SUMMARY: In plants, many trans-acting small interfering RNA (ta-siRNA) regulatory pathways have been identified as significant components of the gene networks involved in development, metabolism, responses to biotic and abiotic stresses and DNA methylation at the TAS locus. To obtain a more comprehensive understanding on the nature of ta-siRNA regulatory pathways, we developed a freely accessible resource, tasiRNAdb, to serve as a repository for the sequences of ta-siRNA regulatory pathway-related microRNAs, TASs, ta-siRNAs and ta-siRNA targets, and for the cascading relations among them. With 583 pathways from 18 species, tasiRNAdb is the largest resource for known ta-siRNA regulatory pathways currently available. tasiRNAdb also provides a tool named TasExpAnalysis that was developed to map user-submitted small RNA and degradome libraries to a stored/input TAS and to perform sRNA phasing analysis and TAS cleavage analysis. AVAILABILITY: The database of plant ta-siRNA regulatory pathways is available at http://bioinfo.jit.edu.cn/tasiRNADatabase/.

MOTIVATION: Trans-acting small interfering RNAs (ta-siRNAs) play an essential role in the regulation of plant gene expression, but relevant reports are still limited. Bioinformatic analyses indicate that many ta-siRNA-producing loci (TASs) are present in plants, implying the existence of as yet undiscovered ta-siRNAs and related regulatory pathways. To expand our knowledge of these plant gene regulators, we applied high-throughput computational and experimental methods to grapevine (Vitis vinifera L.). RESULTS: Based on bioinformatic predictions, we identified 49 TASs from 49 055 small RNA clusters. Using RNA degradome analysis, we experimentally validated 5 TASs, 22 ta-siRNAs and 37 ta-siRNA targets. The cis-activities of ta-siRNAs were also confirmed, which suggested an inactive mechanism of TAS transcription, and a produced mechanism of multiple forms of small RNA from same TAS. We examined the conservation of newly identified ta-siRNA regulatory cascades and found that while the cascade related to vviTAS3 was conserved, cascades related to vviTAS7, vviTAS8, vviTAS9 and vviTAS10 were grape-specific. These results broaden the known scope of ta-siRNA regulation.