Rapid and accurate determination of the long mitochondrial genome of the “Hot-spring frog” (Ryukyu Kajika frog, Buergeria japonica)

A paper written by Yuka Asaeda, a graduate student (M2) as the first author, has been published in the journal PLoS One. In this paper we rapidly and accurately determined a long mitochondrial genome of the “Hot-spring frog” (Buergeria japonica) using a Nanopore sequencer. The genome was approximately 23,000 base pair mitochondrial circular genome, which contains a repeat region that repeats the same sequence over 200 times.

Asaeda Y, Shiraga K, Suzuki M, Sambongi Y, Ogino H, *Igawa T, Rapid and collective determination of the complete “hot-spring frog” mitochondrial genome containing long repeat regions using Nanopore sequencing. PLoS One 18: e0280090 October 2023 [ DOI | http | PDF ]

Nowadays, it is easy to obtain large-scale data from short-read sequencers, and it is thought that mitochondrial genomes can be easily determined. However, we demonstrated that repeat regions were misassembled even using thousands of times as many short-read data. In fact, the mitochondrial genomes of anuran amphibians often contain such repeat regions in their control regions, and some of the genomes assembled using only short read data may happen to be omitted the important elements from the actual sequences.

In addition, one of the mysteries behind the hot spring frog’s adaptation to high temperatures is that it is not well understood how energy metabolism, especially aerobic metabolism in high water temperatures. The data obtained this time is an important first step towards solving the mystery of how gene expression is regulated in mitochondria, which are the center of aerobic metabolism.