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Multiplex detection, distribution, and genetic diversity of Hop stunt viroid and Citrus exocortis viroid infecting citrus in Taiwan. 2015

Chun-Yi Lin, and Meng-Ling Wu, and Tang-Long Shen, and Hsin-Hung Yeh, and Ting-Hsuan Hung
Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan. f97633012@ntu.edu.tw.

BACKGROUND Two citrus viroids, Citrus exocortis viroid (CEVd) and Hop stunt viroid (HSVd), have been reported and become potential threats to the citrus industry in Taiwan. The distributions and infection rates of two viroids have not been investigated since the two diseases were presented decades ago. The genetic diversities and evolutionary relationships of two viroids also remain unclear in the mix citrus planted region. METHODS Multiplex RT-PCR was used to detect the two viroids for the first time in seven main cultivars of citrus. Multiplex real-time RT-PCR quantified the distributions of two viroids in four citrus tissues. Sequence alignment and phylogenetic analysis were performed using the ClustalW and MEGA6 (neighbor-joining with p-distance model), respectively. RESULTS HSVd was found more prevalent than CEVd (32.2% vs. 30.4%). Both CEVd and HSVd were commonly found simultaneously in the different citrus cultivars (up to 55%). Results of the multiplex quantitative analysis suggested that uneven distributions of both viroids with twig bark as the most appropriate material for studies involving viroid sampling such as quarantine inspection. Sequence alignment against Taiwanese isolates, along with analysis of secondary structure, revealed the existence of 10 and 5 major mutation sites in CEVd and HSVd, respectively. The mutation sites in CEVd were located at both ends of terminal and variability domains, whereas those in HSVd were situated in left terminal and pathogenicity domains. A phylogenetic analysis incorporating worldwide viroid isolates indicated three and two clusters for the Taiwanese isolates of CEVd and HSVd, respectively. CONCLUSIONS Moderately high infection and co-infection rates of two viroids in certain citrus cultivars suggest that different citrus cultivars may play important roles in viroid infection and evolution. These data also demonstrate that two multiplex molecular detection methods developed in the present study provide powerful tools to understand the genetic diversities among viroid isolates and quantify viroids in citrus host. Our field survey can help clarify citrus-viroid relationships as well as develop proper prevention strategies.

UI MeSH Term Description Entries
D008969 Molecular Sequence Data Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D010935 Plant Diseases Diseases of plants. Disease, Plant,Diseases, Plant,Plant Disease
D002957 Citrus A plant genus of the family RUTACEAE. They bear the familiar citrus fruits including oranges, grapefruit, lemons, and limes. There are many hybrids which makes the nomenclature confusing. Citron Tree,Fruit, Citrus,Lemon Tree,Orange Tree, Bitter,Orange Tree, Mandarin,Orange Tree, Seville,Orange Tree, Sour,Pomelo Tree,Pummelo Tree,Tangerine Tree,Citrus Fruit,Citrus aurantium,Citrus bergamia,Citrus grandis,Citrus hystrix,Citrus limon,Citrus maxima,Citrus medica,Citrus reticulata,Kaffir Lime,Bitter Orange Tree,Bitter Orange Trees,Citron Trees,Citrus aurantiums,Citrus bergamias,Citrus grandi,Citrus hystrices,Citrus medicas,Citrus reticulatas,Lemon Trees,Lime, Kaffir,Mandarin Orange Tree,Mandarin Orange Trees,Orange Trees, Bitter,Orange Trees, Mandarin,Orange Trees, Seville,Orange Trees, Sour,Pomelo Trees,Pummelo Trees,Seville Orange Tree,Seville Orange Trees,Sour Orange Tree,Sour Orange Trees,Tangerine Trees,Tree, Bitter Orange,Tree, Citron,Tree, Lemon,Tree, Mandarin Orange,Tree, Pomelo,Tree, Pummelo,Tree, Seville Orange,Tree, Sour Orange,Tree, Tangerine,Trees, Bitter Orange,Trees, Citron,Trees, Lemon,Trees, Mandarin Orange,Trees, Pomelo,Trees, Pummelo,Trees, Seville Orange,Trees, Sour Orange,Trees, Tangerine,aurantium, Citrus,bergamia, Citrus,hystrices, Citrus,maxima, Citrus,medicas, Citrus,reticulata, Citrus
D005838 Genotype The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS. Genogroup,Genogroups,Genotypes
D013624 Taiwan Country in eastern Asia, islands bordering the East China Sea, Philippine Sea, South China Sea, and Taiwan Strait, north of the Philippines, off the southeastern coast of China. The capital is Taipei. The alternate country name is Republic of China. Formosa,Republic of China
D014644 Genetic Variation Genotypic differences observed among individuals in a population. Genetic Diversity,Variation, Genetic,Diversity, Genetic,Diversities, Genetic,Genetic Diversities,Genetic Variations,Variations, Genetic
D014772 Viroids A group of pathogens comprising the smallest known agents of infectious disease. They are unencapsulated and are capable of replicating autonomously in susceptible cells. Positively identified viroids composed of single-stranded RNA have been isolated from higher plants, but the existence of DNA viroids pathogenic to animals is suspected. Viroid
D017385 Sequence Homology The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species. Homologous Sequences,Homologs, Sequence,Sequence Homologs,Homolog, Sequence,Homologies, Sequence,Homologous Sequence,Homology, Sequence,Sequence Homolog,Sequence Homologies,Sequence, Homologous,Sequences, Homologous
D017422 Sequence Analysis, DNA A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis. DNA Sequence Analysis,Sequence Determination, DNA,Analysis, DNA Sequence,DNA Sequence Determination,DNA Sequence Determinations,DNA Sequencing,Determination, DNA Sequence,Determinations, DNA Sequence,Sequence Determinations, DNA,Analyses, DNA Sequence,DNA Sequence Analyses,Sequence Analyses, DNA,Sequencing, DNA

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