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Identification of equine mitochondrial DNA variants using long read sequencing

ABSTRACT: Identification of equine mitochondrial DNA variants using long-read sequencing

PROVIDER: PRJEB35937 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3774120_1.fastq.gz	Fastqsanger.gz
	ERR3774130_1.fastq.gz	Fastqsanger.gz
	ERR3774111_1.fastq.gz	Fastqsanger.gz
	ERR3774121_1.fastq.gz	Fastqsanger.gz
	ERR3774131_1.fastq.gz	Fastqsanger.gz

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

Project description:BackgroundMitochondrial 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.ResultsWe 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.ConclusionsOur 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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Gene expression profiling in equine polysaccharide storage myopathy

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Project description:The PDE12 gene codes for the poly(A)-specific exoribonuclease, involved in the quality control of mitochondrial non-coding RNAs. Here, we report that disease-causing PDE12 variants in three unrelated families are associated with mitochondrial respiratory chain deficiencies. Clinically, they presented in utero and within the neonatal period with muscle and brain involvement leading to marked cytochrome c oxidase (COX) deficiency in muscle and severe lactic acidosis. To analyze perturbations in specific cellular pathways contributing to pathogenesis in our patient cohort, we used Affymetrix Clariom D transcriptome arrays to study the RNA levels in fibroblasts derived from two patient (Patient 2 and patient 3), comparing these to age-matched controls.

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