DOI: 10.5061/dryad.5x69p8dgv
title: A chromosome-level genome assembly of the snow leopard, Panthera uncia

description: The snow leopard (Panthera uncia), a vulnerable big cat native to Central
 Asia, faces an ongoing population decline due to habitat loss and human
 activities. Despite its conservation importance, genomic resources for
 this species remain limited. High-quality reference genomes are essential
 for assessing genetic diversity, structural variation, and evolutionary
 history. To address this gap, we have generated a long-read-based and
 proximity-ligation scaffolded de novo genome assembly of a male snow
 leopard. The final assembly has a total length of 2.46 Gb in 280
 scaffolds, of which the 19 largest correspond to the 18 autosomes and the
 X chromosome. The scaffold N50 is 145.76 Mb, and the L50 is seven
 scaffolds. BUSCO and compleasm scores are 98.7 % and 98.9 % of identified
 Carnivora orthologs. Telomeric sequences were identified on at least one
 end of 18 out of 19 chromosomes. Scaffolds corresponding to the Y
 chromosome were identified and mapped. Additionally, the assembly's
 annotation identified a repeat content of 42.27 % and 25,391 genes. We
 produced a high-quality, long-read-based chromosome-level assembly of a
 male snow leopard, as evidenced by the data above. As a first assembly of
 a male genome, it can serve as a suitable reference genome for the
 species. The Y chromosome scaffolds provide a glimpse into the chromosome
 organization and interspecies differences.
description: # A chromosome-level genome assembly of the snow leopard, Panthera uncia.
 Dataset DOI: [10.5061/dryad.5x69p8dgv](10.5061/dryad.5x69p8dgv) ##
 Description of the data and file structure The here presented dataset is
 the accompanying annotation results for a Genome report of the same title
 submitted published in the Journal of Heredity. A de novo assembly for the
 snow leopard (*Panthera uncia*) was generated from PacBio HiFi reads using
 hifiasm v.0.19.7. The pseudohaploid assembly was then scaffolded using
 available Hi-C data from the DNAZoo
 ([www.dnazoo.org](http://www.dnazoo.org)) using the Arima Hi-C mapping
 pipeline used by the Vertebrate Genomes Project and YaHS v.1.1. Gaps in
 scaffolds were filled with TGS-GapCloser v.1.1.1 using the PacBio HiFi
 reads. Repeats in the assembly were annotated using a de novo repeat
 library generated with RepeatModeler v.2.0.1 and a Felidae-specific repeat
 dataset from Dfam_3.1 and RepBase release 20181026 and masked using
 RepeatMasker v.4.1.0. In addition to hardmasking all repeats we generated
 a masked assembly with hardmasked Transposable Elements and softmasked
 simple repeats as input for gene annotation with the  GeMoMA pipeline
 v.1.7.1. Furthermore, we used the following eight assemblies and
 corresponding annotations as references: *Mus musculus*
 (GCF_000001635.27), *Homo sapiens *(GCF_000001405.40) , *Canis lupus
 familiaris* (GCF_011100685.1), *Felis catus *(GCF_018350175.1), *Panthera
 onca* (GCF_028533385.1), *Panthera uncia* (GCF_023721935.1) , *Panthera
 tigris* (GCF_018350195.1), and *Panthera leo* (GCF_018350215.1). The
 predicted proteins were then functionally annotated with a BLASTP search
 against the Swiss-Prot database and using InterProScan. ### Files and
 variables **Usage Note:** compressed directories (.zip) can be
 decompressed using built-in tools on Windows (right-click &gt;
 "Extract All"), macOS (double-click), and Linux (using the
 `unzip`command in the terminal or archive managers). The remaining files
 (.fasta) as well as all files (except of .cat.gz) within the compressed
 directories (.out, .gff, .fasta, .fai, .masked, .tbl, .log)  can be read
 with any text editor; however some are large files that might require a
 command line tool such as the Linux "less" command to be read
 properly. Files with ".cat.gz" can be read with linux command
 line tools such as "less" or "zcat" or decompressed
 using "gunzip" and subsequently read with any text editor. ####
 File: Irbis_yahs_gapclosed.scaff_seqs_updated.fasta **Description:** 
 final genome assembly file after scaffolding and gap-closing #### File:
 hardmasked_all.zip **Description:** RepeatMasker output, hardmasking all
 repeats, including full repeat table * Irbis_repeatmasker_onesteponly.log
 #Repeatmasker logfile for run hardmasking all repeats *
 Irbis_masked_db-families.fa #consensus sequences of repeat families *
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.tbl #summary table of
 repeatcontent of the assembly by repeat class *
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.out.gff #gff annotation file
 of repeats in the assembly *
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.out #list of all repeats in
 the assembly * Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.masked
 #assembly fasta with all repeats hardmasked (Ns) *
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.fai #assembly fai index file
 * Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.cat.gz #list of repeat
 family consensus sequences used by repeatmasker for masking #### File:
 Irbis_yahs_gapclosed.scaff_seqs_updated_TEs_hm_SR_sm.fasta
 **Description:**  final assembly with hardmasked TEs and softmasked simple
 repeats #### File: GeMoMa_results.zip **Description:**  GeMoMa gene
 prediction results * final_annotation.cds.bed #bedfile containing
 positions of coding sequences in the assembly * final_annotation.gene.bed
 #bedfile containing positions of predicted genes in the assembly *
 final_annotation.gff #annotation gff file  * final_annotation.gff_summary
 #summary of annotation results * final_annotation.mrna.bed #containing
 positions of predicted mrna transcripts * predicted_cds.fasta #fasta file
 containing coding sequences of predicted proteins *
 predicted_genomic.fasta #fasta file containing the complete sequence of
 predicted genes including introns, exons, etc. * predicted_proteins.fasta
 #fasta file containing translated protein sequences *
 protocol_GeMoMaPipeline.txt #GeMoMA logfile #### File: hardmasked_TEs.zip
 **Description:**  RepeatMasker output, hardmasking all TEs *
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.tbl #summary table of
 repeatcontent of the assembly by repeat class that were hardmasked *
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.out.gff #gff annotation file
 of hardmasked repeats in the assembly *
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.out #list of hardmasked
 repeats in the assembly *
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.masked #assembly fasta with
 TEs hardmasked (Ns) * Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.cat.gz
 #list of repeat family consensus sequences used by repeatmasker for
 masking #### File: SwissProt_results.zip **Description:** BLASTP hits of
 the predicted proteins against Swiss-Prot *
 Irbis_annotation_swiss-prot_blast.out #BLASTP results #### File:
 InterProScan.zip **Description:** Results of functional annotation with
 InterProScan * predicted_proteins_nostop.fasta.tsv #interproscan output
 file with annotation of GO-terms, motifs etc. of the proteins predicted by
 GeMoMa * functional_annotation_results.txt #results summary generated by
 custom stripts #### File: hardmasked_TEs_softmasked_SR.zip
 **Description:** RepeatMasker output, softmasking simple repeats
 (following the hardmasking of TEs) *
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.masked.tbl #summary table of
 repeatcontent of the assembly by repeat class that were softmasked -
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.masked.out.gff #gff
 annotation file of softmasked repeats in the assembly -
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.masked.out #list of
 softmasked repeats in the assembly -
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.masked.masked #assembly
 fasta with TEs hardmasked (Ns) and simple repeats softmasked (lowercase) -
 Irbis_yahs_gapclosed.scaff_seqs_updated.fasta.masked.cat.gz #list of
 repeat family consensus sequences used by repeatmasker for masking