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

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

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. High-quality chromosome-level genome assembly of Tibetan fox (Vulpes ferrilata). Zoological Research, 2022, 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. High-quality chromosome-level genome assembly of Tibetan fox (Vulpes ferrilata). Zoological Research, 2022, 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

doi: 10.24272/j.issn.2095-8137.2021.399

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

Funds: This work was supported by the National Natural Science Foundation of China (31872242, 32070405)
More Information
  • 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。
  • Figure  1.  Statistics and data analysis of genome assembly of Vulpes ferrilata

    A: Genome-wide all-by-all Hi-C interaction identified 18 linkage groups. B: Synteny analysis of V. ferrilata and Canis lupus familiaris genomes. C: Gene family evolution between genomes of V. ferrilata and 10 other species, orange and red numbers indicate gene family expansions and contractions, respectively. Length of branch indicates divergence time. MRCA: Most Recent Common Ancestor. Ma: Million years ago. D: Significant KEGG enrichment in expanded gene families. Value around each bar indicates number involved in each KEGG pathway. E: GO classification of expanded gene families, including top 20 significant GO categories (P<0.05). BP: Biological process; CC: Cellular component; MF: Molecular function.

    Table  1.   Comparison of genome assemblies between V. ferrilata and other Vulpes species

    FeatureV. ferrilataV. vulpesV. lagopus
    Assembly levelChromosomeScaffoldChromosome
    Total length (bp)2 379 658 6492 421 568 0722 345 550 353
    Number of scaffolds23482 424929
    Scaffold N50 (bp)133 960 47712 472 085131 537 142
    Number of contigs379183 8981 456
    Contig N50 (bp)52 909 67455 45033 460 300
    GC content (%)41.2541.341.28
    下载: 导出CSV
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出版历程
  • 收稿日期:  2021-12-31
  • 录用日期:  2022-03-29
  • 网络出版日期:  2022-03-31
  • 刊出日期:  2022-05-18

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