家蚕基因组中SnoRNA（Box C/D）的生物信息学分析与研究

【目的】探索生物信息方法在家蚕基因组 snoRNA 预测中的应用，了解snoRNA在家蚕基因组的分布和结构特征。【方法】利用已有和自行设计的生物信息工具对家蚕基因组中Box C/D snoRNA 进行预测和手工校正。【结果】获到家蚕基因组中的 70 个 snoRNA 和 56 个推测的甲基化位点。结构分析发现 D′box 和末端茎环结构的不保守性；分析 snoRNA 在基因组上的分布，未发现普遍的成簇分布的现象，且内含子和基因间隔区的 snoRNA 数目接近；预测得到的家蚕 Box C/D snoRNA 与已报道果蝇 Box C/D snoRNA进行相似性分析，表明两个物种的 Box C/D snoRNAs 在一级结构上存在较大的差异。【结论】基于结构特征预测的方法有利于逐步揭示家蚕基因组中存在的 snoRNA 信息；但与家蚕同源关系较近的物种，其 snoRNA 在序列上可能有较大变化，故可能不适合以序列同源来对其进行预测。

Bioinformatics Identification and Analysis for Box C/D SnoRNAs in Silkworm Genome

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.