ARS | Publication request: Comparative analyses of endogenous Small RNAs in Sclerotinia sclerotiorum and S. trifoliorum

Submitted to: Phytopathology
Publication Type: Abstract Only
Publication Acceptance Date: May 1, 2011
Publication Date: June 1, 2011
Citation: Qiu, D., Vandemark, G.J., Chen, W. 2011. Comparative analyses of endogenous Small RNAs in Sclerotinia sclerotiorum and S. trifoliorum. Phytopathology. 101:S148.

Technical Abstract: Endogenous small RNAs (sRNAs) of Sclerotinia sclerotiorum and S. trifoliorum were compared to gain insight into the biology of the two closely related plant pathogens. Random samples of 53 unique sRNAs of S. sclerotiorum and 55 unique sRNAs of S. trifoliorum had, respectively, 221 and 229 target loci in the S. sclerotiorum genome database. More than half of the sRNAs targeted to exons in both species. The sRNA target loci were not evenly distributed among the 37 supercontigs of the S. sclerotiorum genome. The sRNA target loci from S. trifoliorum had the highest frequency per megabase sequence in Supercontig 35, whereas Supercontig 36 had the highest frequency of sRNA target loci of S. sclerotiorum, suggesting that supercontigs 35 and 36 are hot-spots for sRNA biogenesis. Four sRNAs were found in both species (four pairs). Two pairs targeted five orthologs of the same Tf2 retrotransposon. The other two pairs targeted exons, one of which is a microRNA-like sRNA. However, BLAST searches found no similar sequences in the microRNA database (MIR-BASE), suggesting fungi have different mechanisms of sRNA biogenesis than other eukaryotes. Two putative dicer-like (DCL) genes were identified, and DCL-2 was expressed at higher levels than DCL-1 in both species. Similarly, among three putative Argonaut protein gene transcripts, AGO1 was the highest expressed Argonaut protein gene in both species, suggesting prominent roles of DCL-2 and AGO1 in sRNA biogenesis of Sclerotinia species.