Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors

Abstract

The geographical centre of domestication and species diversity for sheep (Ovis aries) lies around the Kurdistan region of Northern Iraq, within the ‘Fertile Crescent’. From whole genome sequence reads, we assembled the mitochondrial genomes (mtDNA or mitogenome) of five animals of the two main Kurdistani sheep breeds Hamdani and Karadi and found they fitted into known sheep haplogroups (or matrilineages), with some SNPs. Haplotyping 31 animals showed presence of the main Asian (hpgA) and European (hpgB) haplogroups, as well as the rarer Anatolian haplogroup hpgC. From the sequence reads, near-complete genomes of mitochondria from wild sheep species (or subspecies), and even many sequences similar to goat (Capra) mitochondria, could be extracted. Analysis suggested that these polymorphic reads were nuclear mitochondrial DNA segments (numts). In situ hybridization with seven regions of mitochondria chosen from across the whole genome showed strong hybridization to the centromeric regions of all autosomal sheep chromosomes, but not the Y. Centromeres of the three submetacentric pairs and the X chromosomes showed fewer copies of numts, with varying abundance of different mitochondrial regions. Some mitochondrial-nuclear transfer presumably occurred before species divergence within the genus, and there has been further introgression of sheep mitochondrial sequences more recently. This high abundance of nuclear mitochondrial sequences is not reflected in the whole nuclear genome assemblies, and the accumulation near major satellite sequences at centromeres was unexpected. Mitochondrial variants including SNPs, numts and heteroplasmy must be rigorously validated to interpret correctly mitochondrial phylogenies and SNPs.

Keywords:

• Nuclear mitochondrial DNA segments (numts)
• mitogenome diversity
• massively parallel sequencing
• fluorescent in situ hybridization
• sheep domestication

Acknowledgements

We would like to thank Prof. Jaladet Mohammed Saleh and Dilan Jasim Khalil for letting us use their laboratory facilities in the Research Center at the University of Duhok for DNA extraction. We thank Joseph Morris Butchers Ltd, Lutterworth for blood samples for short-term lymphocyte cultures. We also thank Ashti I. Abdulrahman for producing the map in Figure 1.

Geolocation information: Blood and DNA samples for the present study were collected from different sheep farms originating from different geographical locations in Iraqi Kurdistan Region. Coordinates for Duhok Governorate are (36.8679 N, 42.9488 W); Erbil Governorate (36.1911 N, 44.0091 W); and Sulaymaniyah Governorate (35.5641 N, 45.3756 W), Iraq.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

Data availability statement

The annotated mitochondrial DNA sequences are available in GenBank under accession numbers MF004242, MF004243, MF004244, MF004245 and MF004246.

Additional information

Funding

This project was supported by a PhD scholarship (HCDP; Human Capacity Development Program) by the Kurdistan Regional Government-Iraq to Sarbast Mustafa.