Summary Whole-genome duplications (WGDs) of Schizothoracinae are believed to have played a significant role in speciation and environmental adaptation on the Qinghai-Tibet Plateau (QTP). Here, we present a genome for Schizothorax o'connori , a QTP endemic fish and showed the species as a young tetraploid with a recent WGD later than ∼1.23 mya. We exhibited that massive insertions between duplicated genomes caused by transposon bursts could induce mutagenesis in adjacent sequences and alter the expression of neighboring genes, representing an early re-diploidization process in a polyploid genome after WGD. Meanwhile, we found that many genes involved in DNA repair and folate transport/metabolism experienced natural selection and might contribute to the environmental adaptation of this species. Therefore, the S. o'connori genome could serve as a young tetraploid model for investigations of early re-diploidization in polyploid genomes and offers an invaluable genetic resource for environmental adaptation studies of the endemic fish of the QTP.

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AbstractsBackgroundMechanisms for high-altitude adaption have attracted widespread interest among evolutionary biologists. Several genome-wide studies have been carried out for endemic vertebrates in Tibet, including mammals, birds, and amphibians. However, little information is available about the adaptive evolution of highland fishes. Glyptosternon maculatum (Regan 1905), also known as Regan or barkley and endemic to the Tibetan Plateau, belongs to the Sisoridae family, order Siluriformes (catfishes). This species lives at an elevation ranging from roughly 2,800 m to 4,200 m. Hence, a high-quality reference genome of G. maculatum provides an opportunity to investigate high-altitude adaption mechanisms of fishes.FindingsTo obtain a high-quality reference genome sequence of G. maculatum, we combined Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, 10X Genomics linked-reads, and BioNano optical map techniques. In total, 603.99 Gb sequencing data were generated. The assembled genome was about 662.34 Mb with scaffold and contig N50 sizes of 20.90 Mb and 993.67 kb, respectively, which captured 83% complete and 3.9% partial vertebrate Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 35.88% of the genome, and  22,066 protein-coding genes were predicted from the genome, of which 91.7% have been functionally annotated.ConclusionsWe present the first comprehensive de novo genome of G. maculatum. This genetic resource is fundamental for investigating the origin of G. maculatum and will improve our understanding of high-altitude adaption of fishes. The assembled genome can also be used as reference for future population genetic studies of G. maculatum.

A 10‐week feeding trial with four dietary protein levels (400, 450, 500 and 550 g kg−1 crude protein) and two dietary lipid levels (80 and 160 g kg−1 crude lipid) was conducted to assess optimum dietary protein and lipid levels for the growth, feed utilization and body composition of juvenile Manchurian trout (initial weight 11.80 ± 0.15 g). Fish were fed twice daily (08:30 and 16:30 h) to apparent satiation. The results showed that fish fed the diet with 500 g kg−1 protein and 80 g kg−1 lipid had the highest growth and feed efficiency. However, fish fed the diet with 450 g kg−1 protein and 160 g kg−1 lipid showed comparable growth to that of the fish fed diet 5 (500/80) and had higher protein efficiency ratio (PER), nitrogen retention (NR) and energy retention (ER) than other groups (P < 0.05). Growth, PER, NR and ER of fish fed the 160 g kg−1 lipid diet was significantly higher (P < 0.05) than that of fish fed the 80 g kg−1 lipid diet at 400 and 450 g kg−1 protein diet, whereas these values showed an opposite trend at 500 and 550 g kg−1 protein diet, and the lowest PER, NR and ER was found by fish fed the 400 g kg−1 protein diet with 80 g kg−1 lipid. Fish fed diets with 400 g kg−1 protein had lower feed intake (FI) than that of other groups. Feed intake of fish fed 80 g kg−1 lipid level was significantly lower than that of fish fed 160 g kg−1 lipid diet at 400 g kg−1 protein (P < 0.05), while no significant differences were observed at 450, 500 and 550 g kg−1 protein‐based diets. Contrary to moisture content, lipid content of whole body and muscle increased significantly (P < 0.05) with increasing lipid levels. The results of this study indicated that the diet containing 450 g kg−1 protein and 160 g kg−1 lipid, with a P/E ratio of 23.68 g protein MJ−1 would be suitable for better growth and feed utilization of juvenile Manchurian trout under the experimental conditions and design level used in this study.

Animal genomes in the Qinghai-Tibetan Plateau provide valuable resources for scientists to understand the molecular mechanism of environmental adaptation. Tibetan fish species play essential roles in the local ecology; however, the genomic information for native fishes was still insufficient. Oxygymnocypris stewartii, belonging to Oxygymnocypris genus, Schizothoracinae subfamily, is a native fish in the Tibetan plateau living within the elevation from roughly 3,000 m to 4,200 m. In this report, PacBio and Illumina sequencing platform were used to generate ~385.3 Gb genomic sequencing data. A genome of about 1,849.2 Mb was obtained with a contig N50 length of 257.1 kb. More than 44.5% of the genome were identified as repetitive elements, and 46,400 protein-coding genes were annotated in the genome. The assembled genome can be used as a reference for future population genetic studies of O. stewartii and will improve our understanding of high altitude adaptation of fishes in the Qinghai-Tibetan Plateau.