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吕天舒, 韦钦国, 王立东, 周生扬, 石鲁鹏, 董悦欢, 窦华山, 沙未来, 尕塔, 张洪海. 2022: 藏狐的高质量染色体基因组. 动物学研究, 43(3): 362-366. DOI: 10.24272/j.issn.2095-8137.2021.399
引用本文: 吕天舒, 韦钦国, 王立东, 周生扬, 石鲁鹏, 董悦欢, 窦华山, 沙未来, 尕塔, 张洪海. 2022: 藏狐的高质量染色体基因组. 动物学研究, 43(3): 362-366. DOI: 10.24272/j.issn.2095-8137.2021.399
Tian-Shu Lyu, Qin-Guo Wei, Li-Dong Wang, Sheng-Yang Zhou, Lu-Peng Shi, Yue-Huan Dong, Hua-Shan Dou, Wei-Lai Sha, Ta Ga, Hong-Hai Zhang. 2022: High-quality chromosome-level genome assembly of Tibetan fox (Vulpes ferrilata). Zoological Research, 43(3): 362-366. DOI: 10.24272/j.issn.2095-8137.2021.399
Citation: Tian-Shu Lyu, Qin-Guo Wei, Li-Dong Wang, Sheng-Yang Zhou, Lu-Peng Shi, Yue-Huan Dong, Hua-Shan Dou, Wei-Lai Sha, Ta Ga, Hong-Hai Zhang. 2022: High-quality chromosome-level genome assembly of Tibetan fox (Vulpes ferrilata). Zoological Research, 43(3): 362-366. DOI: 10.24272/j.issn.2095-8137.2021.399

藏狐的高质量染色体基因组

High-quality chromosome-level genome assembly of Tibetan fox (Vulpes ferrilata)

  • 摘要: 藏狐是青藏高原独有的犬科动物,广泛分布于青藏高原海拔3500米以上的区域,对维持青藏高原的生态平衡起着重要的作用。在该研究中,我们采用Oxford Nanopore以及Hi-C技术,组装了第一个染色体级别的藏狐基因组。基因组大小约为2.38 Gb, N50的长度为133 960 477 bp,共注释到了21 715个蛋白编码基因。系统发育关系表明藏狐与赤狐的分化时间约为3.27个百万年左右。基因家族扩张分析的结果表明,藏狐扩张的基因家族主要与缺氧响应以及能量代谢相关。此外,正选择分析的结果表明藏狐的正选择基因RWDD3, MAX, VEGFA, MGME1, HTATIP2, EGFL6, FANCG, PGF以及SIRT4与DNA损伤修复以及血管生成相关。这些结果揭示了藏狐可能存在的高原适应机制。高质量的基因组有助于我们更好的理解藏狐以及其高原适应机制,丰富了我们对高原物种的认知,也为将来的研究提供了一个良好的资源。

     

    Abstract: Using Oxford Nanopore and Hi-C sequencing technology, we successfully assembled a chromosome-level genome of the Tibetan fox (Vulpes ferrilata), with a total size of 2.38 Gb and N50 length of 133 960 477 bp. The 157 contigs were further assembled into 18 chromosomes with a sequence length of 2 378.42 Mb, accounting for 99.95% of the total length. A total of <number>21715</number> protein-coding genes were predicted in the assembled genome, 86.47% of which were functionally annotated. Phylogenetic analysis showed that V. ferrilata and the red fox (V. vulpes) formed a clade, with an estimated divergence time of 3.27 million years ago (Ma). Significantly enriched pathways and Gene Ontology terms associated with the expanded gene families in the V. ferrilata genome were mainly related to hypoxia response and energy metabolism, indicating the mechanistic strategy of V. ferrilata for high-altitude adaptation. Furthermore, selection signature analysis identified genes associated with DNA damage repair and angiogenesis in V. ferrilata. Construction of the V. ferrilata genome provides valuable information for further genetic analysis of important biological processes, which will facilitate the study of genetic changes during evolution.

     

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