Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2019 Oct 4;4(2):3368–3369. doi: 10.1080/23802359.2019.1674215

The complete mitochondrial genome of a wild edible mushroom, Russula griseocarnosa

Fei Yu a, Yongjie Zhang b, Jie Song a, Junfeng Liang a,✉
PMCID: PMC7707367  PMID: 33365997

Abstract

Russula griseocarnosa is a wild edible ectomycorrhizal mushroom in southern China. In this study, we assembled the complete mitochondrial genome of R. griseocarnosa. Its total length was 60995 bp with a GC content of 21% and contained a total of 52 genes, including 14 standard protein-coding genes, two rRNA genes, 21 tRNA genes and 15 free-standing open reading frames (ORFs). Phylogenetic analysis reflected that the evolutionary processes between R. griseocarnosa and some agaricomycetes.

Keywords: Russula griseocarnosa, mitochondrion, phylogenetic analysis

Russula griseocarnosa is an important wild edible mycorrhizal fungus in southern China (Wang et al. 2009). Previous studies confirmed that the chemical properties played a great role in the antioxidant and anti-tumor activities of R. griseocarnosa (Chen et al. 2010; Chen et al. 2018; Liu et al. 2018; Yu et al. 2019). Mitochondria are presumed to be derived from bacteria through endosymbiosis (Muñoz-Gómez et al). Many mitochondrial genomes (mitogenomes) contribute to systemic evolution, population genetics, and taxonomy (Carpi et al. 2016; Ramos et al. 2018). MtDNA analysis has been carried out for six species of Russula (Li et al. 2018), but the mitochondrial genome of R. griseocarnosa has not been reported.

Fruiting bodies of R. griseocarnosa (strain LJ24) were collected from Linjing Town, Teng County, Guangxi Province, China (110°38′E, 23°8′N), frozen rapidly in liquid nitrogen, brought back to the laboratory and placed at −80 °C in the Research Institute of Tropical Forestry, Chinese Academy of Forestry. The genomic DNA was extracted with the Omega Fungal DNA Kit D3390-02, and then sequenced on Illumina HiSeq X-ten sequencing platform at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, China.

The assembly of the mitogenome of R.griseocarnosa were carried out using MITObim V1.9.1 (Hahn et al. 2013) by using the mitogenome of Russula compacta (MH138072) as the initial reference. The complete mitogenome was annotated with the MFannot V1.33 (Valach et al. 2014) and MITOS2 (Bernt et al. 2013). Protein coding gene and ORFs were corrected using the NCBI open reading frame finder (https://www.ncbi.nlm.nih.gov/orffinder). tRNA genes were predicted using tRNAscan-SE 2.0 (Lowe and Chan 2016). Individual sequences of 14 protein-coding genes (atp6, atp8, atp9, cob, cox1,cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5 and nad6) were aligned using MEGA v6.06, concatenated using SequenceMatrix v1.8, and then a neighbor-joining phylogenetic tree was constructed using MEGA v6.06 with 1000 bootstrap replicates.

The mitogenome of Russula griseocarnosa was assembled as a 60995-bp circular molecule with a GC content of 21% (GenBank accession No. MN427435). It contains 52 genes, including 14 protein-coding genes, two rRNA genes, 21 tRNA genes and 15 open reading frames (ORFs). The start codon of 14 protein coding gene was ATG, and the termination codon was TAA. The R. griseocarnosa mitogenome contained two tRNA genes with different anticodons for leucine and serine, and three tRNAs with the same anticodons for methionine. The mitogenome of R. griseocarnosa contains six introns, which are located at nad5 (1 intron), cob (2 introns) and cox1 (3 introns).

To examine the phylogenetic evolution of R. griseocarnosa, a neighbor-joining phylogenetic analysis was applied for 14 agaricomycetes mitogenomes (including R. griseocarnosa) based on 14 protein-coding genes and rooted with Neurospora crassa (Figure 1). The phylogenetic evolution indicats a close relationship between R. griseocarnosa and other Russula. It will help us to understanding the evolutionary processes.

Figure 1.

Figure 1.

