The mitochondrial genome of a wild edible mushroom, Russula rosea

Abstract

Russula rosea is a common wild edible ectomycorrhizal fungus, which is widely distributed all over the world. We assembled the complete mitochondrial genome of R. rosea with the total length was 54177 bp and the GC content of 22.34%. It contains a total of 57 genes, including 14 standard protein-coding genes, one conserved ribosomal protein S3 gene (rps3), two rRNA genes, 24 tRNA genes, 15 free-standing open reading frames (ORFs) and one DNA polymerase gene (dpo). Mitochondrial genome found a close evolutionary relationship between Russula rosea and Russula lepida, which was helpful to study the genetic evolutionary relationship of edible fungi.

Russula rosea (Pers. 1796) is one of the important wild edible ectomycorrhizal fungi in the world (Karliński et al. 2007, Kolmakov 2015), which also has antioxidant, anti-tumor and other medicinal effects (Kostić et al. 2020). It is a functional food with high protein, rough fiber and low fat with high nutritional and economic value (Karliński et al. 2007). Mitochondria, as an important organelle of eukaryotic cells, have their own genome and genetic mechanism, and play an important role in cell energy metabolism and biosynthesis, activation of drug resistance (Sandor et al. 2018). The mitochondrial genome has contributed to system evolution and population genetics (Li et al. 2018), but the mitochondrial genome of R. rosea not been described. In this study, we sequenced and annotated the mitochondrial genome of R. rosea to provide theoretical basis for phylogenetic relationships.

Fruiting bodies of R. rosea (strain F10) (Figure 1(A)) were collected from Huangshan, Anhui Province, China (118°18′ E, 30°9′ N), collected and identified by Fei Yu (email: yufei_1007@163.com). The materials were collected according to the guidelines of China, Anhui Province and the Research Institute of Tropical Forestry, Chinese Academy of Forestry, while the voucher specimen (RITF5754) was stored in the Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou City, Guangdong Province, China (http://ritf.caf.ac.cn/, Junfeng Liang, jfliang2000@163.com). R. rosea fruiting bodies were divided into two fractions: one fraction was stored in a − 80 °C refrigerator, and the other fraction was 50 °C dried brought back to the laboratory. The specimen genomic DNA was extracted by Omega Fungal DNA Kit D3390-02, and species identification was performed, then genomic sequenced using Illumina NovaSeq 6000 at Novogene Bioinformatic Technology Co., Ltd, China.

Figure 1.

Phylogenetic tree (A) Russula rosea; (B) Phylogenetic tree of R.rosea and 18 fungi based on 14 standard protein coding genes.

The assembly of the mitogenomic of R.rosea were carried out using GetOrganelle v 1.7.5 (Jin et al. 2020), which based on bowtie2 v 2.3.5.1 (Langmead and Salzberg 2012) map reads to fungal mitogenomes (fungus_mt) database in NCBI and producted the de novo assembly using SPAdes v 3.13.0 (Bankevich et al. 2012), eventually generating the complete circular mitogenomes. The K-mer gradient was set to ‘-k 21, 45, 65, 85,105’ according to the sequenced read length of 150 bp. The mitogenomic was automatically annotated with online tool MFannot (Valach et al. 2014) based on mold mitochondrial genetic code (genetic code 4) (Li et al. 2018). Open Reading Frames (ORFs) were corrected using the online tool NCBI open reading frame finder, tRNA genes were predicted using online tRNAscan-SE 2.0 (Lowe and Chan 2016), and then perform a manual check to correct possible errors.

The mitogenomic of R. rosea was assembled as a 54177-bp circular molecule with a GC content of 22.34% (GenBank accession No. OL117025). It contains 57 genes, including 14 protein-coding genes (atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5 and nad6), one conserved ribosomal protein S3 gene (rps3), two rRNA genes (rns and rnl), 24 tRNA genes, 15 free-standing open reading frames (ORFs) and one DNA polymerase gene (dpo). The initiation codon of 14 protein coding genes and conserved ribosomal protein S3 gene were ATG and the termination codon were TAA. The R. rosea mitogenome contains three tRNA genes with two different anticodons for arginine, leucine and serine, and two tRNA genes with the same anticodons for methionine. The mitogenome of R. rosea contains nine introns, which were located at cob (2 introns), cox1 (4 introns), cox2 (1 introns), nad1 (1 intron) and nad5 (1 intron). The overall nucleotide composition was A: 39.01%, T: 38.65%, C: 10.43%, and G: 11.91%.

To understand the evolution of R. rosea, we selected the mitochondrial genomes of 17 edible fungi published on NCBI website, took Neurospora crassa as outgroup, aligned the sequences of 14 protein-coding genes respectively, then concatenated alignments with SequenceMatrix v1.8 (Li et al. 2018), and finally constructed a neighbor-joining phylogenetic tree with Mega v7 by using 1000 bootstrap replicates (Figure 1(B)). Based on the neighbor-joining phylogenetic tree constructed by the nucleotide sequences of 14 protein coding genes, it was found that there was a close genetic relationship between Russula rosea and Russula lepida.

Funding Statement

This study was supported by the Scientific and Technological Innovation Project of Colleges and Universities in Shanxi Province [2021L107], the Award for Excellent Doctoral to work in Shanxi [SXBYKY2021035] and the Science and technology innovation fund of Shanxi Agricultural University [2020BQ85].

Disclosure statement

The authors report no potential conflict of interest.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov under the accession no. OL117025. The associated BioProject, BioSample, and SRA numbers are PRJNA800019, SAMN25224323 and SRR17717762, respectively.

Author contributions

Fei Yu: collection and identification of samples, assemble, annotate and write the mitochondrial genome. Junfeng Liang: study design and modified the manuscript.