Return of the Mitochondrial DNA
This is a project associated with a poster presented at the 29th Fungal Genetics Conference (14-19 March 2017, Pacific Grove, CA, USA). It contains more information on the methods used than the poster itself. You can also find a downloadable copy of the poster here and links to related information (entry on ResearchGate and GitHub repositories).
In the 1990s, the barcoding of life project was started, aiming to use a single sequence to identify animals, fungi and plants to the species level. The first marker that was proposed was a mitochondrial marker: the mitochondrially encoded cytochrome oxidase I (cox1 in filamentous fungi).
However, amplifying the cox1 sequence proved problematic in many fungal groups, because the frequent insertions of introns into the region made universal primer design difficult. Hence, the mitochondrial marker was abandoned and the barcoding community chose the ITS region as official barcode for fungi. Unfortunately, the ITS barcode proved to have insufficient resolution in many closely related species. Thus, multi-locus analysis became the new standard, most of which included at least one mitochondrial marker. There has been no consensus on which mitochondrial loci to include.
With next generation sequencing and new assembly tools it is possible to assemble the complete mitochondrial genome of isolates, which provide all the benefits that are associated with using mitochondrial markers. In addition, using the complete mitochondrial genome offers better resolution for phylogenetic analyses and with sufficient sampling it can be placed in the context of previous works done on mitochondrial barcoding markers.
Take home message
- Mitochondrial genomes can be efficiently assembled from NGS data
- It is feasible to analyze the mitogenome of a large number of strains
- Complete miotgenomes offer sufficient information to delineate even closely related species
- A detailed analysis of the mitogenomes may offer new insights into the biology of the organism
- Complete mitochondrial genomes should be added to whole genome sequencing projects
Methods
All the different regions used for the analysis was assembled using GRAbB. GRAbB is a program designed to assemble selected regions of the genome or transcriptome using reference sequences and NGS data.
Phylogenetic species were identified using the programmatic implementation of the genealogical concordance phylogenetic species recognition (GCPSR).
More details are coming after the publication of the research article. Until then, if you wish to know more about the methods, feel free to contact me via ResearchGate, LinkedIn or GitHub.
Reference
The article that was used as reference is not yet published. So the citation information below is temporary and will be updated when the work is published.