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

Maternal diversity based on a sub-region of mitochondrial genome or variants were commonly used to understand past demographic events in livestock. Additionally, there is growing evidence of direct association of mitochondrial genetic variants with a range of phenotypes. Therefore, this study used complete bovine mitogenomes from a large sequence database to explore the full spectrum of maternal diversity. Mitogenome diversity was evaluated among 1883 animals representing 156 globally important cattle breeds. Overall, the mitogenomes were diverse: presenting 11 major haplogroups, expanding to 1309 unique haplotypes, with nucleotide diversity 0.011 and haplotype diversity 0.999. A small proportion of African taurine (3.5%) and indicine (1.3%) haplogroups were found among the European taurine breeds and composites. The haplogrouping was largely consistent with the population structure derived from alternate clustering methods (e.g. PCA and hierarchical clustering). Further, we present evidence confirming a new indicine subgroup (I1a, 64 animals) mainly consisting of breeds originating from China and characterised by two private mutations within the I1 haplogroup. The total genetic variation was attributed mainly to within-breed variance (96.9%). The accuracy of the imputation of missing genotypes was high (99.8%) except for the relatively rare heteroplasmic genotypes, suggesting the potential for trait association studies within a breed.

Section: Discussionsupporting

confidence: 58%

Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle

Dorji

Jagt

Chamberlain

et al. 2022

“…To minimize the effects of nucleotide mis-incorporations on building a consensus mitogenome sequence, the first two bases on each end of the read were clipped with BamUtil ver. 1.0.14 37 according to our previous bioinformatics procedure 38 Deamination is considerably repaired by using PreCR Repair Mix, but even if it is repaired, it is difficult to completely repair it. Because the damage still remains, both ends are clipped.…”

Section: Methodsmentioning

confidence: 99%

Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences

Mizuno

Gojobori

Kumagai

et al. 2021

Self Cite

The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

“…To minimize the effects of nucleotide mis-incorporations on building a consensus mtDNA sequence, the first two bases on each end of the read were clipped with BamUtil ver. 1.0.14 21 according to our previous bioinformatics procedure 22 . Then, reads with a significant hit (E-value < = 1e − 15) to non-human genomes (e.g., fungal or bacterial genomes) were identified by BLASTN and then were also filtered out.…”

Section: Methodsmentioning

confidence: 99%

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

Mizuno

Ishiya

Matsushita³

et al. 2020

Self Cite

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.