Background

RNA interference (RNAi) is involved in genome defence and diverse cellular, developmental, physiological processes. Key components of RNAi are Argonaute, Dicer, and RNA-dependent RNA Polymerase (RdRP), which have been functionally characterized mainly in model organisms. The key components are believed to exist throughout the eukaryotes, however, no systematic platform is present for archiving and dissecting these important gene families. In addition, only a few fungi are studied to date, limiting our understanding of RNAi in fungi. Here we present funRNA (http://funrna.riceblast.snu.ac.kr/), a fungal kingdom-wide genomics platform for putative genes encoding Argonaute, Dicer, and RdRP.

Description

To identify and archive the genes encoding the key components, protein domain profiles were determined from the characterized sequences. The domain profiles were searched on fungal, metazoan, and plant genomes as well as bacterial and archaeal ones. In total of 1,163 Argonaute, 442 Dicer, and 678 RdRP-encoding genes were predicted. Based on the identification results, active site variation of Argonautes, diversification of Dicers, and structural conserveness of RdRP were discussed in a fungi-oriented manner. funRNA provides results from diverse bioinformatics programs and job submission forms for BLAST, BLASTMatrix, and ClustalW. Furthermore, sequence collections created in funRNA are synced with several family analysis portals and databases, offering further analysis opportunities.

Conclusions

By providing the identification results from a broad range of taxonomy and diverse analysis functions, funRNA could be used in diverse comparative and evolutionary studies. Therefore, funRNA would serve as a versatile genomics workbench for key components of RNAi.