Further insight into genetic variation and haplotype diversity of Cherry virus A from China

Autor: Yunxiao Xu, Rui Gao, Thierry Candresse, Yuxin Ma, Shifang Li, Meiguang Lu, Zhen He
Přispěvatelé: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Chinese Academy of Agricultural Sciences (CAAS), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Yangzhou University
Jazyk: angličtina
Rok vydání: 2017
Předmět:
0301 basic medicine
haplotype
Heredity
Virologie
lcsh:Medicine
Genome
Plant Viruses
santé des plantes
lcsh:Science
Cherries
pathologie végétale
Phylogeny
Data Management
Recombination
Genetic

Genetics
Multidisciplinary
Phylogenetic tree
Nucleotides
Database and informatics methods
Sequence analysis
Eukaryota
Phylogenetic Analysis
Plants
Phylogenetics
Genetic Mapping
arbre fruitier à noyau
GenBank
[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Prunus
Research Article
Computer and Information Sciences
China
Bioinformatics
Phytopathology and phytopharmacy
cerisier
Genome
Viral

Biology
Real-Time Polymerase Chain Reaction
analyse phylogénétique
Fruits
03 medical and health sciences
Sequence Motif Analysis
Virology
Genetic variation
Evolutionary Systematics
DNA sequence analysis
Taxonomy
Plant Diseases
chine
Evolutionary Biology
Genetic diversity
virus phytopathogène
RNA sequence analysis
Base Sequence
lcsh:R
Haplotype
Organisms
Biology and Life Sciences
Genetic Variation
Sequence Analysis
DNA

Phytopathologie et phytopharmacie
variation génétique
[SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Research and analysis methods
030104 developmental biology
Haplotypes
Evolutionary biology
lcsh:Q
cherry virus a
Sequence Alignment
Reference genome
Zdroj: PLoS ONE
PLoS ONE, Public Library of Science, 2017, 12 (10), pp.e0186273. ⟨10.1371/journal.pone.0186273⟩
Plos One 10 (12), e0186273. (2017)
PLoS ONE, Vol 12, Iss 10, p e0186273 (2017)
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0186273⟩
Popis: UMR BFP - Equipe Virologie; International audience; Cherry virus A (CVA) infection appears to be prevalent in cherry plantations worldwide. In this study, the diversity of CVA isolates from 31 cherry samples collected from different orchards around Bohai Bay in northeastern China was analyzed. The complete genome of one of these isolates, ChYT52, was found to be 7,434 nt in length excluding the poly (A) tail. It shares between 79.9-98.7% identity with CVA genome sequences in GenBank, while its RdRp core is more divergent (79.1-90.7% nt identity), likely as a consequence of a recombination event. Phylogenetic analysis of ChYT52 genome with CVA genomes in Genbank resulted in at least 7 major clusters plus additional 5 isolates alone at the end of long branches suggesting the existence of further phylogroups diversity in CVA. The genetic diversity of Chinese CVA isolates from 31 samples and GenBank sequences were analyzed in three genomic regions that correspond to the coat protein, the RNA-dependent RNA polymerase core region, and the movement protein genes. With few exceptions likely representing further recombination impact, the trees various trees are largely congruent, indicating that each region provides valuable phylogenetic information. In all cases, the majority of the Chinese CVA isolates clustering in phylogroup I, together with the X82547 reference sequence from Germany. Statistically significant negative values were obtained for Tajima's D in the three genes for phylogroup I, suggesting that it may be undergoing a period of expansion. There was considerable haplotype diversity in the individual samples and more than half samples contained genetically diverse haplotypes belonging to different phylogroups. In addition, a number of statistically significant recombination events were detected in CVA genomes or in the partial genomic sequences indicating an important contribution of recombination to CVA evolution. This work provides a foundation for elucidation of the epidemiological characteristics and evolutionary history of CVA populations.
Databáze: OpenAIRE
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