The complete mitochondrial genome of nematophagous fungus Esteya vermicola

Abstract

The complete mitochondrial genome of the Nematophagous fungus Esteya vermicola CBS 115803 was determined using the PacBio RS II sequencing technology. The circular molecule is 47,282bp in length with a GC content of 24.85%. Annotated genes including 14 conserved protein-coding genes, the large and the small rRNA subunit (rnl and rns) and 27 tRNAs. The phylogenetic analysis showed that E. vermicola had close genetic relationship with the genus Sporothrix.

Keywords:

• Mitochondrial genome
• Esteya vermicola
• phylogenetic analysis

Esteya vermicola is known as the recorded endoparasitic nematophagous fungus that attacks pine wood nematode (PWN, Bursaphelenchus xylophilus) (Liou et al. 1999). Adhesive lunate conidia produced by E. vermicola can attach to and penetrate the cuticle of PWN and consume contents of the infected nematode’s body, and then kill nematode and produce new lunate conidia for the next infection cycle (Wang et al. 2011, 2010, 2008). Up to now, there are six strains of E. vermicola around the world (Chu et al. 2015). However, the complete mitochondrial genome of E. vermicola has not been reported. Sequencing the complete mitochondrial genome of E. vermicola will enhance our understanding of the evolutionary relationships between E. vermicola and its related closed species.

The strain of E. vermicola CBS 115803 was originally isolated from Scolytus intricatus and its galleries in oak trees in Czech Republic (Chu et al. 2015) and was stored in the CBS-KNAW culture collection in the Netherlands. Here, we present the complete mitochondrial genome of E. vermicola CBS 115803 (GenBank accession number: KY644696). Total genomic DNA was extracted using Genomic-tip Kit 500G (Cat No./ID: 10262) following the manufacturer’s instructions, then was build up 20kb genomic library and sequenced using PacBio RS II platform. Sequencing depth was 104.66 × coverage. Mitochondrial reads of E. vermicola were filtered depending on the database of fungal mitogenome, and assembled using HGAP2.3.0 (SMRT Analysis). The mitochondrial genome of E. vermicola was assembled as a 47,282bp single circular molecule, which encoded 16 genes including three cytochrome oxidases (cox), seven subunits of NAD dehydrogenase (nad), the large and the small rRNA subunit (rnl and rns), three ATP synthases (atp), and one cytochrome b (cob).

A total of 27 tRNA genes were predicted in the mitochondrial genome of E. vermicola corresponding to 21 amino acids using tRNAscan software, including 19 common amino acids tRNA (three tRNA-Met), extraordinary 21st selenocysteine tRNA which takes part in proteins involved in antioxidant activity (Byun & Kang 2011) and one suppressor tRNA. The base composition of mitochondrial genome of E. vermicola is 38.08% A, 37.06% T, 14.05% G, and 10.81% C, with a low GC content of 24.85%. The gene order of all conserved protein-coding genes and tRNA was Cys, Arg, cox1, nad1, nad4, atp8, atp6, rns, Tyr, Asn, cox3, Lys, Asp, Ser, SeC, nad6, Sup, Val, Ile, Ser, Pro, rnl, Lys, Thr, Glu, Met, Met, Leu, Gly, Ala, Phe, Leu, Gln, His, Met, nad2, nad3, atp9, cox2, Arg, nad4L, nad5, cob.

To validate the phylogenetic position of E. vermicola, phylogenetic analyses using maximum-likelihood (ML) method were conducted in MEGA7 using GTR + G + I model with 1000 bootstrap replicates (Figure 1). 15 species were used to construct phylogenetic tree, and they are Beauveria bassiana D1-5 mit, Cordyceps bassiana isolate Bb147, B. pseudobassiana NC 022708.1, C. militaris strain EFCC-C2, Metarhizium anisopliae strain ME1, Hirsutella minnesotensis strain 3608, H. rhossiliensis isolate USA-87-5, Fusarium graminearum strain CBS 110263, Aspergillus nidulans FGSC A4, Neurospora crassa OR74A, Esteya vermicola CBS115803, Sporothrix brasiliensis 5110 Cont23, S. schenckii KMU2052, S. schenckii ATCC 10268, and S. schenckii NC 015923.1. Phylogenetic analysis based on whole mitochondria genome sequences clustered E. vermicola with the genus Sporothrix, so it confirms E. vermicola has close genetic relationship with the genus Sporothrix according to phylogenetic analysis (Figure 1).

Figure 1. Phylogenetic relationships (maximum likelihood) of Esteya vermicola based on the nucleotide sequence of 14 conserved protein-coding genes (atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, nad6) in the mitochondrial genomes. The numbers beside the nodes are percentages of 1000 bootstrap values.

Disclosure statement

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

Additional information

Funding

This work was supported by the Institute Special Fund for Basic Research, Institute of Forest Ecology, Environment, and Protection, Chinese Academy of Forestry (grant no. CAFRIFEEP201403) and the State 863 Project funded by Ministry of Science and Technology (grant no. 2012AA101503).