Genome survey sequence of black carp provides insights into development‐related gene duplications

Abstract

AbstractAs one of the traditional "Four Domesticated Fishes" in China, black carp (Mylopharyngodon piceus) is an important species in freshwater aquaculture, an important fishery resource in China, and an invasive species in the United Sates. Here, we reported the draft genome of black carp with an estimated size of 975 Mb and 27,541 predicted protein‐coding genes. The genome of black carp exhibited a high synteny with those of grass carp and zebrafish. Phylogenetic estimation suggested that black carp likely diverged from grass carp and zebrafish around 13 and 57 million years ago, respectively. The comparison of expanded gene families among eight fish species identified functional genes involved in skeletal growth, hormone regulation and rhythmic control, cellular differentiation and other development‐related pathways underwent the duplications in the large body fishes such as black carp and grass carp. Further analysis of functional interaction networks of the proteins encoded by these duplicated genes revealed their important role associated with regulation of development pathways. In addition, Sox and TLR gene families were found to have diverse subfamily evolution among different fishes. The first draft genome of black carp offers insights into its genomic structure, function, and evolution and provides an additional resource for improved molecular selection and breeding.