Skip to main content
SpringerLink
Log in

The complete genome sequence and phylogenetic analysis of the mitochondrial DNA of the wood-decaying fungus Fomitopsis palustris

  • Research Article
  • Published:
Genes & Genomics Aims and scope Submit manuscript

Abstract

The complete mitochondrial genome sequence of the wood-decaying fungus Fomitopsis palustris (Basidiomycete, Agaricomycotina) was determined by next-generation sequencing technology. The complete sequence of the circular mitochondrial DNA of F. palustris was 63,479 bp in length with a 75.98% AT content. The mitochondrial genome encoded 14 conserved proteins, 2 ribosomal RNAs, 26 transfer RNAs, and 19 additional open reading frames. The coxI and cob genes contained six and one group I introns, respectively, and encoded eight open reading frames, including seven intron-encoded endonucleases. The complete mitochondrial genome of F. palustris presented herein represents the first such report for brown rot basidiomycetes. In addition, the BLAST score ratio and phylogenetic analysis may open new avenues to understanding the evolutionary status of this fungus .

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Aguileta G, de Vienne DM, Ross ON, Hood ME, Giraud T, Petit E, Gabaldón T (2014) High variability of mitochondrial gene order among fungi. Genome Biol Evol 6:451–465

    Article  PubMed  PubMed Central  Google Scholar 

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Binder M, Justo A, Riley R, Salamov A, Lopez-Giraldez F, Sjökvist E, Copeland A, Foster B, Sun H, Larsson E, Larsson KH, Townsend J, Grigoriev IV, Hibbett DS (2013) Phylogenetic and phylogenomic overview of the Polyporales. Mycologia 105:1350–1373

    Article  CAS  PubMed  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bullerwell CE, Burger G, Lang BF (2000) A novel motif for identifying Rps3 homologs in fungal mitochondrial genomes. Trends Biochem Sci 25:363–365

    Article  CAS  PubMed  Google Scholar 

  • Crusoe MR, Alameldin HF, Awad S, Boucher E, Caldwell A, Cartwright R, Charbonneau A, Constantinides B, Edvenson G, Fay S et al (2015) The khmer software package: enabling efficient nucleotide sequence analysis. F1000Res 4:900

    PubMed  PubMed Central  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochem Bull 19:11–15

    Google Scholar 

  • Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M et al (2017) InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res 4:D190–D199

    Article  Google Scholar 

  • Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martínez AT, Otillar R, Spatafora JW, Yadav JS et al (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 29:1715–1719

    Article  Google Scholar 

  • Formighieri EF, Tiburcio RA, Armas ED, Medrano FJ, Shimo H, Carels N, Góes-Neto A, Cotomacci C, Carazzolle MF, Sardinha-Pinto N et al (2008) The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109 kb in size and contains a stable integrated plasmid. Mycol Res 112:1136–1152

    Article  CAS  PubMed  Google Scholar 

  • Hildén K, Martinez AT, Hatakka A, Lundell T (2005) The two manganese peroxidases Pr-MnP2 and Pr-MnP3 of Phlebia radiata, a lignin-degrading basidiomycete, are phylogenetically and structurally divergent. Fungal Genet Biol 42:403–419

    Article  PubMed  Google Scholar 

  • Hofrichter M, Lundell T, Hatakka A (2001) Conversion of milled pine wood by manganese peroxidase from Phlebia radiata. Appl Environ Microbiol 67:4588–4593

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hunt M, Silva N, Otto T, Parkhill J, Keane J, Harris S (2015) Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol 16:294

    Article  PubMed  PubMed Central  Google Scholar 

  • Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C et al (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649

    Article  PubMed  PubMed Central  Google Scholar 

  • Kuuskeri J, Mäkelä MR, Isotalo J, Oksanen I, Lundell T (2015) Lignocellulose-converting enzyme activity profiles correlate with molecular systematics and phylogeny grouping in the incoherent genus Phlebia (Polyporales, Basidiomycota). BMC Microbiol 15:217

    Article  PubMed  PubMed Central  Google Scholar 

  • Kuuskeri J, Häkkinen M, Laine P, Smolander OP, Tamene F, Miettinen S, Nousiainen P, Kemell M, Auvinen P, Lundell T (2016) Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose. Biotechnol Biofuels 9:192

