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.

Gymnocypris namensis, the only commercial fish in Namtso Lake of Tibet in China, is rated as nearly threatened species in the Red List of China's Vertebrates. As one of the highest-altitude schizothorax fish in China, G. namensis has strong adaptability to the plateau harsh environment. Although being an indigenous economic fish with high value in research, the biological characterization, genetic diversity, and plateau adaptability of G. namensis are still unclear. Here, we used Pacific Biosciences single molecular real time long read sequencing technology to generate full-length transcripts of G. namensis. Sequences clustering analysis and error correction with Illumina-produced short reads to obtain 319,044 polished isoforms. After removing redundant reads, 125,396 non-redundant isoforms were obtained. Among all transcripts, 103,286 were annotated to public databases. Natural selection has acted on 42 genes for G. namensis, which were enriched on the functions of mismatch repair and Glutathione metabolism. Total 89,736 open reading frames, 95,947 microsatellites, and 21,360 long non-coding RNAs were identified across all transcripts. This is the first study of transcriptome in G. namensis by using PacBio Iso-seq. The acquisition of full-length transcript isoforms might accelerate the transcriptome research of G. namensis and provide basis for further research. The Tibetan Plateau, a harsh environment with an average altitude of 4,500 m, is home to the highest and largest high-altitude lakes in the world 1,2. The area of lakes on the Tibetan Plateau are more than 50,900 km 2 , and 1,091 lakes are larger than 1.0 km 2,3. With an area of 1,920 km 2 and an altitude of 4,718 m, Namtso Lake in the North Tibet is the highest great lake in the world and is the second biggest salt water lake in China 4,5. As a highly natural, rare, fragile and representative lake, Namtso Lake imposes many inhospitable living conditions on most of organisms, such as the high pH and alkalinity, severe cold (with an annual average temperature of 0°C, five-month ice-covered period), the low primary productivity and oligotrophic conditions 3-7. Because of the lower temperatures and oligotrophic conditions of Namtso Lake, only two endemic fish species (Gymnocypris namensis and Triplophysa stewarti) have been found in the lake 6. G. namensis, the only economic fish in Namtso Lake, is known as one of the highest-altitude schizothorax fish in China and it has strong ability to adapt to the plateau harsh environment 6,8. However, systematic biological studies on G. namensis are chronically lacked due to extremely harsh environments on the plateau 8,9. In previous transcriptome studies in other fish of geneus Gymnocypris, such as Gymnocypris selincuoensis 10 , Gymnocypris przewalskii 11 , Gymnocypris eckloni 12 , some progress has been made. In transcriptome studies of G. selincuoensis, a full-length reference transcriptome has been generated by using PacBio Iso-Seq and Illumina RNA-seq technologies. But the most of other transcriptome studies us...

Ghrelin, a non-amidated peptide hormone, is a potent anorectic neuropeptide implicated in feeding regulation in mammals and non-mammalian vertebrates. However, the involvement of ghrelin in the feeding behavior of teleosts has not been well understood. To better understand the role of ghrelin in the regulation of appetite in fish, in this study, we cloned the cDNAs encoding ghrelin and investigated their mRNA distributions in gibel carp tissues. We also assessed the effects of different nutritional status on ghrelin mRNA abundance. Ghrelin mRNAs were ubiquitously expressed in ten tissues (intestine, liver, brain, mesonephron, head kidney, spleen, skin, heart, muscle, gill and pituitary gland), and relatively high expression levels were detected in the gut. Postprandial studies analysis revealed a significant postprandial decrease in ghrelin mRNA expression in the gut (1 and 3 h after the regular feeding time). In addition, ghrelin mRNA expression in the gut significantly increased at day 7 after fasting and declined sharply after refeeding, which suggested that ghrelin might be involved in the regulation of appetite in gibel carp. Overall, our result provides basis for further investigation into the regulation of feeding in gibel carp.

Several studies have demonstrated that the neuropeptide peptide YY (PYY) plays an important role in feeding in mammals and fish. However, thus far, the feeding regulation function of PYY in Schizothorax davidi has not been well understood. Here, we identified the full-length cDNA sequence of PYY in S. davidi for the first time. S. davidi PYY contains 803 bp nucleotides including a 328 bp 3' untranslated region (UTR), a 181 bp 5' UTR, and a 294 bp open reading frame encoding a peptide of 97 amino acids. S. davidi PYY expression was observed in almost all tissues, with the highest expression detected in the hypothalamus. PYY mRNA expression in the hypothalamus was significantly elevated after a meal (P < 0.01), and significantly decreased after fasting (P < 0.01). PYY expression levels were increased sharply following refeeding after 9 days (P < 0.01), suggesting that it might function as a satiety factor in S. davidi.

