Single-molecule sequencing of an animal mitochondrial genome reveals chloroplast-like architecture and repeat-mediated recombination

Joel Sharbrough; Laura Bankers; Emily Cook; Peter D Fields; Joseph Jalinsky; Kyle E McElroy; Maurine Neiman; John M Logsdon; Jeffrey L Boore

doi:10.1093/molbev/msad007

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Single-molecule sequencing of an animal mitochondrial genome reveals chloroplast-like architecture and repeat-mediated recombination

Journal article

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Single-molecule sequencing of an animal mitochondrial genome reveals chloroplast-like architecture and repeat-mediated recombination

Joel Sharbrough, Laura Bankers, Emily Cook, Peter D Fields, Joseph Jalinsky, Kyle E McElroy, Maurine Neiman, John M Logsdon and Jeffrey L Boore

Molecular biology and evolution, Vol.40(1), msad007

01/10/2023

DOI: 10.1093/molbev/msad007

PMCID: PMC9874032

PMID: 36625177

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Abstract

Recent advances in long-read sequencing technology have allowed for single-molecule sequencing of entire mitochondrial genomes, opening the door for direct investigation of mitochondrial genome architecture and recombination. We used PacBio sequencing to re-assemble mitochondrial genomes from two species of New Zealand freshwater snails, Potamopyrgus antipodarum and Potamopyrgus estuarinus. These assemblies revealed a ∼1.7 kb structure within the mitochondrial genomes of both species that was previously undetected by assembly of short reads and likely corresponding to a large non-coding region commonly present in mitochondrial genomes. The overall architecture of these Potamopyrgus mitochondrial genomes is reminiscent of the chloroplast genomes of land plants, harboring a large single-copy region (LSC) and a small single-copy region (SSC) separated by a pair of inverted repeats (IRa and IRb). Individual sequencing reads that spanned across the Potamopyrgus IRa-SSC-IRb structure revealed the occurrence of "flip-flop" recombination. We also detected evidence for two distinct IR haplotypes and recombination between them in wild-caught P. estuarinus, as well as extensive intermolecular recombination between SNPs in the LSC region. The chloroplast-like architecture and repeat-mediated mitochondrial recombination we describe here raise fundamental questions regarding the origins and commonness of inverted repeats in cytoplasmic genomes and their role in mitochondrial genome evolution.

heteroplasmy

repeat-mediated recombination

Flip-flop recombination

PacBio sequencing

mitochondrial DNA

Details

Title: Subtitle: Single-molecule sequencing of an animal mitochondrial genome reveals chloroplast-like architecture and repeat-mediated recombination
Creators: Joel Sharbrough - New Mexico Institute of Mining and Technology
Laura Bankers - University of Iowa
Emily Cook - New Mexico Institute of Mining and Technology
Peter D Fields - University of Basel
Joseph Jalinsky - Department of Biology, University of Iowa, Iowa City, IA 52242, USA
Kyle E McElroy - Iowa State University
Maurine Neiman - University of Iowa
John M Logsdon - University of Iowa
Jeffrey L Boore - Phenome Health and Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA 98109, USA
Resource Type: Journal article
Publication Details: Molecular biology and evolution, Vol.40(1), msad007
DOI: 10.1093/molbev/msad007
PMID: 36625177
PMCID: PMC9874032
NLM abbreviation: Mol Biol Evol
ISSN: 0737-4038
eISSN: 1537-1719
Language: English
Date published: 01/10/2023
Academic Unit: Office Of The Provost; Gender, Women's and Sexuality Studies; Biology
Record Identifier: 9984357457102771

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