Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA

Andrews, Richard M.; Kubacka, Iwona; Chinnery, Patrick F.; Lightowlers, Robert N.; Turnbull, Douglass M.; Howell, Neil

doi:10.1038/13779

Cited by 2,955 publications

(2,422 citation statements)

References 9 publications

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“…Reads originating from four of the 18 dental calculus libraries were impacted by chimera formation during pooled post-capture amplification (Hawkins et al 2015; Kircher et al 2012) and were excluded from further analysis (NF-15c KAPA HiFi Uracil+, NF-108c Phusion HS II, and NF-47c Phusion HS II and KAPA HiFi Uracil+). The resulting analysis-ready reads were mapped to the revised Cambridge Reference Sequence (rCRS) (Andrews et al 1999) using the Burrows Wheeler Aligner (BWA aln) v. 0.7.5 (Li and Durbin 2009) with default parameters except that seeding was disabled (−1 1000) and edit distance was increased (−n 0.01) to improve mapping accuracy of ancient DNA reads, as recommended by (Schubert et al 2012). Nuclear mitochondrial Sequences (NumtS) were identified as any reads exhibiting superior alignment to the human nuclear genome, and removed.…”

Section: Methodsmentioning

confidence: 99%

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

Ozga

Nieves-Colón

Honap

et al. 2016

American J Phys Anthropol

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Objectives Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. Materials and Methods Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. Results Full mitogenomes (7-34x) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92–100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. Discussion Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains.

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Section: Methodsmentioning

confidence: 99%

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

Ozga

Nieves-Colón

Honap

et al. 2016

American J Phys Anthropol

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“…The segments examined covered parts of the tRNA Pro gene, hypervariable segment (HVS) 1 (nucleotide positions [np] 15,999–16,141, 16,121–16,238, and 16,209–16,366, relative to the revised Cambridge reference sequence [rCRS: Andrews et al, 1999]), and HVS 2 (128–256).…”

Section: Methodsmentioning

confidence: 99%

Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

Adachi

Kakuda

Takahashi

et al. 2017

American J Phys Anthropol

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ObjectivesThe Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern‐day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large‐scale immigration into Hokkaido about 150 years ago, should be examined. Moreover, the samples should be collected from all over Hokkaido.Materials and methodsMitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era were successfully determined by analyzing haplogroup‐defining polymorphisms in the hypervariable and coding regions. Thereafter, their frequencies were compared to those of other populations.ResultsOur findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan.DiscussionOur results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual‐structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people.

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“…All footprints that started from the very 5’ terminus to 5 nucleotides downstream of the of the start codon, were mapped to their nucleotide position of the mtDNA reference sequence 29 , irrespective of their individual lengths (x-axis represents the nucleotide position in the reference mtDNA). These footprints were mapped as blocks where the depth (y axis) of the block is proportional to the frequency with which that specific length of footprint, in that position, is found as part of the selected sequences from the library.…”

Section: Methodsmentioning

confidence: 99%

Using mitoribosomal profiling to investigate human mitochondrial translation

et al. 2017

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Background: Gene expression in human mitochondria has various idiosyncratic features. One of these was recently revealed as the unprecedented recruitment of a mitochondrially-encoded tRNA as a structural component of the large mitoribosomal subunit. In porcine particles this is mt-tRNA Phe whilst in humans it is mt-tRNA Val. We have previously shown that when a mutation in mt-tRNA Val causes very low steady state levels, there is preferential recruitment of mt-tRNA Phe. We have investigated whether this altered mitoribosome affects intra-organellar protein synthesis. Methods: By using mitoribosomal profiling we have revealed aspects of mitoribosome behaviour with its template mt-mRNA under both normal conditions as well as those where the mitoribosome has incorporated mt-tRNA Phe. Results: Analysis of the mitoribosome residency on transcripts under control conditions reveals that although mitochondria employ only 22 mt-tRNAs for protein synthesis, the use of non-canonical wobble base pairs at codon position 3 does not cause any measurable difference in mitoribosome occupancy irrespective of the codon. Comparison of the profile of aberrant mt-tRNA Phe containing mitoribosomes with those of controls that integrate mt-tRNA Val revealed that the impaired translation seen in the latter was not due to stalling on triplets encoding either of these amino acids. The alterations in mitoribosome interactions with start codons was not directly attributable to the either the use of non-cognate initiation codons or the presence or absence of 5’ leader sequences, except in the two bicistronic RNA units, RNA7 and RNA14 where the initiation sites are internal. Conclusions: These data report the power of mitoribosomal profiling in helping to understand the subtleties of mammalian mitochondrial protein synthesis. Analysis of profiles from the mutant mt-tRNA Val cell line suggest that despite mt-tRNA Phe being preferred in the porcine mitoribosome, its integration into the human counterpart results in a suboptimal structure that modifies its interaction with mt-mRNAs.

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Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA

Cited by 2,955 publications

References 9 publications

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

Using mitoribosomal profiling to investigate human mitochondrial translation

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