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SnoPatrol: how many snoRNA genes are there?

Gardner PP, Bateman A, Poole AM - J. Biol. (2010)

Bottom Line: Small nucleolar RNAs (snoRNAs) are among the most evolutionarily ancient classes of small RNA.Two experimental screens published in BMC Genomics expand the eukaryotic snoRNA catalog, but many more snoRNAs remain to be found.

View Article: PubMed Central - HTML - PubMed

Affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB101SA, UK. pg5@sanger.ac.uk

ABSTRACT
Small nucleolar RNAs (snoRNAs) are among the most evolutionarily ancient classes of small RNA. Two experimental screens published in BMC Genomics expand the eukaryotic snoRNA catalog, but many more snoRNAs remain to be found.

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The taxonomic distribution of existing snoRNA annotations. The figure displays a tree derived from the top three levels of the National Center for Biotechnology Information (NCBI) taxonomy. Mapped onto this are counts of: (1) the snoRNP-associated Pfam 24.0 domains Nop, Nop10p, Gar1, SHQ1, fibrillarin and TruB_N (blue); (2) the small subunit (SSU) rRNA regions annotated by Rfam 10.0 (green); (3) genome projects registered as completed, draft or in progress from the GOLD database (version 3.0, October 22, 2009) (gold); (4) all snoRNA regions annotated by Rfam 10.0 (red); (5) EMBL sequences annotated as snoRNAs that are also annotated by Rfam 10.0 (pink). We only show here the lineages where a significant amount of sequencing effort has been directed (see Supplementary Table 1 in Additional data file 1 for the full results). Lengths of the bars correspond to counts in each taxa for each category. The shortest bar length corresponds to counts between 1 and 10 (exclusive), the next shortest is between 10 and 100 (exclusive), and so on.
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Figure 2: The taxonomic distribution of existing snoRNA annotations. The figure displays a tree derived from the top three levels of the National Center for Biotechnology Information (NCBI) taxonomy. Mapped onto this are counts of: (1) the snoRNP-associated Pfam 24.0 domains Nop, Nop10p, Gar1, SHQ1, fibrillarin and TruB_N (blue); (2) the small subunit (SSU) rRNA regions annotated by Rfam 10.0 (green); (3) genome projects registered as completed, draft or in progress from the GOLD database (version 3.0, October 22, 2009) (gold); (4) all snoRNA regions annotated by Rfam 10.0 (red); (5) EMBL sequences annotated as snoRNAs that are also annotated by Rfam 10.0 (pink). We only show here the lineages where a significant amount of sequencing effort has been directed (see Supplementary Table 1 in Additional data file 1 for the full results). Lengths of the bars correspond to counts in each taxa for each category. The shortest bar length corresponds to counts between 1 and 10 (exclusive), the next shortest is between 10 and 100 (exclusive), and so on.

Mentions: To investigate the taxonomic distribution of the known snoRNAs and highlight where potential new discoveries can be made, we have gathered data from the Pfam (protein families), Rfam (RNA families), Genomes Online (GOLD) and EMBL databases (Figure 2). The Rfam database uses experimentally validated ncRNA sequences that have been deposited in EMBL to search for homologous sequences across all nucleotide sequences (see the red and pink bars in Figure 2). The results show that for many major taxonomic clades there are few or no known snoRNAs annotated.


SnoPatrol: how many snoRNA genes are there?

Gardner PP, Bateman A, Poole AM - J. Biol. (2010)

The taxonomic distribution of existing snoRNA annotations. The figure displays a tree derived from the top three levels of the National Center for Biotechnology Information (NCBI) taxonomy. Mapped onto this are counts of: (1) the snoRNP-associated Pfam 24.0 domains Nop, Nop10p, Gar1, SHQ1, fibrillarin and TruB_N (blue); (2) the small subunit (SSU) rRNA regions annotated by Rfam 10.0 (green); (3) genome projects registered as completed, draft or in progress from the GOLD database (version 3.0, October 22, 2009) (gold); (4) all snoRNA regions annotated by Rfam 10.0 (red); (5) EMBL sequences annotated as snoRNAs that are also annotated by Rfam 10.0 (pink). We only show here the lineages where a significant amount of sequencing effort has been directed (see Supplementary Table 1 in Additional data file 1 for the full results). Lengths of the bars correspond to counts in each taxa for each category. The shortest bar length corresponds to counts between 1 and 10 (exclusive), the next shortest is between 10 and 100 (exclusive), and so on.
© Copyright Policy
Related In: Results  -  Collection

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Figure 2: The taxonomic distribution of existing snoRNA annotations. The figure displays a tree derived from the top three levels of the National Center for Biotechnology Information (NCBI) taxonomy. Mapped onto this are counts of: (1) the snoRNP-associated Pfam 24.0 domains Nop, Nop10p, Gar1, SHQ1, fibrillarin and TruB_N (blue); (2) the small subunit (SSU) rRNA regions annotated by Rfam 10.0 (green); (3) genome projects registered as completed, draft or in progress from the GOLD database (version 3.0, October 22, 2009) (gold); (4) all snoRNA regions annotated by Rfam 10.0 (red); (5) EMBL sequences annotated as snoRNAs that are also annotated by Rfam 10.0 (pink). We only show here the lineages where a significant amount of sequencing effort has been directed (see Supplementary Table 1 in Additional data file 1 for the full results). Lengths of the bars correspond to counts in each taxa for each category. The shortest bar length corresponds to counts between 1 and 10 (exclusive), the next shortest is between 10 and 100 (exclusive), and so on.
Mentions: To investigate the taxonomic distribution of the known snoRNAs and highlight where potential new discoveries can be made, we have gathered data from the Pfam (protein families), Rfam (RNA families), Genomes Online (GOLD) and EMBL databases (Figure 2). The Rfam database uses experimentally validated ncRNA sequences that have been deposited in EMBL to search for homologous sequences across all nucleotide sequences (see the red and pink bars in Figure 2). The results show that for many major taxonomic clades there are few or no known snoRNAs annotated.

Bottom Line: Small nucleolar RNAs (snoRNAs) are among the most evolutionarily ancient classes of small RNA.Two experimental screens published in BMC Genomics expand the eukaryotic snoRNA catalog, but many more snoRNAs remain to be found.

View Article: PubMed Central - HTML - PubMed

Affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB101SA, UK. pg5@sanger.ac.uk

ABSTRACT
Small nucleolar RNAs (snoRNAs) are among the most evolutionarily ancient classes of small RNA. Two experimental screens published in BMC Genomics expand the eukaryotic snoRNA catalog, but many more snoRNAs remain to be found.

Show MeSH