Dataset Information

The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes.

ABSTRACT: Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized for genetics research including population studies. However, the reconstruction of the mitogenome is complicated by nuclear mitochondrial DNA (mtDNA) segments (NUMTs) that co-align with the mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% and 10%, were assessed for the ability to produce authentic mitogenome haplotypes from a previously generated WGS dataset. Variants associated with NUMTs were detected in the mtDNA alignments for 91 of 917 (~8%) Swedish samples when the 5% frequency threshold was applied. The 413 observed NUMT variants were predominantly detected in two regions (nps 12,612-13,105 and 16,390-16,527), which were consistent with previously documented NUMTs. The number of NUMT variants was reduced by ~97% (400) using a 10% frequency threshold. Furthermore, the 5% frequency data were inconsistent with a platinum-quality mitogenome dataset with respect to observed heteroplasmy. These analyses illustrate that a 10% variant detection threshold may be necessary to ensure the generation of reliable mitogenome haplotypes from WGS data resources.

SUBMITTER: Sturk-Andreaggi K

PROVIDER: S-EPMC8876724 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes.

Sturk-Andreaggi Kimberly K Ring Joseph D JD Ameur Adam A Gyllensten Ulf U Bodner Martin M Parson Walther W Marshall Charla C Allen Marie M

International journal of molecular sciences 20220217 4

Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized for genetics research including population studies. However, the reconstruction of the mitogenome is complicated by nuclear mitochondrial DNA (mtDNA) segments (NUMTs) that co-align with the mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% and 10%, were assessed for the ability to produce authentic mitogenome ha ...[more]

PMID: 35216360

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Project description:Stocking hatchery fish can lead to disturbance and extinction of the local indigenous population. Masu salmon Oncorhynchus masou masou, which is endemic across Japan, is a commonly stocked fish for recreational fishing in Japan. To conserve the indigenous resource, their genetic information is required, however, especially on Kyushu Island, the paucity of genetic information for this species has hindered proper resource management. Here, to identify hatchery mitogenome haplotypes of this species, stocked in the Kase River system, Kyushu Island, Japan, and to provide mitogenomic information for the resource management of this species, we analyzed the whole-mitogenome of masu salmon in this river system and several hatcheries potentially used for stocking. Whole-mitogenome sequencing clearly identified hatchery haplotypes, like fingerprints: among the 21 whole-mitogenome haplotypes obtained, six were determined to be hatchery haplotypes. These hatchery haplotypes were distributed in 13 out of 17 sites, suggesting that informal stocking of O. m. masou has been performed widely across this river system. The population of no hatchery haplotypes mainly belonged to clade I, a clade not found in Hokkaido Island in previous studies. Sites without hatchery haplotypes, and the non-hatchery haplotypes in clade I might be candidates for conservation as putative indigenous resources. The whole-mitogenome haplotype analysis also clarified that the same reared strain was used in multiple hatcheries. Analysis of molecular variance suggested that stocked hatchery haplotypes reduce the genetic variation among populations in this river system. It will be necessary to pay attention to genetic fluctuations so that the resources of this river system will not deteriorate further. The single nucleotide polymorphism data obtained here could be used for resource management in this and other rivers: e.g., for monitoring of informal stocking and stocked hatchery fishes, and/or putative indigenous resources.

Dataset Information

The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes.

Publications

The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes.

Similar Datasets

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