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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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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
Feature V. ferrilata V. vulpes V. lagopus Assembly level Chromosome Scaffold Chromosome Total length (bp) 2 379 658 649 2 421 568 072 2 345 550 353 Number of scaffolds 234 82 424 929 Scaffold N50 (bp) 133 960 477 12 472 085 131 537 142 Number of contigs 379 183 898 1 456 Contig N50 (bp) 52 909 674 55 450 33 460 300 GC content (%) 41.25 41.3 41.28 
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