title: Experimental RNomics and genomic comparative analysis reveal a large group of species-specific small non-message RNAs in the silkworm Bombyx mori.
abstract: Accumulating evidences show that small non-protein coding RNAs (ncRNAs) play important roles in development, stress response and other cellular processes. The silkworm is an important model for studies on insect genetics and control of lepidopterous pests. Here, we have performed the first systematic identification and analysis of intermediate size ncRNAs (50-500 nt) in the silkworm. We identified 189 novel ncRNAs, including 141 snoRNAs, six snRNAs, three tRNAs, one SRP and 38 unclassified ncRNAs. Forty ncRNAs showed significantly altered expression during silkworm development or across specific stage transitions. Genomic comparisons revealed that 123 of these ncRNAs are potentially silkworm-specific. Analysis of the genomic organization of the ncRNA loci showed that 32.62% of the novel snoRNA loci are intergenic, and that all the intronic snoRNAs follow the pattern of one-snoRNA-per-intron. Target site analysis predicted a total of 95 2'-O-methylation and pseudouridylation modification sites of rRNAs, snRNAs and tRNAs. Together, these findings provide new clues for future functional study of ncRNA during insect development and evolution.
authors.affiliation: Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, China.
authors.forename: Dandan
authors.initials: D
authors.lastname: Li
authors.forename: Yanhong
authors.initials: Y
authors.lastname: Wang
authors.forename: Kun
authors.initials: K
authors.lastname: Zhang
authors.forename: Zhujin
authors.initials: Z
authors.lastname: Jiao
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerboe
authors.forename: Xiangqian
authors.initials: X
authors.lastname: Guo
authors.forename: Viswanathan
authors.initials: V
authors.lastname: Chinnusamy
authors.forename: Lijun
authors.initials: L
authors.lastname: Bi
authors.forename: Yongping
authors.initials: Y
authors.lastname: Huang
authors.forename: Shuanglin
authors.initials: S
authors.lastname: Dong
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
authors.forename: Yunchao
authors.initials: Y
authors.lastname: Kan
mesh_terms: D000818:Animals; D001483:Base Sequence; D012831:Bombyx / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D049750:Genome, Insect; D023281:Genomics; D008969:Molecular Sequence Data; D020537:RNA, Small Nucleolar / Q000235:genetics / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000235:genetics / Q000378:metabolism*; D013045:Species Specificity
chemical_list: D020537:RNA, Small Nucleolar; D058727:RNA, Small Untranslated