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 de..., The presented data is related to the eponymous publication \"A chromosome-scale high-contiguity genome assembly of the threatened cheetah (Acinonyx jubatus)\" soon to be published in the Journal of Heredity. 
Any questions regarding this dataset or the publication can be addressed to the corresponding authors, Sven Winter ([e-mail]) and Pamela Burger ([e-mail]).
Assembly: 
The assembly was generated from one PacBio CLR library sequenced on one SMRTCell on a Sequel IIe using Flye v. 2.9, including one iteration of long-read polishing followed by one iteration of short-read polishing with pilon v.1.23 using trimmed standard Illumina short-reads generated on the Illumina Novaseq 6000 platform. Subsequently, the contigs of the polished assembly were anchored into chromosome-scale scaffolds with YaHS v.1.1 using publically available Hi-C data for the cheetah (SRR8616936, SRR8616937) that were prepared following the Arima Hi-C mapping pipeline (https://gi...,

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动物。历史上，它们曾广泛栖息于非洲、阿拉伯半岛及亚洲西南部的开阔草原；但时至今日，仅存少量碎片化的种群。本研究报道了基于PacBio连续长读长测序（PacBio continuous long reads）与Hi-C邻位连接测序数据（Hi-C proximity ligation data）构建的猎豹从头基因组组装（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条染色体级支架（scaffold）。该组装的重叠群（contig）与支架N50长度分别为96.8 Mb与144.4 Mb，BUSCO完整度达95.4%，k-mer完整度达98.4%，上述指标均彰显了本次基因组组装的高质量。此外，对该组装的基因注释共鉴定出23622个编码基因，重复序列占比为40.4%。这款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分析，是极具价值的研究资源，例如可用于开展从头……。
本数据集相关的同名研究论文《受威胁物种猎豹的染色体级高连续性基因组组装》（A chromosome-scale high-contiguity genome assembly of the threatened cheetah (Acinonyx jubatus)）即将发表于《遗传学期刊》（Journal of Heredity）。
关于本数据集或该论文的任何疑问，请联系通讯作者斯文·温特（[e-mail]）与帕梅拉·伯格（[e-mail]）。
基因组组装流程：本组装基于单个PacBio CLR文库构建，该文库在Sequel IIe测序平台的单个SMRT细胞（SMRT Cell）上完成测序，使用Flye v.2.9软件进行初始组装，随后进行一轮长读长校正，再利用Pilon v.1.23软件，基于Illumina NovaSeq 6000平台测序得到的经修剪的标准Illumina短读长数据进行一轮短读长校正。之后，研究人员借助YaHS v.1.1软件，将已公开的猎豹Hi-C数据（SRR8616936、SRR8616937）用于将校正后的重叠群锚定至染色体级支架，上述Hi-C数据按照Arima Hi-C定位流程（https://gi……）制备得到。