Background A considerable fraction of microRNAs (miRNAs) are highly conserved, and certain miRNAs correspond to genomic clusters. The clustering of miRNAs can be advantageous, possibly by allowing coordinated expression. However, little is known about the evolutionary forces responsible for the loss and acquisition of miRNA and miRNA clusters. Results The results demonstrated that several novel miRNAs arose throughout grass carp evolution. Duplication and de novo production were critical strategies for miRNA cluster formation. Duplicates accounted for a smaller fraction of the expansion in the grass carp miRNA than de novo creation. Clustered miRNAs are more conserved and change slower, whereas unique miRNAs usually have high evolution rates and low expression levels. The expression level of miRNA expression in clusters is strongly correlated. Conclusions This study examines the genomic distribution, evolutionary background, and expression regulation of grass carp miRNAs. Our findings provide novel insights into the genesis and development of miRNA clusters in teleost.

Background A considerable fraction of miRNAs are highly conserved, and certain miRNAs correspond to genomic clusters. The clustering of microRNAs can be advantageous, possibly by allowing coordinated expression. However, little is known about the evolutionary forces responsible for the loss and acquisition of microRNA and microRNA clusters. Results The results demonstrated that several novel miRNAs arose throughout grass carp evolution. Duplication and de novo production were critical strategies for miRNA cluster formation. Duplicates accounted for a smaller fraction of the expansion in the grass carp miRNA than de novo creation. Clustered miRNAs are more conserved and change slower, whereas unique miRNAs usually have high evolution rates and low expression levels. The expression level of miRNA expression in clusters is strongly correlated. Conclusions This study examines the genomic distribution, evolutionary background, and expression regulation of grass carp microRNAs. Our findings provide novel insights into the genesis and development of microRNA clusters in teleost.

Grass carp (Ctenopharyngodon idella) is an important economic and ecological freshwater fish. Grass carp is a highly adaptive and has been introduced around the world, making it a good model to explore genomic divergence in diverse ecosystems. Habitat colonization often requires extensive adaptation to cope with environmental challenges from temperature and light variations; however, the associated genomic mechanisms underlying evolution are unclear. To evaluate the genetic diversity and selective adaptation in this species, we improved the draft genome of female grass carp using a fine genetic map and performed whole-genome resequencing to generalize genetic differentiations and variations among eight populations across its distributional range in Asia. Population structures analysis using principal component, linkage disequilibrium decay, and admixture analyses revealed that the Asian grass carp comprises two independent and genetically distinct populations, which might have resulted from geographical distributions with contrasting environments. The South Asia population exhibited reduced genetic diversity and a distinct population structure compared with those of the China and Vietnam populations. Genome selected sweep analysis revealed many diverged genomic regions containing genes enriched for the nervous system and epigenetic diversity-related genetic variation. Finally, among 27 candidate genes located in selected regions, the oxytocin gene had the highest Fst value, and is involved in parturition, social behavior, growth, and developmental processes, possibly contributing to the local adaptation of South Asia grass carp. Our results suggested that grass carp genomic divergence has been triggered and maintained by geographic isolation, revealing the genomic basis of adaptation in this species.