title: Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs.
abstract: BACKGROUND
  Small nucleolar RNAs (snoRNAs) represent one of the largest groups of functionally diverse trans-acting non-protein-coding (npc) RNAs currently known in eukaryotic cells. Chicken snoRNAs have been very poorly characterized when compared to other vertebrate snoRNAs. A genome-wide analysis of chicken snoRNAs is therefore of great importance to further understand the functional evolution of snoRNAs in vertebrates.
  
  
  RESULTS
  Two hundred and one gene variants encoding 93 box C/D and 62 box H/ACA snoRNAs were identified in the chicken genome and are predicted to guide 86 2'-O-ribose methylations and 69 pseudouridylations of rRNAs and spliceosomal RNAs. Forty-four snoRNA clusters were grouped into four categories based on synteny characteristics of the clustered snoRNAs between chicken and human. Comparative analyses of chicken snoRNAs revealed extensive recombination and separation of guiding function, with cooperative evolution between the guiding duplexes and modification sites. The gas5-like snoRNA host gene appears to be a hotspot of snoRNA gene expansion in vertebrates. Our results suggest that the chicken is a good model for the prediction of functional snoRNAs, and that intragenic duplication and divergence might be the major driving forces responsible for expansion of novel snoRNA genes in the chicken genome.
  
  
  CONCLUSIONS
  We have provided a detailed catalog of chicken snoRNAs that aids in understanding snoRNA gene repertoire differences between avians and other vertebrates. Our genome-wide analysis of chicken snoRNAs improves annotation of the 'darkness matter' in the npcRNA world and provides a unique perspective into snoRNA evolution in vertebrates.
authors.affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Zhongshan University, Guangzhou, PR China. lsssp@mail.sysu.edu.cn
authors.forename: Peng
authors.initials: P
authors.lastname: Shao
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Yang
authors.forename: Hui
authors.initials: H
authors.lastname: Zhou
authors.forename: Dao-Gang
authors.initials: DG
authors.lastname: Guan
authors.forename: Liang-Hu
authors.initials: LH
authors.lastname: Qu
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D019295:Computational Biology; D019143:Evolution, Molecular; D015723:Gene Library; D016678:Genome; D006801:Humans; D020537:RNA, Small Nucleolar / Q000235:genetics*; D016415:Sequence Alignment; D026801:Synteny
chemical_list: D020537:RNA, Small Nucleolar