DOI: 10.5061/dryad.0000000c4
title: Data from: Red, gold and green: Comparative genomics of polymorphic leopards from South Africa

description: An important goal of comparative and functional genomics is to connect
 genetic polymorphisms to phenotypic variation. Leopards (Panthera pardus)
 from northern South Africa are particularly diverse, as here a unique
 colour morph occurs, as well as two deeply diverged southern (SA) and
 central African (CA) mitochondrial clades, stemming from two Pleistocene
 refugia. Here, we present the first whole genomes of a red leopard and a
 black (captive) leopard, and wildtypes belonging to the CA and SA
 mitochondrial clades, to evaluate genome-wide diversity, divergence, and
 high impact mutations that may relate to their phenotype. In the black
 leopard, we found long runs of homozygosity (ROHs), low nucleotide
 diversity across the genome, and a large number of homozygous structural
 variants, likely resulting from inbreeding to maintain this colour morph
 in captivity. In red leopards, ROHs were slightly longer compared to
 wildtype leopards, with potential deleterious mutations relating to its
 phenotype, including impaired vision. When assessing population structure,
 we found no divergence between CA and SA leopards and the rest of Africa,
 whether comparing single nucleotide or structural variants. This
 illustrates the homogenizing effect of introgression, and highlights that
 although leopards in northern South Africa may be phenotypically unique,
 they are not genetically different.
description: DNA extractions of molecular weight &gt;100 kb were sequenced
 on an Illumina HiSeq 2500 platform by a commercial provider using
 paired-end (2 x 150 bp) chemistry following the manufacturer’s
 instruction. We targeted 10X depth of coverage and generated whole-genome
 sequencing data for two leopards that each have unique traits: the red /
 strawberry leopard, and the melanistic / black leopard. Two other whole
 genomes were generated of Wildtype leopards belonging to the SA and CA
 mitochondrial clades, which were merged with another dataset of South
 African leopards (see #). 
description: # Red, gold and green: Comparative genomics of polymorphic leopards from
 South Africa
 [https://doi.org/10.5061/dryad.0000000c4](https://doi.org/10.5061/dryad.0000000c4) ## Description of the data and file structure Four leopard samples were collected in the Mpumalanga province, northern South Africa, including a red leopard, wildtype leopard from the CA mitochondrial clade, wildtype leopard from the SA mitochondrial clade, and a black leopard from Sebaka game reserve. A blood sample was collected from the captive black leopard, whereas tissue samples were collected of the other leopards that were opportunistically collected from roadkills. DNA was isolated using the QIAgen Blood and Tissue kit (Qiagen, Valencia, CA, United States). DNA extractions of molecular weight &gt;100 kb were sequenced on an Illumina HiSeq 2500 platform by a commercial provider using paired-end (2 x 150 bp) chemistry following the manufacturer’s instruction. We targeted 10X depth of whole-genome sequencing data. | Sample | Reference | Location | Longitude | Latitude | Gender | Date | | :----- | :-------- | :--------- | :-------- | :------- | :----- | :----- | | Black | | Sebaka | -25.545 | 29.331 | Female | Nov-23 | | Red | | Ohrigstad | -24.749 | 30.574 | Female | Aug-10 | | SA | MPL1 | Loskop Dam | -25.406 | 29.335 | Female | Aug-17 | | CA | MPL4 | Malelane | -25.463 | 31.548 | Male | Aug-19 | ### Files and variables #### File: Redleopard.zip **Description:** Red2_EKDN230008909-1A_HW7JKDSX5_L3_1.fq, Red2_EKDN230008909-1A_HW7JKDSX5_L3_2.fq #### File: Blackleopard.tar.gz **Description:** M44_EKDN230043202-1AHFLT5DSX7_L1_1.fq.gz, M44_EKDN230043202-1AHFLT5DSX7_L1_2.fq.gz, M44_EKDN230043202-1AHFLT5DSX7_L3_1.fq.gz, M44_EKDN230043202-1AHFLT5DSX7_L3_2.fq.gz ## Code/software The data is raw sequencing data. For use, the files must be unzipped: tar -xf Blackleopard.tar.gz gunzip Redleopard.zip The files are the .fq.gz files, or better known as fastq files. There are usually two files: one R1 and one R2. Sometimes the provider choses to change the R1/R2 nomenclature for read files L1/L2, but in either way you can combine R1 files together and R2 files together by using: cat R1_file1.fq.gz R1_file2.fq.gz &gt; R1_one.fq.gz