Complete genome analysis of a novel recombinant isolate of potato virus Y from China

Gao, Fangluan; Fei, Chang; Shen, Jianguo; Shi, Fengyang; Xie, Liji; Zhan, Jiasui

doi:10.1007/s00705-014-2184-2

Cited by 17 publications

(12 citation statements)

References 15 publications

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“…Total RNAs were extracted using an RNAsimple Kit according to the manufacturer's instructions (TianGen, Beijing, China). Full‐length cDNAs were synthesized by RT‐PCR using Oligo(dt) 18 and TransScript ® First‐Strand cDNA Synthesis SuperMix (TransGen, Beijing, China) and amplified with two pairs of degenerate primers as described previously (Gao et al., ). PCR amplifications of cDNAs were performed in a total volume of 50 μl composed of 5.0 μl of TransTaq™ 10× HiFi Buffer II, 4.0 μl of dNTPs (2.5 mM), 2.0 μl of forward primer (10 μmol/l), 2.0 μl of reverse primer (10 μmol/l), 34.5 μl of ddH 2 O, 0.5 μl of TransTaq™ HiFi Polymerase (5 U/μl), and 2.0 μl of template cDNA.…”

Section: Methodsmentioning

confidence: 99%

Adaptive evolution and demographic history contribute to the divergent population genetic structure of Potato virus Y between China and Japan

Gao

Zou

Xie

et al. 2017

Evolutionary Applications

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Potato virus Y (PVY) is an important plant pathogen causing considerable economic loss to potato production. Knowledge of the population genetic structure and evolutionary biology of the pathogen, particularly at a transnational scale, is limited but vital in developing sustainable management schemes. In this study, the population genetic structure and molecular evolution of PVY were studied using 127 first protein (P1) and 137 coat protein (CP) sequences generated from isolates collected from potato in China and Japan. High genetic differentiation was found between the populations from the two countries, with higher nucleotide diversity in Japan than China in both genes and a KST value of .216 in the concatenated sequences of the two genes. Sequences from the two countries clustered together according to their geographic origin. Further analyses showed that spatial genetic structure in the PVY populations was likely caused by demographic dynamics of the pathogen and natural selection generated by habitat heterogeneity. Purifying selection was detected at the majority of polymorphic sites although some clade‐specific codons were under positive selection. In past decades, PVY has undergone a population expansion in China, whereas in Japan, the population size of the pathogen has remained relatively constant.

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Section: Methodsmentioning

confidence: 99%

Adaptive evolution and demographic history contribute to the divergent population genetic structure of Potato virus Y between China and Japan

Gao

Zou

Xie

et al. 2017

Evolutionary Applications

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“…When whole genomes are compared, there is apparent agreement between PVY C , PVY O and PVY N isolates defined by inoculation to potato cultivar differentials with genes Nc or Ny , and to tobacco, with their placement within one or other of the phylogenetic PVY C , PVY O and PVY N subgroups, respectively (e.g. Karasev & Gray, and references therein; Gao et al ., ; Jones, and references therein). Whole genome sequences of three PVY Z isolates and PVY E isolate Mon were placed within PVY NTN (PVY Z ) or a separate group between PVY N/NA‐N and PVY NTN lineages (PVY E ) (Chikh‐Ali et al ., ; Karasev & Gray, and references therein; Quintero‐Ferrer et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Improving Potato virus Y strain nomenclature: lessons from comparing isolates obtained over a 73‐year period

Kehoe

Jones

2015

Plant Pathology

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Biological and whole genome properties were compared between eight historical European (1943European ( -1984 and five Australian (2003Australian ( -2012 Potato virus Y (PVY) isolates. Based on eliciting hypersensitivity genes Nc, Ny or Nz, the former belonged to biological strain groups PVY C (CT, CRM1), PVY O (CRN, KE, RS) or PVY Z (CM2, CRM2, DS). The latter were inoculated to differential and other potato cultivars, tobacco and tomato. Two belonged to PVY O (BL, DEL3), one to PVY Z (ATL1), and one (KIP1) to suggested strain group (PVY D ) which elicited putative hypersensitivity gene Nd. Tomato isolate CN1 (and unsequenced CN2), which were poorly adapted to infect potato, were not grouped. Next-generation sequencing (NGS) of samples containing all isolates except CN2, yielded 13 complete sequences of 9592-9700 nucleotides (nt), and one partial sequence of 9002 nt, none being recombinants. Comparing the former with 60 other PVY complete genomes, found one (CRM2) in phylogenetic subgroup Y O , eight in Y O5 (CM2, CRN, DS, KE, RS, ATL1, BL, DEL3), three in Y C2 (CRM1, CT, KIP1) and one in Y C1 (CN1). Thus, biologically defined PVY O (5) and PVY Z (4) isolates were within phylogenetic subgroups Y O or Y O5 , biological PVY C isolates (2) within Y C2 , biological PVY D isolate KIP1 in Y C2 and tomato isolate CN1 in Y C1 . NGS identified KIP1 and partial sequence KIP from mixed infection. KIP was in Y O5 . Grouping of four PVY Z isolates within phylogenetic PVY O , and the PVY D isolate within phylogenetic PVY C , reveals disagreement between current biological and phylogenetic PVY nomenclature systems. Using Latinized numerals for phylogenetic group names resolved this.

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“…These coat protein‐based phylogenetic relationship results were different from those based on the whole genome (Gao et al . ). The PVY NTN clade was clearly divided from other clades such as PVY N , PVY O and PVY C .…”

Section: Resultsmentioning

confidence: 97%

Potato virus Y (PVY) detection in a single aphid by one‐step RT‐PCR with boiling technique

Kim

Jea²,

Kwon³

et al. 2016

Entomological Research

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Potato virus Y (PVY) (Potyviridae: potyvirus) is a serious emerging virus affecting seed potato worldwide. It affects the seed potato by transmitting non‐persistently via aphids. Sometimes this virus induces symptomless infection and is hard to detect in potato. So, it requires a specific and quick diagnosis for efficient examination. Recently, a reverse‐transcription polymerase chain reaction (RT‐PCR)‐based PVY detection method has been developed from plant as well as insect vectors. However, it is a complex and time consuming method. Here, we developed a simple PVY detection method that uses boiling for releasing the viral RNA from aphid stylets, and amplification by PVY‐specific primers located in the viral coat protein gene. The method is suitable for various strains. This simplified method could save time compared to earlier detection methods because of the simplified RNA extraction step. Following this procedure, we tested this one‐step RT‐PCR‐based PVY detection method by using three PVY vectoring aphid species (Myzus persicae, Aphis gossypii and Macrosiphum euphorbiae) as well as other sucking insects such as thrips, Frankliniella occidentalis. The reliability of a newly developed primer set was suitable for RT‐PCR and procedures were successfully demonstrated for virus detection. This PVY detection method is rapid, easy to use and suitable for large‐scale testing in laboratories of seed potato, and could potentially be applied to virus‐free seed potato production.

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Complete genome analysis of a novel recombinant isolate of potato virus Y from China

Cited by 17 publications

References 15 publications

Adaptive evolution and demographic history contribute to the divergent population genetic structure of Potato virus Y between China and Japan

Adaptive evolution and demographic history contribute to the divergent population genetic structure of Potato virus Y between China and Japan

Improving Potato virus Y strain nomenclature: lessons from comparing isolates obtained over a 73‐year period

Potato virus Y (PVY) detection in a single aphid by one‐step RT‐PCR with boiling technique

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