed by maximum likelihood (ML) method using nucleotide sequences of coding regions. In addition, phylogeny-trait association analysis was used to evaluate the relationship between PVY isolate and the reported stains. [Result]The complete sequence of ShX14 had 9 724 nucleotides, excluding the 3′- terminal poly (A) tail. It contains a single open reading frame of 9 186 nucleotides and encodes a polyprotein of 3 061 amino acids. An additional protein, termed ‘PIPO’, is also translated by +2 nucleotide frame shifting within the P3 cistron. The isolate shares 98%-99% nucleotide identity and 98%-100% amino acid identity with HN2 and SYR-NB-16 (PVYNTN-NW strain, SYR-I genotype), respectively. Similar to the PVYNTN-NW (SYR-I) genomic structure, three recombination breakpoints were identified at nucleotide positions 2 318, 5 674 and 8 385 in the P1, HC-Pro/P3 and the 5′-terminus of CP gene respectively with high confidence. Phylogenetic analysis indicated that ShX14 was clustered together with HN2 and SYR-NB-16, suggesting that it shared high sequence homology with PVYNTN-NW (SYR-I) strain. Association index (AI), parsimony score (PS) and maximum monophyletic clade (MC) all indicated that ShX14 was strongly associated with the PVYNTN-NW (SYR-I) group. Three fragments of about 1 000, 600 and 400 bp in size were also amplified from the isolate by a multiplex RT-PCR, consisting with the expected band of the PVYNTN-NW (SYR-I) strain. Overall, these analyses strongly indicate that ShX14 is likely to be a PVYNTN-NW strain (SYR-I).[Conclusion] ShX14 is a N×O recombinant isolate, classified to PVYNTN-NW strain (SYR-I). It will provide useful information in the further study of the biology of this pathogen.关键词
马铃薯Y病毒/全基因组/重组/系统发育/系统发育与性状关联分析Key words
Potato virus Y/complete genome/recombination/phylogeny/phylogeny-trait association analysis引用本文复制引用
高芳銮,常飞,沈建国,谢联辉,詹家绥..PVYNTN-NW榆林分离物的全基因组序列测定与分析[J].中国农业科学,2015,(2):270-279,10.基金项目
国家现代农业马铃薯产业技术体系（CARS-10）、福建省自然科学基金（2013J01088）、国家质检总局科技计划（2013IK094）、质检公益性行业科研专项 （）
