The intron landscape of the mtDNA cytb gene among the Ascomycota: introns and intron-encoded open reading frames

Abstract

Fungal mitochondrial genes are frequently noted for the presence of introns. These introns are self-splicing and can be assigned to either group I or II introns and they can encode open reading frames (ORFs). This study examines the introns present within the cytochrome b (cytb) gene of ascomycetes fungi. Cytochrome b gene sequences were sampled from GenBank and supplemented with our own data for species of Leptographium and Ophiostoma. Group I introns were encountered most frequently, many encoding either LAGLIDADG or GIY-YIG homing endonucleases (HEs). Numerous examples of different intron/ORF arrangements were observed including nested ORFs, multiple ORFs within a single intron and intron ORFs at various stages of erosion due to the accumulation of mutations. In addition, we noted one example of a nested intron and one complex group II intron that could potentially allow for alternative splicing. Documenting the distribution of introns within the same gene across a range of species allows for a better understanding of the evolution of introns and intronic ORFs. Intron landscapes also are a resource that can help in annotating genes and in bioprospecting for potentially active HEs, which are rare-cutting DNA endonucleases with applications in biotechnology.

Keywords:

• Group I and II introns
• nested introns
• homing endonucleases
• evolution

Acknowledgements

We would like to acknowledge Dr. Steve Zimmerly (University of Calgary) for his valuable advice on folding group II introns and the contribution of Hay M, La D, Carta A, Chen T, and Corkery T, with regards to obtaining sequence data for Leptographium and Ophiostoma strains. Valuable comments by two anonymous reviewers were greatly appreciated.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this paper.

Additional information

Funding

GH would like to acknowledge funding from an Natural Sciences and Engineering Research Council of Canada [Discovery Grant RGPIN-2015-06658]. In addition, TKG and AW would like to acknowledge funding from the University of Manitoba GETS Program.