Virus isolates with different pathogenetic properties have distinctive effects on small RNA profiles and expression of RNA silencing genes in tomato (Solanum lycopersicum (Abstract/Comunicazione in atti di convegno)

Type
Label
  • Virus isolates with different pathogenetic properties have distinctive effects on small RNA profiles and expression of RNA silencing genes in tomato (Solanum lycopersicum (Abstract/Comunicazione in atti di convegno) (literal)
Anno
  • 2014-01-01T00:00:00+01:00 (literal)
Alternative label
  • De Paola D., Finetti-Sialer M.M., Catalano D., Tecce T., Cillo F. (2014)
    Virus isolates with different pathogenetic properties have distinctive effects on small RNA profiles and expression of RNA silencing genes in tomato (Solanum lycopersicum
    in Epigenetics, coding and non-coding RNAs - Challenging NGS data, Bari, italy, 25-27/06/2014
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • De Paola D., Finetti-Sialer M.M., Catalano D., Tecce T., Cillo F. (literal)
Note
  • Comunicazione (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • Tecce T., Università degli Studi di Bari (literal)
Titolo
  • Virus isolates with different pathogenetic properties have distinctive effects on small RNA profiles and expression of RNA silencing genes in tomato (Solanum lycopersicum (literal)
Abstract
  • Potato virus Y (PVY) is a pathogen of pepper, potato, tobacco, tomato and other plant hosts. Two PVY isolates, PVY-Cto and PVY-SON41, induce very different disease phenotypes on tomato (Solanum lycopersicum), the former being responsible of leaf distortions and growth reduction and the latter inducing only mild symptoms. With the aim of investigating the role of RNA silencing mechanisms in the different pathogenic behaviour of the two isolates, we performed a systematic analysis of expression profiles of Dicer-like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) genes that form the core components of the RNA silencing-based plant immune system. The effects on expression profiles of some of these genes were higher in tomato plants infected by the aggressive isolate PVY-Cto in comparison with PVY-SON41-infected and healthy plants. We further investigated on whether effects on expression of silencing genes could lead to a differential accumulation of small RNAs (sRNAs) in plants. Both endogenous microRNA (miRNA) and viral small interfering RNA (vsiRNA) populations were analysed by high-throughput sequencing. SRNAs from tomato plants, healthy or infected by PVY-Cto and PVY-SON41, were isolated at 21 and 30 days post-inoculation (dpi) and sequenced using the Illumina platform. Total reads from samples at 21 dpi ranged between 23 to 28 million, and at 30 dpi between 13 to 17 million. From these data, vsiRNA and miRNA populations were analysed separately. VsiRNA from PVY-Cto-infected or PVY-SON41-infected samples were identified using the Bowtie software (Langmead et al., 2009, Genome Biol 10:R25) by mapping reads to the reference genome of the two viral isolates (EU482153.1, AJ439544). As a result, a non-uniform distribution of VsiRNA was observed. PVY-Cto-infected plants accumulated vsiRNA with a peak of 44% at 21 dpi. Surprisingly, a negligible number of vsiRNA were found in PVY-SON41-infected samples, representing less than 1% of total reads. More than 150 known miRNAs were found to be expressed in our six libraries, some of which had relatively high expression abundance and exhibited evolutionary conservation across multiple plant species. MiRNAs read count was proportional to each library size and varied in a narrow range from 2.8 % of total reads in mock-inoculated at 21 dpi to 4,8% in PVY-Cto samples at the same timepoint. Virus infection affected also the profile of miRNAs expression. MiRNA abundance, in different libraries, was normalized to transcripts per million (TPM) and subjected to a Z-test with a significance value of 0.01. Change in miRNA read counts between virus- and mock-inoculated plants was scored as fold change and recorded. On this basis, PVY-Cto infection was associated to the differential accumulation (either up- or downregulated) of 71 and 39 miRNA at 21 and 30 dpi, respectively. The mild PVY-SON41 isolate affected the composition of miRNA population at significantly lower extent, and a differential accumulation was observed only for 25 (21 dpi) and 6 (30 dpi) miRNAs. Our results provide a comparative analysis, via deep sequencing, of changes in the small RNA profiles and in the genes of RNA silencing machinery induced by different viral isolates. They uncover new mechanisms of virus-host interactions that may have practical implications. (literal)
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