Open in a new tab

Phylogenetic analyses of 15 fungi based on 14 protein coding genes. GenBank accessionn numbers: Agaricus bisporus (JX271275.1), Ganoderma lucidum (NC_021750.1), Ganoderma meredithae (NC_026782.1), Heterobasidion irregulare (KF957635.1), Laccaria bicolour (NC_042773.1), Phlebia radiata (HE613568.1), Russula abietina (MH138073.1), Russula compacta (MH138072.1), Russula foetens (MH138074.1), Russula lepida (MH138075.1), Russula sp. (MH138077.1), Russula virescens (MH138076.1), Trametes hirsuta (MG775432.1) and Neurospora crassa (KY498477.1).

Disclosure statement

No potential conflict of interest was reported by the authors.

References

  1. Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69:313–319. [DOI] [PubMed] [Google Scholar]
  2. Carpi G, Kitchen A, Kim HL, Ratan A, Drautz-Moses DI, McGraw JJ, Kazimirova M, Rizzoli A, Schuster SC. 2016. Mitogenomes reveal diversity of the European Lyme borreliosis vector Ixodes ricinus in Italy. Mol Phylogenet Evol. 101:194–202. [DOI] [PubMed] [Google Scholar]
  3. Chen Q, Qi C, Peng G, Liu Y, Zhang XY, Meng ZL. 2018. Immune-enhancing effects of a polysaccharide PRG1-1 from Russula griseocarnosa on RAW264.7 macrophage cells via the MAPK and NF-κB signalling pathways. Food Agr Immunol. 29:833–844. [Google Scholar]
  4. Chen XH, Xia LX, Zhou HB, Qiu GZ. 2010. Chemical composition and antioxidant activities of Russula griseocarnosa sp. nov. J Agric Food Chem. 58:6966–6971. [DOI] [PubMed] [Google Scholar]
  5. Hahn C, Bachmann L, Chevreux B. 2013. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach. Nucleic Acids Res. 41:e129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Li Q, Wang QF, Chen C, Jin X, Chen ZQ, Xiong C, Li P, Zhao J, Huang WL. 2018. Characterization and comparative mitogenomic analysis of six newly sequenced mitochondrial genomes from ectomycorrhizal fungi (Russula) and phylogenetic analysis of the Agaricomycetes. Int J Biol Macromol. 119:792–802. [DOI] [PubMed] [Google Scholar]
  7. Liu Y, Zhang JJ, Meng ZL. 2018. Purification, characterization and anti-tumor activities of polysaccharides extracted from wild Russula griseocarnosa. Int J Biol Macromol. 109:1054–1060. [DOI] [PubMed] [Google Scholar]
  8. Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 44:W54–W57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Muñoz-Gómez SA, Wideman JG, Roger AJ, Slamovits CH. 2017. The origin of mitochondrial cristae from Alphaproteobacteria. Mol Biol Evol. 34:943–956. [DOI] [PubMed] [Google Scholar]
  10. Ramos B, González-Acuña D, Loyola DE, Johnson WE, Parker PG, Massaro M, Dantas GPM, Miranda MD, Vianna JA. 2018. Landscape genomics: natural selection drives the evolution of mitogenome in penguins. BMC Genomics. 19:53. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Valach M, Burger G, Gray MW, Lang BF. 2014. Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules. Nucleic Acids Res. 42:13764–13777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Wang XH, Yang ZL, Li YC, Knudsen H, Liu PG. 2009. Russula griseocarnosa sp. nov. (Russulaceae, Russulales), a commercially important edible mushroom in tropical China: mycorrhiza, phylogenetic position, and taxonomy. Nova Hedw. 88:269–282. [Google Scholar]
  13. Yu F, Song J, Liang JF, Wang SK, Lu JK. 2019. Whole genome sequencing and genome annotation of the wild edible mushroom, Russula griseocarnosa. Genomics. doi: 10.1016/j.ygeno.2019.04.012 [DOI] [PubMed] [Google Scholar]

Articles from Mitochondrial DNA. Part B, Resources are provided here courtesy of Taylor & Francis

RESOURCES