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SmallRNA NGS revealed the presence of CVA and LCHV1 on apricot in Hungary

ABSTRACT: Fruit trees, as apricots, can be infected by and are constantly exposed to the attack of viruses. As they are propagated on a vegetative way, this risk is present not only at the field, where they exists for decades, but also during propagation. Metagenomic diagnostic methods, based on next generation sequencing, offer unique possibilities to reveal all the presenting pathogens in the investigated sample. Using small RNA NGS, a special fields of this technique, we tested leaf samples of different varieties of apricot in isolator house and at open air stock nursery. As a result, we identified Cherry Virus A (CVA) and Little Cherry Virus1 (LChV1) first time in Hungary. Gained results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral PCR products enabled us to investigate their phylogenetic relationships. Our results demonstrate, that small RNA NGS can offer a sensitive virus diagnostics method, moreover beside obligatory tested viruses we could detect CVA and LChV1. However as these pathogens haven’t been described in our country before, their role in symptom development and modification during coinfection with other viruses requires further investigations.

ORGANISM(S): Prunus armeniaca

PROVIDER: GSE114251 | GEO | 2018/06/20

REPOSITORIES: GEO

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Project description:The aim of this study was to elucidate the potential use of microarray technology, developed in model species, in related, yet phenotypically distinct, species where few or no information are available. Considering the high degree of sequence conservation within the Rosaceae family and, in particular, among the Prunus species we employed the first available peach oligonucleotide microarray (µPEACH 1.0) for studying the transcrptomic profile during apricot fruit development (Prunus armeniaca L., cv. 'Goldrich'). Fruit material was harvested at three distinct stages, corresponding to immature-green stage (6 weeks before fully-ripe stage), mature-firm-ripe stage (change of peel color, 1 week before fully-ripe stage) and at fully-ripe stage and designated as S1, S2 and S3 stages, respectively. Apricot targets cDNA, when applied the µPEACH1.0, were showing significant hybridization with an average of 43% of spotted targets validating the use of μPEACH1.0 to profile the transcriptome of apricot fruit during development and ripening. Microarray analysis carried out on immature and ripe peach and apricot fruit separately pointed out that 70% of genes differentially expressed was detectable the same pattern of expression in both species. This result indicates that the transcriptome of immature and ripe fruit are quite similar in apricot and peach, but also highlighted the presence of transcript changes specie-specific. When μPEACH1.0 was used to profile apricot developing fruit were identified 400 and 74 genes differetially expressed during the transition from S1 to S2 stage and from S2 to S3 stage, respectively. Intriguingly, a considerable number of auxin action regulators (AUX/IAA) and of genes coding heat shock proteins (hsp) were highly up-regulated at the onset and late of ripening phase, respectively.The comparison between the expression profiles of these apricot genes and their peach hortologues showed a similar pattern for AUX/IAA and quite different for hsps. This result suggests a similar role for AUX/IAA in both species and a more important involvement for hsps in the apricot fruit ripening.

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SmallRNA NGS revealed the presence of CVA and LCHV1 on apricot in Hungary

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