DOI: 10.5061/dryad.4581cc7
title: Data from: Evolutionary divergence of 3’ UTRs in cichlid fishes

description: Background: Post-transcriptional regulation is crucial for the control of
 eukaryotic gene expression and might contribute to adaptive divergence.
 The three prime untranslated regions (3’ UTRs), that are located
 downstream of protein-coding sequences, play important roles in
 post-transcriptional regulation. These regions contain functional elements
 that influence the fate of mRNAs and could be exceptionally important in
 groups such as rapidly evolving cichlid fishes. Results: To examine
 cichlid 3’ UTR evolution, we 1) identified gene features in nine teleost
 genomes and 2) performed comparative analyses to assess evolutionary
 variation in length, functional motifs, and evolutionary rates of 3’ UTRs.
 In all nine teleost genomes, we found a smaller proportion of repetitive
 elements in 3’ UTRs than in the whole genome. We found that the 3’ UTRs in
 cichlids tend to be longer than those in non-cichlids, and this was
 associated, on average, with one more miRNA target per gene in cichlids.
 Moreover, we provided evidence that 3’ UTRs on average have evolved faster
 in cichlids than in non-cichlids. Finally, analyses of gene function
 suggested that both the top 5% longest and 5% most rapidly evolving 3’
 UTRs in cichlids tended to be involved in ribosome-associated pathways and
 translation. Conclusions: Our results reveal novel patterns of evolution
 in the 3’ UTRs of teleosts in general and cichlids in particular. The data
 suggest that 3’ UTRs might serve as important meta-regulators, regulators
 of other mechanisms governing post-transcriptional regulation, especially
 in groups like cichlids that have undergone extremely fast rates of
 phenotypic diversification and speciation.
description: Astyanax mexicanus
 updated annotationThe PASA v2.0.2
 annotation pipeline was employed to incorporate gene structures, including
 UTRs, into the existing Astyanax mexicanus gene annotation, based on
 RNA-Seq data.Astmex.pasa2.gff3Danio rerio updated annotationThe PASA v2.0.2 annotation pipeline was employed to incorporate gene structures, including UTRs, into the existing Danio rerio gene annotation, based on RNA-Seq data.Danrer.pasa2.gff3Haplochromis burtoni updated annotationThe PASA v2.0.2 annotation pipeline was employed to incorporate gene structures, including UTRs, into the existing Haplochromis burtoni gene annotation, based on RNA-Seq data.Hapbur.pasa2.gff3Maylandia zebraThe PASA v2.0.2 annotation pipeline was employed to incorporate gene structures, including UTRs, into the existing Maylandia zebra gene annotation, based on RNA-Seq data.Metzeb.pasa2.gff3Neolamprologus brichardi updated annotationThe PASA v2.0.2 annotation pipeline was employed to incorporate gene structures, including UTRs, into the existing Neolamprologus brichardi gene annotation, based on RNA-Seq data.Neobri.pasa2.gff3Oreochromis niloticus updated annotationThe PASA v2.0.2 annotation pipeline was employed to incorporate gene structures, including UTRs, into the existing Oreochromis niloticus gene annotation, based on RNA-Seq data.Orenil.pasa2.gff3Oryzias latipes updated annotationThe PASA v2.0.2 annotation pipeline was employed to incorporate gene structures, including UTRs, into the existing Oryzias latipes gene annotation, based on RNA-Seq data.Orylat.pasa2.gff3Poecilia formosa updated annotationThe PASA v2.0.2 annotation pipeline was employed to incorporate gene structures, including UTRs, into the existing Poecilia formosa gene annotation, based on RNA-Seq data.Poefor.pasa2.gff3Pundamilia nyererei updated annotationThe PASA v2.0.2 annotation pipeline was employed to incorporate gene structures, including UTRs, into the existing Pundamilia nyererei gene annotation, based on RNA-Seq data.Punnye.pasa2.gff3