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Abstract
Ribosomal protein genes (RPGs) are a powerful tool for studying intron evolution. They exist in all three domains of life and are much conserved. Accumulating genomic data suggest that RPG introns in many organisms abound with non-protein-coding-RNAs (ncRNAs). These ancient ncRNAs are small nucleolar RNAs (snoRNAs) essential for ribosome assembly. They are also mobile genetic elements and therefore probably important in diversification and enrichment of transcriptomes through various mechanisms such as intron/exon gain/loss. snoRNAs in basal metazoans are poorly characterized. We examined 449 RPG introns, in total, from four demosponges: Amphimedon queenslandica, Suberites domuncula, Suberites ficus and Suberites pagurorum and showed that RPG introns from A. queenslandica share position conservancy and some structural similarity with “higher” metazoans. Moreover, our study indicates that mobile element insertions play an important role in the evolution of their size. In four sponges 51 snoRNAs were identified. The analysis showed discrepancies between the snoRNA pools of orthologous RPG introns between S. domuncula and A. queenslandica. Furthermore, these two sponges show as much conservancy of RPG intron positions between each other as between themselves and human. Sponges from the Suberites genus show consistency in RPG intron position conservation. However, significant differences in some of the orthologous RPG introns of closely related sponges were observed. This indicates that RPG introns are dynamic even on these shorter evolutionary time scales.
Highlights
The ribosome is a protein-RNA complex, fundamentally the same in all three domains of life, and is the crucial cell component for protein synthesis
Because small nucleolar RNAs (snoRNAs) were identified in Archaea and Eukarya, it was surprising that the only systematic non-protein-coding RNAs (ncRNAs) genome annotation among basal metazoans found merely eight snoRNAs, showing that host genes of snoRNAs in Trichoplax adhaerens are not conserved in human [21]
Full-length cDNA sequences coding for 79 ribosomal proteins (RPs) were identified in the marine sponge A. queenslandica (AQ) genome, and the gene structure for 78 of them was completely ascertained
Summary
The ribosome is a protein-RNA complex, fundamentally the same in all three domains of life, and is the crucial cell component for protein synthesis. The accumulating genomic data strongly confirm tendency of snoRNAs to colonize RPGs and ribosome related genes in eukaryotes [13] and suggest that these genes have conserved snoRNAs across mammals [14] These snoRNAs are involved in the modification of rRNAs, small nuclear RNAs (snRNAs) and transfer RNAs (tRNAs) in archaea [15,16,17]. Because snoRNAs were identified in Archaea and Eukarya, it was surprising that the only systematic ncRNA genome annotation among basal metazoans found merely eight snoRNAs, showing that host genes of snoRNAs in Trichoplax adhaerens are not conserved in human [21] This number is exceedingly lower than in ‘‘higher’’ animals. Even though the intron positions in the Suberites genus are conserved, there are significant differences in certain RPG introns which indicate that they are dynamic even on these shorter evolutionary time scales
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