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Home / Equine Research Bank / BMC Genomics / A new method for long-read sequencing of animal mitochondria...
BMC genomics2020; 21(1); 785; doi: 10.1186/s12864-020-07183-9

A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants.

Abstract: Mitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes. We present here an approach to sequence whole mitochondrial genomes using nanopore long-read sequencing. Our method relies on the selective elimination of nuclear DNA using an exonuclease treatment and on the amplification of circular mitochondrial DNA using a multiple displacement amplification step. Results: We optimized each preparative step to obtain a 100 million-fold enrichment of horse mitochondrial DNA relative to nuclear DNA. We sequenced these amplified mitochondrial DNA using nanopore sequencing technology and obtained mitochondrial DNA reads that represented up to half of the sequencing output. The sequence reads were 2.3 kb of mean length and provided an even coverage of the mitochondrial genome. Long-reads spanning half or more of the whole mtDNA provided a coverage that varied between 118X and 488X. We evaluated SNPs identified using these long-reads by Sanger sequencing as ground truth and found a precision of 100.0%; a recall of 93.1% and a F1-score of 0.964 using the Twilight horse mtDNA reference. The choice of the mtDNA reference impacted variant calling efficiency with F1-scores varying between 0.947 and 0.964. Conclusions: Our method to amplify mtDNA and to sequence it using the nanopore technology is usable for mitochondrial DNA variant analysis. With minor modifications, this approach could easily be applied to other large circular DNA molecules.
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Publication Date: 2020-11-11 PubMed ID: 33176683PubMed Central: PMC7661214DOI: 10.1186/s12864-020-07183-9Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

In this research study, scientists have developed a new method for sequencing entire mitochondrial genomes from animals using nanopore long-read sequencing. They applied this method to identify mitochondrial DNA variations in horses and achieved a high level of precision in their results.

Research Methodology

  • The research methodology involved sequencing whole mitochondrial genomes using nanopore long-read sequencing. This technique relies on high-speed electronic reading of DNA sequences as they pass through tiny nanopore channels.
  • The method consisted of two main steps. Firstly, the nuclear DNA was selectively removed using an exonuclease treatment. Secondly, circular mitochondrial DNA was amplified using a process known as multiple displacement amplification.
  • The researchers optimized each step of the process to obtain a 100 million-fold enrichment of horse mitochondrial DNA relative to nuclear DNA.

Results

  • After amplifying the mitochondrial DNA, the researchers sequenced it using nanopore sequencing technology. The mitochondrial DNA reads represented up to 50% of the total sequencing output.
  • The average sequence read length was 2.3 kilobases, providing an even coverage of the mitochondrial genome.
  • Long-reads spanning half or more of the whole mitochondrial DNA provided a coverage that varied between 118X and 488X.
  • The researchers evaluated single nucleotide polymorphisms (SNPs) identified using these long-reads with Sanger sequencing, which is a method used to determine the precise sequence of a certain part of DNA.
  • The precision was 100.0%, recall was 93.1%, and the F1-score (which measures the balance between precision and recall) was 0.964 using the Twilight horse mtDNA reference. The mtDNA reference used impacted variant calling efficiency with F1 scores ranging from 0.947 to 0.964.

Conclusions

  • The authors concluded that their method for amplifying mitochondrial DNA and sequencing it using nanopore technology is useful for studying mitochondrial DNA variant analysis.
  • With minor modifications, the authors suggest their method could also be applied to other large circular DNA molecules.

Cite This Article

APA
Dhorne-Pollet S, Barrey E, Pollet N. (2020). A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants. BMC Genomics, 21(1), 785. https://doi.org/10.1186/s12864-020-07183-9

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 21
Issue: 1
Pages: 785
PII: 785

Researcher Affiliations

Dhorne-Pollet, Sophie
  • Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
Barrey, Eric
  • Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
Pollet, Nicolas
  • Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France. Nicolas.Pollet@egce.cnrs-gif.fr.

MeSH Terms

  • Animals
  • DNA, Mitochondrial / genetics
  • Genome, Mitochondrial / genetics
  • High-Throughput Nucleotide Sequencing
  • Horses / genetics
  • Nanopores
  • Sequence Analysis, DNA

Conflict of Interest Statement

The authors declare no competing interests.

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