Computational discovery enables broad taxonomic examination

A recent IGNITE-supported study presents a computational approach that enabled a taxonomically broad examination of the 28S rRNA molecules of the eukaryotes for the presence of the hidden break. 

In some eukaryotes, a ‘hidden break’ has been described in which the 28S ribosomal RNA molecule is cleaved into two subparts. The break is common in protostome animals (arthropods, molluscs, annelids etc.), but a break has also been reported in some vertebrates and non-metazoan eukaryotes. A new computational approach can determine the presence of the hidden break in 28S rRNAs using mapping of RNA-Seq data. Researchers find a homologous break is present across protostomes although it has been lost in a small number of taxa. Rare breaks in vertebrate 28S rRNAs are not homologous to the protostome break. A break is found in just 4 out of 331 species of non-animal eukaryotes studied and, in three of these, the break is located in the same position as the protostome break suggesting a striking instance of convergent evolution. RNA Integrity Numbers (RIN) rely on intact 28S rRNA and will be consistently underestimated in the great majority of animal species with a break.

This paper was written by ESR Project 12: Comparative genomics and phylogenetics of the Deuterostomes. The team aims at clarifying the relationships between groups of deuterostomes will allow subsequent mapping of the evolutionary history of diverse genomic, developmental and morphological characters and is essential to understand the route from invertebrates to vertebrates. The Deuterostomes are one of the two major branches of bilaterian animals and are of particular interest to humans as we are members of one of its phyla - the Chordata. While the clade itself is very widely accepted, there is uncertainty over several important aspects of deuterostomes phylogeny including, surprisingly, a weak signal supporting their monophyly. To reconstruct the tree, genomes of some significant missing clades will be assembled and annotated allowing both tree reconstruction and subsequent mapping of genomic characters.

Original source: Natsidis, P., Schiffer, P.H., Salvador-Martínez, I. et al. Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers. Sci Rep 9, 19477 (2019). https://doi.org/10.1038/s41598-019-55573-1