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. 2023 Oct 31;18(10):e0280090.
doi: 10.1371/journal.pone.0280090. eCollection 2023.

Rapid and collective determination of the complete "hot-spring frog" mitochondrial genome containing long repeat regions using Nanopore sequencing

Yuka Asaeda  1 , Kento Shiraga  1 , Makoto Suzuki  1   2 , Yoshihiro Sambongi  1 , Hajime Ogino  1   2 , Takeshi Igawa  1   2
Affiliations

Rapid and collective determination of the complete "hot-spring frog" mitochondrial genome containing long repeat regions using Nanopore sequencing

Yuka Asaeda et al. PLoS One. .

Abstract

The mitochondrial genome (mt-genome) is one of the promising molecular markers for phylogenetics and population genetics. Recently, various mt-genomes have been determined rapidly by using massively parallel sequencers. However, the control region (CR, also called D-loop) in mt-genomes remain difficult to precisely determine due to the presence of repeat regions. Here, using Nanopore sequencing, we succeeded in rapid and collective determination of complete mt-genome of the hot-spring frog, Buergeria japonica, and found that its mt-genome size was 22,274 bp including CR (6,929 bp) with two types of tandem repeat motifs forming repeat regions. Comparison of assembly strategies revealed that the long- and short-read data combined together enabled efficient determination of the CR, but the short-read data alone did not. The B. japonica CR was longer than that of a congenic species inhabiting cooler climate areas, Buergeria buergeri, because of the long repeat regions in the former. During the thermal adaptation of B. japonica, the longer repeat regions in its CR may have accumulated within a period after divergence from B. buergeri.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Flowchart of mitochondrial genome assembly of B. japonica using Illumina and Nanopore sequence data.
Fig 2
Fig 2. Representative histogram showing length distribution of the raw reads from the control region.
Fig 3
Fig 3. Distribution of repeat motifs in the control region of B. japonica mitochondrial genome.
The upper and lower numbers indicate nucleotide positions from the 5’ end of the control region and from 5’ end of the ND5 gene, respectively.
See this image and copyright information in PMC

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