Using Oxford Nanopore and Hi-C sequencing technology, we successfully assembled a chromosome-level genome of the Tibetan fox (Vulpesferrilata), 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.
Clark HO Jr, Newman DP, Murdoch JD, Tseng J, Wang ZH, Harris RB. 2008. Vulpes ferrilata (Carnivora: Canidae). Mammalian Species, 821: 1−6. doi: 10.1644/821.1
Fritz SA, Bininda-Emonds ORP, Purvis A. 2009. Geographical variation in predictors of mammalian extinction risk: big is bad, but only in the tropics. Ecology Letters, 12(6): 538−549. doi: 10.1111/j.1461-0248.2009.01307.x
Harris RB, Zhou JK, Ji YQ, Zhang K, Yang CY, Yu DW. 2014. Evidence that the Tibetan fox is an obligate predator of the plateau pika: conservation implications. Journal of Mammalogy, 95(6): 1207−1221. doi: 10.1644/14-MAMM-A-021
Humphreys AM, Barraclough TG. 2014. The evolutionary reality of higher taxa in mammals. Proceedings of the Royal Society B:Biological Sciences, 281(1783): 20132750. doi: 10.1098/rspb.2013.2750
Kukekova AV, Johnson JL, Xiang XY, Feng SH, Liu SP, Rando HM, et al. 2018. Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. Nature Ecology & Evolution, 2(9): 1479−1491.
Li L, Stoeckert CJ Jr, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research, 13(9): 2178−2189. doi: 10.1101/gr.1224503
Liu N. 2013. Estimation of Tibetan Fox Population Size Using Fecal DNA Technology and Line Transects. Master thesis, East China Normal University, Shanghai. (in Chinese)
Peng YD, Li H, Liu ZZ, Zhang CS, Li KQ, Gong YF, et al. 2021. Chromosome-level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi-C technology. Molecular Ecology Resources, 21(6): 2093−2108. doi: 10.1111/1755-0998.13397
Yang ZH. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24(8): 1586−1591. doi: 10.1093/molbev/msm088
Zhong D, Ding, L. 1996. Process and mechanism of uplift of Qinghai-Tibet Plateau. ScienceinChina (SeriesD), 26(4): 289–295.