Data from: Red, gold and green: Comparative genomics of polymorphic leopards from South Africa
Data files
Dec 06, 2024 version files 29.15 GB
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Blackleopard.tar.gz
16.90 GB
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README.md
2.32 KB
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Redleopard.zip
12.25 GB
Abstract
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.
README: Red, gold and green: Comparative genomics of polymorphic leopards from South Africa
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 >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 |
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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 > R1_one.fq.gz
Methods
DNA extractions of molecular weight >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 #).