Characterization and Phylogenetic Analysis of the Mitochondrial Genome of Glarea lozoyensis Indicates High Diversity within the Order Helotiales

Abstract

Background Glarea lozoyensis is a filamentous fungus used for the industrial production of non-ribosomal peptide pneumocandin B0. In the scope of a whole genome sequencing the complete mitochondrial genome of the fungus has been assembled and annotated. It is the first one of the large polyphyletic Helotiaceae family. A phylogenetic analysis was performed based on conserved proteins of the oxidative phosphorylation system in mitochondrial genomes.ResultsThe total size of the mitochondrial genome is 45,038 bp. It contains the expected 14 genes coding for proteins related to oxidative phosphorylation,two rRNA genes, six hypothetical proteins, three intronic genes of which two are homing endonucleases and a ribosomal protein rps3. Additionally there is a set of 33 tRNA genes. All genes are located on the same strand. Phylogenetic analyses based on concatenated mitochondrial protein sequences confirmed that G. lozoyensis belongs to the order of Helotiales and that it is most closely related to Phialocephala subalpina. However, a comparison with the three other mitochondrial genomes known from Helotialean species revealed remarkable differences in size, gene content and sequence. Moreover, it was found that the gene order found in P. subalpina and Sclerotinia sclerotiorum is not conserved in G. lozoyensis. ConclusionThe arrangement of genes and other differences found between the mitochondrial genome of G. lozoyensis and those of other Helotiales indicates a broad genetic diversity within this large order. Further mitochondrial genomes are required in order to determine whether there is a continuous transition between the different forms of mitochondrial genomes or G. lozoyensis belongs to a distinct subgroup within Helotiales.

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

“…Given that the mitochondrial (mt) genome evolves more rapidly than the nuclear genome and has been shown to produce reliable phylogenetic trees, it has been established as an effective evolutionary marker in fungi (Wu et al 2009, Duò et al 2012, Youssar et al 2013, Shen et al 2015. Fungal mt genomes are frequently circular molecules consisting of 14 highly conserved protein coding genes related to oxidative phosphorylation (OXPHOS), one large (rrnL) and one small (rrnS) ribosomal RNA (rRNA) gene, and a set of transfer RNA (tRNA or trn) genes which can vary between species (Gray et al 1999, Lavín et al 2008.…”

“…Since the beginning of this global initiative, 347 fungal mt genomes have been deposited and made publicly available via NCBI's Organelle Genome database, 220 of which have been curated. However, there are only 9 sequenced mt genomes from the order Helotiales and just 14 total from the class Leotiomycetes (Ascomycota) (Duò 2012, Youssar 2013. Given that very few mt genomes from the order Helotiales have been annotated, the P. scopiformis mt genome presented herein will serve as a basis for further exploration into the relationships among helotialean fungal mitochondrial genomes.…”

Complete mitochondrial genome of the Verticillium-wilt causing plant pathogen Verticillium nonalfalfae

“…The use of mitochondrial genomes for phylogenetic studies has become a generally well-adopted approach, and is commonly used to gain important insights into both basidio- [ 16 – 18 ] and asco- [ 19 , 20 ] mycete divisions. The most common approach for phylogenetic studies of mitochondrial sequences is to utilize a set of conserved proteins from their annotated sequences [ 9 , 21 , 22 , 23 ].…”

The 203 kbp Mitochondrial Genome of the Phytopathogenic Fungus Sclerotinia borealis Reveals Multiple Invasions of Introns and Genomic Duplications

“…Currently more than 100 complete fungal mitochondrial genomes are available, but only nine represent the order Helotiales of ascomycetes ( Phialocephala subalpina , Sclerotinia sclerotiorum , Botrytis cinerea (teleomorph Botryotinia fuckeliana ), Glarea lozoyensis , Marssonina brunnea, and four Rhynchosporium species) [16], [21], [22]. Only two mitochondrial genomes belong to members of the Sclerotiniaceae family, B. fuckeliana and S. sclerotiorum .…”