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 |
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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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