A chromosome-scale high-contiguity genome assembly of the threatened cheetah (Acinonyx jubatus)

The cheetah (Acinonyx jubatus, SCHREBER 1775) is a large felid and is considered the fastest land animal. Historically, it inhabited open grassland across Africa, the Arabian Peninsula, and southwestern Asia; however, only small and fragmented populations remain today. Here, we present a de novo genome assembly of the cheetah based on PacBio continuous long reads and Hi-C proximity ligation data. The final assembly (VMU_Ajub_asm_v1.0) has a total length of 2.38 Gb, of which 99.7% are anchored into the expected 19 chromosome-scale scaffolds. The contig and scaffold N50 values of 96.8 Mb and 144.4 Mb, respectively, a BUSCO completeness of 95.4% and a k-mer completeness of 98.4%, emphasize the high quality of the assembly. Furthermore, annotation of the assembly identified 23,622 genes and a repeat content of 40.4%. This new highly contiguous and chromosome-scale assembly will greatly benefit conservation and evolutionary genomic analyses and will be a valuable resource, e.g., to gain a detailed understanding of the function and diversity of immune response genes in felids.

猎豹（Acinonyx jubatus，SCHREBER 1775）是大型猫科动物，被公认为陆地上奔跑速度最快的物种。历史上，其栖息地遍布非洲、阿拉伯半岛以及亚洲西南部的开阔草原；但如今仅存少量且碎片化的种群。本研究基于PacBio连续长读长测序（PacBio continuous long reads）和Hi-C邻位连接技术（Hi-C proximity ligation）数据，完成了猎豹的从头基因组组装（de novo genome assembly）。最终组装版本（VMU_Ajub_asm_v1.0）总长度达2.38 Gb，其中99.7%的序列被锚定至预期的19条染色体级骨架序列（scaffold）。该组装的重叠群（contig）N50与骨架N50分别为96.8 Mb和144.4 Mb，通用单拷贝同源物基准测试集（BUSCO）完整度达95.4%，k-mer完整度为98.4%，充分彰显了该组装的高质量水平。此外，对该组装的基因组注释共鉴定出23622个基因，重复序列占比为40.4%。这一全新的高连续性染色体级基因组组装，将极大助力保护基因组学与进化基因组学相关研究，同时也将成为宝贵的研究资源，例如用于深入解析猫科动物免疫应答基因的功能与多样性。