Species-specific variation in mitochondrial genome tandem repeat polymorphisms in hares (Lepus spp., Lagomorpha, Leporidae) provides insight into their evolution

Riikka Tapanainen, Koit Aasumets, Zsófia Fekete, Steffi Goffart, Eric Dufour, Jaakko L. O. Pohjoismäki

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Abstract

The non-coding regions of the mitochondrial DNAs (mtDNAs) of hares, rabbits, and pikas (Lagomorpha) contain short (∼20 bp) and long (130–160 bp) tandem repeats, absent in related mammalian orders. In the presented study, we provide in-depth analysis for mountain hare (Lepus timidus) and brown hare (L. europaeus) mtDNA non-coding regions, together with a species- and population-level analysis of tandem repeat variation. Mountain hare short tandem repeats (SRs) as well as other analyzed hare species consist of two conserved 10 bp motifs, with only brown hares exhibiting a single, more variable motif. Long tandem repeats (LRs) also differ in sequence and copy number between species. Mountain hares have four to seven LRs, median value five, while brown hares exhibit five to nine LRs, median value six. Interestingly, introgressed mountain hare mtDNA in brown hares obtained an intermediate LR length distribution, with median copy number being the same as with conspecific brown hare mtDNA. In contrast, transfer of brown hare mtDNA into cultured mtDNA-less mountain hare cells maintained the original LR number, whereas the reciprocal transfer caused copy number instability, suggesting that cellular environment rather than the nuclear genomic background plays a role in the LR maintenance. Due to their dynamic nature and separation from other known conserved sequence elements on the non-coding region of hare mitochondrial genomes, the tandem repeat elements likely to represent signatures of ancient genetic rearrangements. clarifying the nature and dynamics of these rearrangements may shed light on the possible role of NCR repeated elements in mitochondria and in species evolution.

Original languageEnglish
Article number148644
JournalGene
Volume926
DOIs
Publication statusPublished - 30 Oct 2024
Publication typeA1 Journal article-refereed

Funding

Dr Seppo Helisalmi and Dr Joose Raivo from the Gene diagnostics lab at Genome Center of Eastern Finland are thanked for providing the mtDNA sequencing service. We thank Ms Anita Kervinen for her valuable laboratory assistance in preparing the mtDNA PCRs for the sequencing. Funding: This research was supported by the Academy of Finland (grant no. 329264 for ED and JLOP). The funder had no role in study design; sampling, analysis, and interpretation of data; in the writing of the report; and in the decision to submit the article for publication.

FundersFunder number
Strategic Research Council at the Research Council of Finland329264
Strategic Research Council at the Research Council of Finland

    Keywords

    • Brown hare
    • Mitochondrial DNA replication
    • Mountain hare
    • Non-coding region
    • Population Genetics
    • Regulatory element
    • Strand-slippage

    Publication forum classification

    • Publication forum level 1

    ASJC Scopus subject areas

    • Genetics

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