MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing

Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.

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“…The resulting sequence assembly and haplotype for mitochondrial genome was visualized using MitoSuite ver. 1.0.9 74 .…”

Section: Methodsmentioning

confidence: 99%

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

et al. 2020

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“…34 We then obtained artificial low-coverage mitochondrial genome sequences from these aligned reads with MitoSuite (v. 1.0.9). 35 Finally, we applied our approach 500 times for each mitochondrial DNA lineage and investigated its precision. The precision of the imputation is computed as follows: TP/(TP + FP).…”

Section: Simulated Data Setmentioning

confidence: 99%

MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome

Ishiya

Mizuno

Wang

et al. 2019

Bioinform Biol Insights

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The incompleteness of partial human mitochondrial genome sequences makes it difficult to perform relevant comparisons among multiple resources. To deal with this issue, we propose a computational framework for deducing missing nucleotides in the human mitochondrial genome. We applied it to worldwide mitochondrial haplogroup lineages and assessed its performance. Our approach can deduce the missing nucleotides with a precision of 0.99 or higher in most human mitochondrial DNA lineages. Furthermore, although low-coverage mitochondrial genome sequences often lead to a blurred relationship in the multidimensional scaling analysis, our approach can correct this positional arrangement according to the corresponding mitochondrial DNA lineages. Therefore, our framework will provide a practical solution to compensate for the lack of genome coverage in partial and fragmented human mitochondrial genome sequences. In this study, we developed an open-source computer program, MitoIMP, implementing our imputation procedure. MitoIMP is freely available from https://github.com/omics-tools/mitoimp .

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“…In addition, reads mapped to human nuclear genome sequences of hg19 were also removed as numts (nuclear copies of mtDNA). Mismatch percentage was estimated using MitoSuite ver.1.0.9 23 . Finally, consensus sequences were built using MitoSuite, and their mtDNA haplogroup assignments were called with HaploGrep2 ( https://haplogrep.uibk.ac.at/ ) 24 .…”

Section: Methodsmentioning

confidence: 99%

A biomolecular anthropological investigation of William Adams, the first SAMURAI from England

Mizuno

Ishiya

Matsushita³

et al. 2020

Sci Rep

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William Adams (Miura Anjin) was an English navigator who sailed with a Dutch trading fleet to the far East and landed in Japan in 1600. He became a vassal under the Shogun, Tokugawa Ieyasu, was bestowed with a title, lands and swords, and became the first SAMURAI from England. "Miura" comes from the name of the territory given to him and "Anjin" means "pilot". He lived out the rest of his life in Japan and died in Hirado, Nagasaki Prefecture, in 1620, where he was reportedly laid to rest. Shortly after his death, graveyards designated for foreigners were destroyed during a period of Christian repression, but Miura Anjin’s bones were supposedly taken, protected, and reburied. Archaeological investigations in 1931 uncovered human skeletal remains and it was proposed that they were those of Miura Anjin. However, this could not be confirmed from the evidence at the time and the remains were reburied. In 2017, excavations found skeletal remains matching the description of those reinterred in 1931. We analyzed these remains from various aspects, including genetic background, dietary habits, and burial style, utilizing modern scientific techniques to investigate whether they do indeed belong to the first English SAMURAI.

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MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing

Cited by 31 publications

References 35 publications

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome

A biomolecular anthropological investigation of William Adams, the first SAMURAI from England

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