A 60‐day trial was conducted to investigate the effect of dietary protein on growth, whole‐body composition, hepatopancreas enzymes, digestion and absorption in the juveniles of Schizopygopsis younghusbandi. Six graded levels of dietary protein (200.0, 248.7, 303.5, 351.2, 395.8 and 449.3 g/kg diet) were formulated and assigned to triplicate groups of 60 fish (8.16 ± 0.02) for each aquarium. Results showed a significantly increased specific growth rate (SGR) in fish fed protein containing 351.2 g/kg diet (p < .05). Besides, intestinal ratio (IR), intestinal somatic index (ISI) and hepatosomatic index (HSI) were decreased and the condition factor (CF) was increased with dietary protein up to 351.2 g/kg diet, then altered reversely. Fish fed the optimal dietary protein showed the highest crude protein calcium, phosphorous and lowest crude lipid contents of the whole body in fish. Additionally, plasma ammonia content (PAC), and activities of GOT and GPT were enhanced by dietary protein levels (p < .05). The digestive enzymes of hepatopancreas were generally increased with the quadratic response to dietary protein levels. Optimal dietary protein level increased the intestinal enzyme activities of Na+, K+‐ATPase (NKA), alkaline phosphatase (AKP), gamma‐glutamyl transpeptidase (γ‐GT) and creatine kinase (CK). Based on the 2‐slope broken‐line model analysis of PWG, dietary protein requirement was determined to be 349.6 g/kg diet.

Schizothorax o’connori (S. o’connori) is a representative tetraploid species in the subfamily Schizothoracinae and an important endemic fish in the Qinghai-Tibet Plateau. However, the domestication of S. o’connori remains challenging due to the lack of basic research. Here, we investigated the effects of artificial feeding on the oocytes and liver of S. o’connori by comparing the histological, metabolomic, and transcriptomic data. Histological results showed that the oocytes and liver of captive-reared S. o’connori had abnormal cell morphology. After comparison with the self-built database, a total of 233 metabolites were annotated. In oocytes, a total of 37 differentially accumulated metabolites (DAMs) were detected and two pathways were significantly enriched. There were obvious differences in the metabolites related to ovarian development, including pregnenolone and arachidonic acid. In liver, a total of 70 DAMs were detected and five pathways were significantly enriched. Based on the transcriptomic data, a total of 159 differentially expressed genes (DEGs) were significantly related with cell growth and death pathway in oocytes, while a total of 2841 DEGs were significantly related with 102 pathways in liver. Comparing the metabolomic and transcriptomic data showed that there were three common significant enrichment pathways in liver, including biosynthesis of unsaturated fatty acids, starch and sucrose metabolism, and fatty acid biosynthesis. These results showed that special attention should be given to the composition and intake of fatty acids during the artificial breeding of S. o’connori. In addition, many of metabolite-gene pairs were related to adenosine 5′-diphosphate, adenosine monophosphate, and pregnenolone. In summary, these data provide an overview of global metabolic and transcriptomic resources and broaden our understanding of captive-reared S. o’connori.

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The Gymnocypris chui, a new recorded species in Lange Lake, was grouped into genus Gymnocypris in Schizothoracinae, and had the rare quantity and limited resources on biology and genetics, especially in the mitochondrion. In this study, the complete mitochondrial sequence of G. chui was assembled and phylogenetic relationships with other species in Cyprinidae were analyzed. The whole mitochondrial sequence was 16,864 bp in length, which contained two control regions (D-loop regions), two rRNA genes (12S and 16S rRNA), 13 protein-coding genes and 22 tRNA genes. The D-loop region was separated by tRNA Pro. The 12S rRNA and 16S rRNA located between tRNA Phe and tRNA Leu and were separated by tRNA Val. The 13 mRNAs had three start codons, five termination codons and four overlap regions. The 22 tRNA scattered among the whole mitochondrion, and they were range from 66 (tRNA Cys) to 76 (tRNA Lys andtRNA Leu) in length. To further explore the phylogenetic relationship of the G. chui, we constructed the phylogenetic tree and verified that the G. chui was a part of genus Gymnocypris and had closer relationship with Gymnocypris dobula and was independent from other species of Schizothoracinae, Barbinae and Labeoninae in Cyprinidae. This study provided the valuable evidence on phylogenetic relationship of the G. chui at the molecular level and essential resource for further research on this species.