Draft genome and complete hox-cluster characterization of the sterlet sturgeon (acipenser ruthenus)

Abstract

Background: Sturgeons (Chondrostei: Acipenseridae) are a group of “living fossil” fishes at a basal position among Actinopteri. They have raised great public interest due to their special evolutionary position, species conservation challenges as well as high-prized eggs (caviar). Sterlet sturgeon, (Acipenser ruthenus Linnaeus, 1758), is a relatively small-sized member of sturgeons and has been widely distributing in both Europe and Asia. In this study, we performed whole genome sequencing, de novo assembly and gene annotation of the sterlet to construct its draft genome. Findings: We finally obtained a 1.83-Gb genome assembly (BUSCO completeness of 81.6%) from a total of 316.8-Gb raw reads generated by an Illumina Hiseq 2500 platform. The scaffold N50 and contig N50 values reached 191.06 kb and 18.88 kb, respectively. The sterlet genome is predicted to comprise of 42.84% repeated sequences and contain 22,18422,222 protein-coding genes, in which 21,11221,127 (95.1795.07%) have been functionally annotated with at least one hit in public databases. GeneticGenome-level phylogeny proves that sterlet takes the basal position among ray-finned fishes and 4dTv analysis estimates quite a recent whole genome duplication occurred 21.3 million years ago. Moreover, seven Hox clusters carrying 68 Hox genes were characterized in the sterlet. Phylogeny of HoxA clusters in sterlet and American paddlefish divided these sturgeons into two groups, confirming the independence of each lineage-specific genome duplication in Acipenseridae and Polyodontidae. Conclusions: This draft genome makes up for the lack of genomic and molecular data of the sterlet and its Hox clusters. It also provides a genetic basis for further investigation of lineage-specific genome duplication and early evolution of ray-finned fishes.