Identification and molecular characterization of a novel monopartite geminivirus associated with mulberry mosaic dwarf disease

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Identification and characterization of a novel geminivirus with a monopartite genome infecting apple trees

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Further insight into genetic variation and haplotype diversity of <em>Cherry virus A</em> from China.

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

Global Transcriptomic Changes Induced by Infection of Cucumber (Cucumis sativus L.) with Mild and Severe Variants of Hop Stunt Viroid

Fifteen years after transfer to hops, hop stunt viroid-grapevine (HSVd-g) was replaced by HSVd-hop (HSVd-h), a sequence variant that contains changes at five different positions. HSVd-g54 is a laboratory mutant derived from HSVd-g that differs from its progenitor by a single G to A substitution at position 54. While infection by HSVd-h induces only mild stunting in cucumber (Cucumis sativus L.), HSVd-g54 induces much more severe symptoms in this indicator host. Comparison of transcriptome profiles of cucumber infected with HSVd-h or HSVd-g54 with those of mock-inoculated controls obtained by whole transcriptome shotgun sequencing revealed that many genes related to photosynthesis were down-regulated following infection. In contrast, genes encoding RNA-dependent RNA polymerase 1 (CsRDR1), especially CsRDR1c1 and CsRDR1c2, as well as those related to basal defense responses were up-regulated. Expression of genes associated with phytohormone signaling pathways were also altered, indicating that viroid infection initiates a complex array of changes in the host transcriptome. HSVd-g54 induced an earlier and stronger response than HSVd-h, and further examination of these differences will contribute to a better understanding of the mechanisms that determine viroid pathogenicity

Putative recombination events detected in the CVA complete genome dataset using RDP 4.0.

<p>Putative recombination events detected in the CVA complete genome dataset using RDP 4.0.</p

Phylogenetic analysis of CVA isolates based on nucleotide sequence datasets of the RdRp core region.

<p>Trees were constructed by the neighbor-joining (NJ) method using MEGA5 software. Bootstrap values (1,000 replicates) are given at the branch nodes. Branches corresponding to partitions reproduced in <70% of bootstrap replicates are collapsed. Sequences obtained in this study are marked with a red triangle while those Chinese isolates from GenBank are marked with a black round. <i>Cherry necrotic rusty mottle virus</i> (CNRMV) was used as out-group.</p

Comparison of the ChYT52 isolate with 85 complete CVA genomic sequences in GenBank in different genomic regions.

<p>Comparison of the ChYT52 isolate with 85 complete CVA genomic sequences in GenBank in different genomic regions.</p

Phylogenetic analysis of CVA isolates based on complete genome sequence.

<p>Trees were constructed by the neighbor-joining (NJ) method using MEGA5 software. Bootstrap values (1,000 replicates) are given at the branch nodes. Branches corresponding to partitions reproduced in <75% of bootstrap replicates are collapsed. The isolate for which the complete genome sequence was obtained in the present study (ChYT52) is marked with a red triangle while sequences from Chinese obtained in GenBank are marked with a red round. <i>Cherry necrotic rusty mottle virus</i> (CNRMV) was used as out-group.</p

Metrics for sequences used in the analyses in this study.

<p>Metrics for sequences used in the analyses in this study.</p

Haplotype/nucleotide diversity and neutrality tests in three different genomic regions with respect to phylogroups of CVA isolates.

<p>Haplotype/nucleotide diversity and neutrality tests in three different genomic regions with respect to phylogroups of CVA isolates.</p