The Genomes of Two Invasive Asian Carps Provide Novel Insights into the Evolution of a Hybrid Swarm

Two Asian carps, bighead carp (BC, Hypophthalmichthys nobilis) and silver carp (SC, H. molitrix) are reproductively isolated within their native range. However, when introduced to the US, the two invasive species extensively hybridize. We investigate the genetic architecture of BG, SC and their hybrids through comparative genomic analysis. We conducted de novo genome assembly using approximately 80 Gb Illumina short reads and 10 Gb PacBio long reads for each species. The genome size was estimated 1.00 and 0.97 Gb for BC and SC, respectively, with 53.5% and 35.1% repeats. A total of 26,516 protein-coding genes were predicted for BC and 26,880 for SC. Genomic comparison between Asian carps and 13 published fish genomes revealed 39 and 41 unique gene families in BC and SC, respectively. We mapped the genomic and transcriptomic reads of hybrids to the genomes of parental species, identified a large portion of novel genes from recombination and fusion events, and characterized a set of genes pertaining to behavior and physiology of two Asian carps. The draft genomes of BC and SC provides important insights into the evolution of a hybrid swarm and offers broad implications to control and manage Asian carps in the US.