title: The complete mitochondrial genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 confirms evolutionary division within the fungal Phialocephala fortinii s.l. - Acephala appalanata species complex.
abstract: Despite the recent surge in mitochondrial (mt) genome sequencing, Kingdom Fungi remains underrepresented with respect to mtDNA. We describe the mt genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 (Helotiales, Ascomycota). This strain is of interest to the Canadian forestry industry as it produces the anti-insectan compound rugulosin. Sequence was obtained from whole genome shotgun sequencing. Comparison to the only other published Phialocephala mt genome, Phialocephala subalpina, indicates that the suite of common mt genes - cox1-3, cob, nad1-6 and 4L, atp6, 8 and 9, as well as rrnL and rrnS - has retained an identical order. Nad4L remains one of the most conserved mitochondrial genes within Phialocephala. Members of the closely related Phialocephala fortinii s.l. - Acephala appalanata species complex (PAC) share too much sequence similarity to properly resolve lineages using ITS barcoding alone. Using P. scopiformis sequence as an outgroup, we determined ancestral gene states that help confirm clades within Phialocephala. Our results show: (1) the complete mt genome of P. scopiformis, representing the 10th complete mt genome for the order Helotiales (containing >3800 species), and (2) how large-scale genomic patterns, such as mitochondrial gene order, can be used to confirm lineages within fungal species complexes.
authors.affiliation: Department of Biology, Acadia University, 33 Westwood Ave, Wolfville, NS, B4P 2R6, Canada.
authors.forename: Brent M
authors.initials: BM
authors.lastname: Robicheau
authors.affiliation: Department of Biology, Acadia University, 33 Westwood Ave, Wolfville, NS, B4P 2R6, Canada.
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Young
authors.affiliation: U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Kurt
authors.initials: K
authors.lastname: LaButti
authors.affiliation: U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.affiliation: Department of Biology, Acadia University, 33 Westwood Ave, Wolfville, NS, B4P 2R6, Canada. Electronic address: allison.walker@acadiau.ca.
authors.forename: Allison K
authors.initials: AK
authors.lastname: Walker
mesh_terms: D001203:Ascomycota / Q000145:classification / Q000235:genetics*; D016000:Cluster Analysis; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D060026:Endophytes / Q000145:classification / Q000235:genetics*; D023061:Gene Order; D005800:Genes, Fungal; D016681:Genome, Fungal; D054629:Genome, Mitochondrial; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D026801:Synteny; D064028:Tracheophyta / Q000382:microbiology
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer
keywords: Comparative mitochondrial genomics; Gene duplication; Helotiales; Rugulosin