家蚕基因组中SnoRNA(Box C/D)的生物信息学分析与研究  

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

作　　者：余东亮[1,2] 汪旭升[3] 徐飞[3] 傅衍[1,2] 

机构地区：[1]浙江大学沃森基因组科学研究院 [2]浙江大学动物科学学院,杭州310029 [3]浙江大学农业与生物技术学院生物信息学研究所

出　　处：《中国农业科学》2007年第1期196-203,共8页Scientia Agricultura Sinica

基　　金：国家重点基础研究发展计划"973"项目(2004CB117500)

摘　　要：【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BoxC/DsnoRNA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BoxC/DsnoRNA与已报道果蝇BoxC/DsnoRNA进行相似性分析,表明两个物种的BoxC/DsnoRNAs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。[ Objective ] Attempt to use bioinformatic tools to predict snoRNAs presence in the silkworm genome, and acquire its structure and distribution information. [ Method ] The tool SNOSCAN and our developed script were performed for prediction of Box C/D snoRNA, and the preliminary results were manually verified. [Result] 70 candidate snoRNAs were identified, which were considered to guide 56 sites for methylation. Analysis of the snoRNAs＇ distribution indicated that there are few snoRNA gene clusters scattered through the whole genome. Functional structures of snoRNA have also been annotated, and we found the D＇ boxes and terminal stems were not conserved. Moreover, it suggested that intronic snoRNAs lack canonical terminal stems （possibly compensated with the flanking sequences）. Comparison of the sequences complementary to rRNAs showed the possibility that Box C/D snoRNAs contain similar complementary sequences. These guide 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. [ Conclusion] It is effective to predict the snoRNAs in silkworm genome based on structure feature, however, homology searching seems less helpful because of the high diversity.

关 键 词：家蚕(Bombyx mori) BOX C/D SNORNA 甲基化 计算机预测 非编码RNA 

分 类 号：S881.2[农业科学—特种经济动物饲养]