Comprehensive transcriptome data for endemic Schizothoracinae fish in the Tibetan Plateau

Zhou, Chaowei; Xiao, Shijun; Liu, Yanchao; Mou, Zhenbo; Zhou, Jianshe; Pan, Yingzi; Zhang, Chi; Wang, Jiu; Deng, Xingxing; Zou, Ming; Li, Haiping

doi:10.1038/s41597-020-0361-6

Cited by 17 publications

(16 citation statements)

References 17 publications

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“…The number of unigenes was much higher than genes in most fish species. Similar concern was reported in endemic Schizothoracinae fish [27] and Aristichthys nobilis [28] after de novo transcriptome assembly. But a total of 47,394 and 68,431 genes were annotated separately in D. rerio (GRCz11) and common carp (Cyprynius carpio) according to the NCBI Genome database (https://www.ncbi.nlm.nih.gov/genome, April 29, 2020).…”

Section: Discussionsupporting

confidence: 79%

Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb (Puntius tetrazona)

et al. 2020

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Background Tropical stenothermal fish exhibit special tolerance and response to cold stress. However current knowledge of the molecular mechanisms response to cold stress in aquatic ectotherms is largely drawn from eurythermal or extreme stenothermal species. The tiger barb Puntius tetrazona is a tropical stenothermal fish, with great popularity in aquarium trade and research. Results To investigate the response mechanism of P. tetrazona to low temperature, fish were exposed to increasing levels of acute cold stress. Histopathological analysis showed that the brain, gill, liver and muscle tissues appeared serious damage after cold stress (13 °C). Brain, gill, liver and muscle tissues from control (CTRL) groups (27 °C) and COLD stress groups (13 °C) of eight-month fish (gender-neutral) were sampled and assessed for transcriptomic profiling by high-throughput sequencing. 83.0 Gb of raw data were generated, filtered and assembled for de novo transcriptome assembly. According to the transcriptome reference, we obtained 392,878 transcripts and 238,878 unigenes, of which 89.29% of the latter were annotated. There were 23,743 differently expressed genes (DEGs) been filtered from four pairs of tissues (brain, gill, liver and muscle) between these cold stress and control groups. These DEGs were mainly involved in circadian entrainment, circadian rhythm, biosynthesis of steroid and fatty acid. There were 64 shared DEGs between the four pairs of groups, and five were related to ubiquitylation/deubiquitylation. Our results suggested that ubiquitin-mediated protein degradation might be necessary for tropical stenothermal fish coping with acute cold stress. Also, the significant cold-induced expression of heat shock 70 kDa protein (HSP70) and cold-induced RNA-binding protein (CIRBP) was verified. These results suggested that the expression of the molecular chaperones HSP70 and CIRBP in P. tetrazona might play a critical role in coping with acute cold stress. Conclusions This is the first transcriptome analysis of P. tetrazona using RNA-Seq technology. Novel findings about tropical stenothermal fish under cold stress (such as HSP70 and CIRBP genes) are presented here. This study contributes new insights into the molecular mechanisms of tropical stenothermal species response to acute cold stress.

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Section: Discussionsupporting

confidence: 79%

Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb (Puntius tetrazona)

et al. 2020

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“…The average lengths of transcripts or unigenes obtained in the previous studies in some schizothoracinae were 513-1,323 bp 1,29,[55][56][57] . It is also notable that the mean and N50 length of our transcriptome (1,819 and 2,044 bp) built using PacBio platform was much higher than the latest G. namensis transcriptome (1,267 and 1,825 bp) from NGS sequencing 41 . Longer isoforms implied higher sequence integrity for the species, which was rather important for the following gene function and evolutionary studies.…”

Section: Discussionmentioning

confidence: 79%

“…Meanwhile, we performed homology search against transcripts recently reported for G. namensis, G. selincuoensis, G. pzewalskii and G. eckloni 41 . After searching the gene sequences to the public transcriptome data, we found that more than 96% of isoforms generated from PacBio sequencing could hit homologs in NGS-based transcriptome of G. namensis, G. selincuoensis, G. pzewalskii and G. eckloni.…”

Section: Resultsmentioning

confidence: 99%

“…Based on comparative analysis for orthologous genes pairs among G. namensis, C. carpio and S. rhinocerous, natural selection detection was detected from 42 genes in G. namensis (Table S7). We also performed the phylogenetic analysis using Gymnocypris transcriptome data from the latest data 41 . Based on 346,029 sites from 597 single-copy orthologous genes, we generated the phylogenetic relationship of Gymnocypris species with other teleost.…”

Section: Resultsmentioning

confidence: 99%

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Full-length transcript sequencing accelerates the transcriptome research of Gymnocypris namensis, an iconic fish of the Tibetan Plateau

Luo

Zhang

et al. 2020

Sci Rep

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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...

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“…We downloaded six alkaline intolerant schizothoracine fish transcriptomes (Zhou et al 2020) including…”

Section: Additional Data Retrievalmentioning

confidence: 99%

Genomic signature of shifts in selection and alkaline adaptation in highland fish

Tong

Tang

et al. 2020

Preprint

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Understanding how organisms adapt to aquatic life at high altitude is fundamental in evolutionary biology. This objective has been addressed mainly related to hypoxia adaptation by recent comparative studies, whereas highland fish has also long suffered extreme alkaline environment, insight into the genomic basis of alkaline adaptation has rarely been provided. Here, we compared the genomes or transcriptomes of 15 fish species, including two alkaline tolerant highland fish species and their six alkaline intolerant relatives, three alkaline tolerant lowland fish species and four alkaline intolerant relatives. We found putatively consistent patterns of molecular evolution in alkaline tolerant species in a large number of shared orthologs within highland and lowland fish taxa. Remarkably, we identified consistent signatures of accelerated evolution and positive selection in a set of core shared genes associated with ion transport, apoptosis, immune response and energy metabolisms in alkaline tolerant species within both highland and lowland fish taxa. This is one of the first comparative studies that began to elucidate the consistent genomic signature of alkaline adaptation shared by highland and lowland fish. This finding also highlights the adaptive molecular evolution changes that support fish adapting to extreme environments at high altitude.Significance StatementLittle is known about how wild fish responds to extreme alkaline stress besides hypoxia at high altitude. Comparative genomics has begun to elucidate the genomic basis of alkaline adaptation in lowland fish, such as killifish, but insight from highland fish has lagged behind. The common role of adaptive molecular evolution during alkaline adaptation in highland and lowland fish has rarely been discussed. We address this question by comparing 15 fish omics data. We find numbers of shared orthologs exhibited consistent patterns of molecular evolution in alkaline tolerant species relative to intolerant species. We further identify remarkably consistent signatures of rapidly evolving and positive selection in a substantial shared core of genes in both highland and lowland alkaline tolerant species.

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Comprehensive transcriptome data for endemic Schizothoracinae fish in the Tibetan Plateau

Cited by 17 publications

References 17 publications

Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb (Puntius tetrazona)

Transcriptome analysis reveals molecular mechanisms responsive to acute cold stress in the tropical stenothermal fish tiger barb (Puntius tetrazona)

Full-length transcript sequencing accelerates the transcriptome research of Gymnocypris namensis, an iconic fish of the Tibetan Plateau

Genomic signature of shifts in selection and alkaline adaptation in highland fish

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