Gene family Diversification in conserved miRNAs target sites in Tomato revealed as layers of interaction with a nuclear-replicating virus.

ABSTRACT: In the present study we diagnosed cleaved transcripts in either healthy or virus infected plants, by sRNAome and metagenome of degraded mRNAs. We integrated the experimentally obtained data with publicly available annotations and we gained a deep insight into the parallel evolution of gene families and the transcriptional regulation mediated by miRNAs in Tomato. Gene expression is finely regulated to specific paralogues in gene families such as the squamosa-promoter binding protein-like, the Auxin Response Factor, the Class III homeodomain-leucine zipper, the Argonaute gene families, just to name a few. In some cases, different miRNA are expressed to target different copies of the same family. Size fractionated small RNA from total RNA extracts of Solanum lycopesicum cv. "Money Maker" were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina high throughput pyrosequencing. The kit used is TrueSeq Small RNA kit, Illumina. Please see www.illumina.com for details of the sequencing technology. PARE libraries were generated starting from Poly(A) fraction used for sRNA isolation. The protocol used have been previously described in German et al., 2009, Nature protocols. Please see www.illumina.com for details of the sequencing technology.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE93648 | GEO | 2018/09/28

REPOSITORIES: GEO