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu Y, Steenkamp ET, Brinkmann H, Forget L, Philippe H, Lang BF (2009) Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support. BMC Evol Biol 9:272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rasko DA, Myers GSA, Ravel J (2005) Visualization of comparative genomic analyses by BLAST score ratio. BMC Bioinform 6:2

    Article  Google Scholar 

  • Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, Levasseur A, Lombard V, Morin E, Otillar R et al (2014) Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci USA 111:9923–9928

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rytioja J, Hildén K, Yuzon J, Hatakka A, de Vries RP, Mäkelä MR (2014) Plant-polysaccharide-degrading enzymes from Basidiomycetes. Microbiol Mol Biol Rev 78:614–649

    Article  PubMed  PubMed Central  Google Scholar 

  • Sahl JW, Caporaso JG, Rasko DA, Keim P (2014) The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. PeerJ 2:e332

    Article  PubMed  PubMed Central  Google Scholar 

  • Saitou N, Nei M (1987) Theneighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Salavirta H, Oksanen I, Kuuskeri J, Mäkelä M, Laine P, Paulin L, Lundell T (2014) Mitochondrial genome of Phlebia radiatais the second largest (156 kbp) among fungi and features signs of genome flexibility and recent recombination events. PLoS ONE 9:e97141

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Zeng F, Hon CC, Zhang Y, Leung FC (2008) The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom). FEMS Microbiol Lett 280:34–41

    Article  CAS  PubMed  Google Scholar 

  • Wang XC, Shao J, Liu C (2016) The complete mitochondrial genome of the medicinal fungus Ganoderma applanatum (Polyporales, Basidiomycota). Mitochondr DNA 27:2813–2814

    CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by a research grant from Utsunomiya University (http://www.utsunomiya-u.ac.jp/en/index.php) to the UU-COE. This research was also supported by a Grant-in-Aid for Scientific Research (No. 15K07504) from the Japan Society for the Promotion of Science (JSPS) to N. K. We thank Dr. V. K. Deo (Shizuoka University) for valuable discussions.

Author information

Author notes

  1. Yuki Tanaka and Tomohiro Suzuki have contributed equally to this work.

Authors and Affiliations

  1. Department of Applied Biological Chemistry, Utsunomiya University, 350 Mine-machi, Utsunomiya, Tochigi, 321-8505, Japan

    Yuki Tanaka, Takeshi Kurokura, Masayuki Iigo, Naoto Habu & Naotake Konno

  2. Center for Bioscience Research and Education, Utsunomiya University, 350 Mine-machi, Utsunomiya, Tochigi, 321-8505, Japan

    Tomohiro Suzuki, Takeshi Kurokura, Masayuki Iigo & Naotake Konno

  3. Center for Optical Research and Education, Utsunomiya University, 7-1-2 Yoto, Utsunomiya, Tochigi, 321-8585, Japan

    Masayuki Iigo

  4. Graduate School of Engineering, Utsunomiya University, 7-1-2 Yoto, Utsunomiya, Tochigi, 321-8585, Japan

    Fubito Toyama

  5. Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan

    Hideo Dohra

  6. Faculty of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan

    Naotake Konno

Authors
  1. Yuki Tanaka
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tomohiro Suzuki
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Takeshi Kurokura
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Masayuki Iigo
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Fubito Toyama
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Naoto Habu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Hideo Dohra
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Naotake Konno
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Hideo Dohra or Naotake Konno.

Ethics declarations

Conflict of interest

Yuki Tanaka, Tomohiro Suzuki, Takeshi Kurokura, Masayuki Iigo, Fubito Toyama, Naoto Habu, Hideo Dohra, Naotake Konno declare that they have no conflict of interest.

Ethical approval

This research was conducted in the absence of any ethical issue on animal research.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 173 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tanaka, Y., Suzuki, T., Kurokura, T. et al. The complete genome sequence and phylogenetic analysis of the mitochondrial DNA of the wood-decaying fungus Fomitopsis palustris . Genes Genom 39, 1377–1385 (2017). https://doi.org/10.1007/s13258-017-0603-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13258-017-0603-y

Keywords

Search

Navigation