Abstract: Abstract: Small nucleolar RNAs (snoRNAs) in eukaryotic has been classified into two major families on the basis of conserved motifs, the Box C/D and the Box H/ACA, which involved in pre-ribosomal RNA (pre-rRNA) methylation and pseudouridylations, respectively. A computational screen of Box C/D RNAs in the silkworm genome identified 70 candidate snoRNAs, which were considered to guide 56 sites for methylation. By analyzing the positions and functional regions where snoRNAs located, results indicated that few snoRNA gene clusters in silkworm genome and that the snoRNA genes could diverse in any of the functional regions namely coding region, intergenic region and intron. Functional structures of snoRNA have also been annotated and we found the D' box and terminal stem were not conserved. Moreover, it suggested intronic snoRNAs lacks of canonical terminal stems possibly compensate with the flanking sequences. Similarity comparison of the sequences complementarity to rRNAs showed the possibility that Box C/D snoRNAs contain similar complementary sequences guiding methylation for the same type rRNAs. In addition, the homology analysis of the 70 Box C/D snoRNAs and those reported in Drosophilia melanogaster genome indicated the diversity on primary structure between the two species of animals. With computational screen, the report systematically analyzed the Box C/D snoRNAs in the whole genome of silkworm for the first time and may be helpful to study other non-coding RNAs.

Key words: silkworm, Box C/D snoRNA, methylation, computational screen, ncRNA