Data from: Conservation and novelty in the microRNA genomic landscape of hyperdiverse cichlid fishes

MicroRNAs (miRNAs) play crucial roles in the post-transcriptional control of messenger RNA (mRNA). These miRNA-mRNA regulatory networks are present in nearly all organisms and contribute to development, phenotypic divergence, and speciation. To examine the miRNA landscape of cichlid fishes, one of the most species-rich families of vertebrates, we profiled the expression of both miRNA and mRNA in a diverse set of cichlid lineages. Among these, we found that conserved miRNAs differ from recently arisen miRNAs (i.e. lineage specific) in average expression levels, number of target sites, sequence variability, and physical clustering patterns in the genome. Furthermore, conserved miRNA target sites tend to be enriched at the 5' end of protein-coding gene 3'UTRs. Consistent with the presumed regulatory role of miRNAs, we detected more negative correlations between the expression of miRNA-mRNA functional pairs than in random pairings. Finally, we provide evidence that novel miRNA targets sites are enriched in genes involved in protein synthesis pathways. Our results show how conserved and evolutionarily novel miRNAs differ in their contribution of the genomic landscape and highlight their particular evolutionary roles in the adaptive diversification of cichlids.mRNA_exp_tpm.tableNormalized expression values (TPM) of the 48 mRNA samples included in the study.miRNA_exp_norm.tableNormalized expression values of the 48 microRNA samples included in the study.Aall.strg.faReference-guided transcriptome assembly of the African cichlid species Astatoreochromis alluaudi.Acen.strg.faReference-guided transcriptome assembly of the Neotropical cichlid species Archocentrus centrarchus.Asiq.strg.faReference-guided transcriptome assembly of the Neotropical cichlid species Amatitlania siquia.Azal.strg.faReference-guided transcriptome assembly of the Neotropical cichlid species Amphilophus zaliosus.Hbur.strg.faReference-guided transcriptome assembly of the African cichlid species Astatotilapia burtoni.Mzeb.strg.faReference-guided transcriptome assembly of the African cichlid species Maylandia zebra.Nbri.strg.faReference-guided transcriptome assembly of the African cichlid species Neolamprologus brichardi.Pnye.strg.faReference-based transcriptome assembly of the African cichlid species Pundamilia nyererei.Aall_Trinity.faDe novo transcriptome assembly of the African cichlid species Astatoreochromis alluaudi.Asiq_Trinity.faDe novo transcriptome assembly of the Neotropical cichlid species Amatitlania siquia