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Mitogenome sequences of domestic cats demonstrate lineage expansions and dynamic mutation processes in a mitochondrial minisatellite.

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posted on 2024-01-22, 17:05 authored by Emily C Patterson, Gurdeep Matharu Lall, Rita Neumann, Barbara Ottolini, Chiara Batini, Federico Sacchini, Aiden P Foster, Jon H Wetton, Mark A Jobling
BACKGROUND: As a population genetic tool, mitochondrial DNA is commonly divided into the ~ 1-kb control region (CR), in which single nucleotide variant (SNV) diversity is relatively high, and the coding region, in which selective constraint is greater and diversity lower, but which provides an informative phylogeny. In some species, the CR contains variable tandemly repeated sequences that are understudied due to heteroplasmy. Domestic cats (Felis catus) have a recent origin and therefore traditional CR-based analysis of populations yields only a small number of haplotypes. RESULTS: To increase resolution we used Nanopore sequencing to analyse 119 cat mitogenomes via a long-amplicon approach. This greatly improves discrimination (from 15 to 87 distinct haplotypes in our dataset) and defines a phylogeny showing similar starlike topologies within all major clades (haplogroups), likely reflecting post-domestication expansion. We sequenced RS2, a CR tandem array of 80-bp repeat units, placing RS2 array structures within the phylogeny and increasing overall haplotype diversity. Repeat number varies between 3 and 12 (median: 4) with over 30 different repeat unit types differing largely by SNVs. Five SNVs show evidence of independent recurrence within the phylogeny, and seven are involved in at least 11 instances of rapid spread along repeat arrays within haplogroups. CONCLUSIONS: In defining mitogenome variation our study provides key information for the forensic genetic analysis of cat hair evidence, and for the first time a phylogenetically informed picture of tandem repeat variation that reveals remarkably dynamic mutation processes at work in the mitochondrion.

Funding

Midlands Integrative Biosciences Training Partnership (MIBTP)

Biotechnology and Biological Sciences Research Council

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BBSRC-MIBTP (grant no. BB/M01116X/1) iCASE studentship, co-sponsored by Twycross Zoo (East Midland Zoological Society) and Zoological Society of London.

History

Author affiliation

Department of Genetics and Genome Biology, University of Leicester

Version

  • VoR (Version of Record)

Published in

BMC Genomics

Volume

24

Issue

1

Pagination

690

Publisher

Springer Science and Business Media LLC

eissn

1471-2164

Copyright date

2023

Available date

2024-01-22

Spatial coverage

England

Language

eng

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