DOI: 10.5061/dryad.xksn02vkr
title: A chromosome-scale high-contiguity genome assembly of the threatened cheetah (Acinonyx jubatus)

description: 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.
description: The presented data is related to the eponymous publication
 "A chromosome-scale high-contiguity genome assembly of the threatened
 cheetah (<em>Acinonyx</em> <em>jubatus</em>)"
 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 (sven.winter@vetmeduni.ac.at) and Pamela Burger (pamela.burger@vetmeduni.ac.at). 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://github.com/VGP/vgp-assembly/blob/master/pipeline/salsa/arima_mapping_pipeline.sh). Finally, two iterations of gap-closing were performed with TGS-GapCloser v. 1.1.1 using a different random subset of PacBio reads (25%) for each iteration. Annotation: Repeat Annotation To improve gene prediction, we first identified and masked the repeats in the assembly. A de novo repeat library was generated with RepeatModeler v.2.0.1 and combined with a Felidae-specific repeat library from RepBase. This custom repeat library was then used with RepeatMasker v.4.1.0 to hard-mask interspersed repeats and soft-mask simple repeats.  Gene annotation We predicted genes in the masked assembly based on homology using the GeMoMa pipeline v. 1.7.1 and the following reference assemblies and annotation files: <em>Homo sapiens</em> (GCF_000001405.40), <em>Mus musculus</em> (GCF_000001635.27), Lynx canadensis(GCF_007474595.2), <em>Canis lupus familiaris</em> (GCF_014441545.1), <em>Prionailuris bengalensis</em> (GCF_016509475.1), <em>Leopardus geoffroyi</em> (GCF_018350155.1), <em>Felis catus</em> (GCF_018350175.1), <em>Panthera tigris</em> (GCF_018350195.1), and <em>Panthera leo</em> (GCF_018350215.1). We functionally annotated the predicted proteins using InterProScan v.5.50.84 and a BLASTP v.2.11.0 search against the Swiss-Prot database (release 2021-02).  For more details on assembly quality assessment and comparative analyses to other Felidae assemblies, please read the original manuscript. This dataset comprises the following files: VMU_Ajub_asm_v1.0.fasta (final unmasked assembly, also available at GenBank under accession GCA_027475565.1) VMU_Ajub_asm_v1.0.fasta.masked (final assembly with all repeats hard-masked) VMU_Ajub_asm_v1.0.fasta.out (RepeatMasker output for the fully hard-masked assembly VMU_Ajub_asm_v1.0.fasta.masked) VMU_Ajub_asm_v1.0.fasta.tbl (RepeatMasker output for the fully hard-masked assembly VMU_Ajub_asm_v1.0.fasta.masked) VMU_Ajub_asm_v1.0_hardmaskedTE.fasta (final assembly with all interspersed repeats hard-masked) VMU_Ajub_asm_v1.0_hardmaskedTE.fasta.out (RepeatMasker output for the fully hard-masked assembly VMU_Ajub_asm_v1.0_hardmaskedTE.fasta) VMU_Ajub_asm_v1.0_hardmaskedTE.fasta.tbl (RepeatMasker output for the fully hard-masked assembly VMU_Ajub_asm_v1.0_hardmaskedTE.fasta) VMU_Ajub_asm_v1.0_hardmaskedTE_softmaskedSR.fasta (final assembly with all interspersed repeats hard-masked and simple repeats soft-masked) VMU_Ajub_asm_v1.0_hardmaskedTE_softmaskedSR.fasta.out (RepeatMasker output for the fully hard-masked assembly VMU_Ajub_asm_v1.0_hardmaskedTE_softmaskedSR.fasta) VMU_Ajub_asm_v1.0_hardmaskedTE_softmaskedSR.fasta.tbl (RepeatMasker output for the fully hard-masked assembly VMU_Ajub_asm_v1.0_hardmaskedTE_softmaskedSR.fasta) consensi.fa.classified (de novo repeat library for the final assembly VMU_Ajub_asm_v1.0.fasta generated With RepeatModeler2) Ajub_assembly_commands.txt (List with all commands used to generate the assembly and all related analyses)