Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies

Abstract

BackgroundTransfer RNAs (tRNAs) are ubiquitous in all living organism. They implement the genetic code so that most genomes contain distinct tRNAs for almost all 61 codons. They behave similar to mobile elements and proliferate in genomes spawning both local and non-local copies. Most tRNA families are therefore typically present as multicopy genes. The members of the individual tRNA families evolve under concerted or rapid birth-death evolution, so that paralogous copies maintain almost identical sequences over long evolutionary time-scales. To a good approximation these are functionally equivalent. Individual tRNA copies thus are evolutionary unstable and easily turn into pseudogenes and disappear. This leads to a rapid turnover of tRNAs and often large differences in the tRNA complements of closely related species. Since tRNA paralogs are not distinguished by sequence, common methods cannot not be used to establish orthology between tRNA genes.ResultsIn this contribution we introduce a general framework to distinguish orthologs and paralogs in gene families that are subject to concerted evolution. It is based on the use of uniquely aligned adjacent sequence elements as anchors to establish syntenic conservation of sequence intervals. In practice, anchors and intervals can be extracted from genome-wide multiple sequence alignments. Syntenic clusters of concertedly evolving genes of different families can then be subdivided by list alignments, leading to usually small clusters of candidate co-orthologs. On the basis of recent advances in phylogenetic combinatorics, these candidate clusters can be further processed by cograph editing to recover their duplication histories. We developed a workflow that can be conceptualized as stepwise refinement of a graph of homologous genes. We apply this analysis strategy with different types of synteny anchors to investigate the evolution of tRNAs in primates and fruit flies. We identified a large number of tRNA remolding events concentrated at the tips of the phylogeny. With one notable exception all phylogenetically old tRNA remoldings do not change the isoacceptor class.ConclusionsGene families evolving under concerted evolution are not amenable to classical phylogenetic analyses since paralogs maintain identical, species-specific sequences, precluding the estimation of correct gene trees from sequence differences. This leaves conservation of syntenic arrangements with respect to “anchor elements” that are not subject to concerted evolution as the only viable source of phylogenetic information. We have demonstrated here that a purely synteny-based analysis of tRNA gene histories is indeed feasible. Although the choice of synteny anchors influences the resolution in particular when tight gene clusters are present, and the quality of sequence alignments, genome assemblies, and genome rearrangements limits the scope of the analysis, largely coherent results can be obtained for tRNAs. In particular, we conclude that a large fraction of the tRNAs are recent copies. This prolife...

Diversity of tRNA Clusters in the Chloroviruses

“…The ability of tRNA genes to proliferate is thought to be similar to the mechanism by which mobile elements can lead to intragenomic gene duplications [ 38 ]. Duplications and losses are clearly evident among and within all three chlorovirus clades; for example, the Pbi virus CZ-2 had four tRNA Asn genes that all recognized the same ACC codon, while almost all of the other Pbi viruses had just two copies.…”

SMORE: Synteny Modulator of Repetitive Elements

“…A key step in our workflow is the identification of genomic anchors . Following [ 23 ], we define a genomic anchor as a sequence interval for which orthology between pairs of genomes can be established without ambiguity. As it is key to our approach, we briefly review the concept here in more formal terms:…”

“…Together, these processes can result in a rapid net turn-over of gene copies and sometimes large differences in the number of copies in closely related genomes. This effect has been studied in much detail, in particular for the case of tRNAs [ 19 , 20 , 21 , 22 , 23 ].…”

“…This idea has been exploited in the past, in particular as a means of tracing the evolution of tRNAs [ 19 , 20 , 21 , 22 ]. In [ 23 ], we explored its implication in some detail and proposed a more systematic conceptual workflow for the evolutionary analysis of multicopy genes that can use genome-wide multiple sequence alignments (MSAs), many of which are already publicly available, as a source of synteny information. In the present contribution, we describe an implementation of a fully automatic computational pipeline that serves as a convenient tool for this purpose, and we describe applications to two classes of non-coding RNAs (ncRNAs).…”

“…They show a rapid turnover as the consequence of frequent seeding of new loci compensated for by high rates of pseudogenization [ 19 , 20 , 21 , 22 ]. While gain and loss events can be estimated from changes in the total number of paralogs with often acceptable precision for low-copy-number gene families such as microRNAs [ 34 ], this is not the case for tRNAs, as the number of conserved tRNA loci very quickly decreases with phylogenetic distance [ 19 , 23 ].…”