Data and code from: Sex-biased duplicates are generated during metazoan tRNA repertoire expansion
Year: 2024
Type: article
Abstract: The duplicative nature of the tRNA gene family has been well described, yet how its multi-copy members arise and are naturally selected in eukaryotic genomes and populations remains largely unexplored. We inferred the tempo of D. melanogaster tRNA gene evolution and their mode of origination through comparative genomic analyses of 24 Drosophilid species and observed that Drosophila tRNA isodecoding and isoaccepting genes have been continuously lost and gained throughout 60 million years of evolution at a rate of 1.92 tRNA gene gains and 3.98 losses per million years. We report that 1.03% of the D. melanogaster tRNA gene repertoire duplicated within the last 10 million years resulting in one tRNA gene copy being specific to D. melanogaster. We used site- and haplotype-frequency spectra tests of neutrality to investigate whether adaptive evolution is occurring at tRNA gene loci. We observed departures from neutral expectations in patterns of polymorphisms at loci of 23% of D. melanogaster tRNA genes consistent with purifying selection. Our data suggest the evolutionary process of eukaryotic tRNA gene complements to be characterized by continuous changes in membership rather than simply retention of ancient copies. Pipeline To replicate the analyses of this manuscript run the scripts contained in the zipped folders in the following order: run_tRNAscan-SE_2.09.sh countAnticodonsAndIsotypes.sh getHighConfidencetRNAs.sh getTRNAfa.sh getProtfa.sh makeOrder.sh prepare_ln_command.sh ln_command.sh getAnchors.sh getBlockFasta.sh makeDBs.sh runBlastnBlastp.sh getchrsize.sh searchAnchorRegions.sh ageDating.sh reciprocalRelationship.sh prepare4SelectionTests.sh subset.sh originationAnalysis.sh chromosome_movement.xlsx getTRNAFrequencies.sh tRNAEvolution.R makeGFF4plotting.sh synteny.R selection.R locateSNPs.sh findSNPLocationInTRNAStructure.sh
Authors: Sosa, Dylan, Chen, Jianhai, Long, Manyuan
Institution: University of Chicago
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6911195453
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