Additional file 3.

Silkworm miRNAs identified by Solexa sequencing. In all, 324 miRNA genes (loci) were identified in the silkworm genome, responsible for 209 unique miRNAs and 87 star sequences, which were screened from the raw data through flow data filtration. All known and novel miRNAs have been submitted to the international public DataBase, miRBase. The temporal names of novel miRNAs were replaced by the assigned names. The bmo-mir-276 well mapped to Build 1, but not to the Build2 genome sequence (blast 1e-5). Three new miRNAs, bmo-mir-100, bmo-mir-92b and bmo-mir-216, did not pass the filtering threshold due to their uncanonical hairpin structures, but were finally identified through homolog searches. Another two annotated miRNAs, bmo-mir-1920 and bmo-mir-1921, were not included in this file, since they showed sequential processing in generating mature sequences and no more accumulated reads were observed (Additional file 10). Several novel miRNA genes have duplicated loci within the silkworm genome. The U in the sequence was replaced with T, and sequences presented in the DNA form.

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Liu et al. BMC Genomics 2010 11:148   doi:10.1186/1471-2164-11-148