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Background: SnoRNAs represent an excellent model for studying the structural and functional evolution of small non-coding RNAs involved in the post-transcriptional modification machinery for rRNAs and snRNAs in eukaryotic cells. Identification of snoRNAs from Neurospora crassa, an important model organism playing key roles in the development of modern genetics, biochemistry and molecular biology will provide insights into the evolution of snoRNA genes in the fungus kingdom. Results: Fifty five box C/D snoRNAs were identified and predicted to guide 71 2'-O-methylated sites including four sites on snRNAs and three sites on tRNAs. Additionally, twenty box H/ACA snoRNAs, which potentially guide 17 pseudouridylations on rRNAs, were also identified. Although not exhaustive, the study provides the first comprehensive list of two major families of snoRNAs from the filamentous fungus N. crassa. The independently transcribed strategy dominates in the expression of box H/ACA snoRNA genes, whereas most of the box C/D snoRNA genes are intron-encoded. This shows that different genomic organizations and expression modes have been adopted by the two major classes of snoRNA genes in N. crassa . Remarkably, five gene clusters represent an outstanding organization of box C/D snoRNA genes, which are well conserved among yeasts and multicellular fungi, implying their functional importance for the fungus cells. Interestingly, alternative splicing events were found in the expression of two polycistronic snoRNA gene hosts that resemble the UHG-like genes in mammals. Phylogenetic analysis further revealed that the extensive separation and recombination of two functional elements of snoRNA genes has occurred during fungus evolution. Conclusion: This is the first genome-wide analysis of the filamentous fungus N. crassa snoRNAs that aids in understanding the differences between unicellular fungi and multicellular fungi. As compared with two yeasts, a more complex pattern of methylation guided by box C/D snoRNAs in multicellular fungus than in unicellular yeasts was revealed, indicating the high diversity of post-transcriptional modification guided by snoRNAs in the fungus kingdom. [ABSTRACT FROM AUTHOR]

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. Conclusion: 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. [ABSTRACT FROM AUTHOR]