The complete mitochondrial genome of Hericium erinaceus (Bull.:Fr.) Pers., 1797 (Russulales, Basidiomycota): an edible and medicinal fungus

Abstract Hericium erinaceus (Bull.:Fr.) Pers., 1797, is an edible and medicinal fungus found in China. In this study, specimens of H. erinaceus HE0021 were collected from southeastern China (Yunhe County, Lishui City, Zhejiang Province, 28°7′12″N, 119°34′12″E). The whole mitochondrial genome of H. erinaceus HE0021 was sequenced using next-generation sequencing (NGS) technology, which comprised 15 protein-coding genes (PCGs), 27 transfer RNAs (tRNAs), two ribosomal RNAs, with a total length of 83,518 base pairs (bp). The results of the phylogenetic analysis show that H. erinaceus and H. coralloides were clustered in the same clade. The complete mitogenome sequence provides essential data for the subsequent investigation of Hericium and Russulales.


Introduction
The genus Hericium (within the classification Basidiomycota, Agaricomycetes, Russulales, and Hericiaceae) is a precious medicinal and nutritional resource.Hericium mycelium requires a moist, ventilated environment for growth, with a temperature ranging from 18 to 20 � C, and usually grows upon injured or recently fallen dead hardwood (mostly oak and pine).As a traditional edible and medicinal mushroom, Hericium is also called 'delicacies from the mountains monkey head' in China (Wang et al. 2009).Research has shown that the fruit body of Hericium is rich in protein, fat, polysaccharides, crude fiber, alkaloids, and sterols, among which polysaccharides and sterols were mainly functional compounds and got more attention.Medical research has demonstrated that it has anti-ulcer, anti-inflammation, anti-tumor, anti-aging, and liver protection effects; it is also reported in traditional Chinese medicine theory that its functional compounds possess the potential to control hyperglycemia, hypertension, and hyperlipidemia (Mizuno et al. 1992;Wang 2001;Lee et al. 2009).Four species have been identified in China, Hericium erinaceus (Bull.:Fr.)Pers., Hericium caput-medusae (Bull.:Fr.)Pers., Hericium laciniatum (Leers) Banker, and Hericium coralloides (Scop.:Fr.)Pers.ex Gray.Among them, H. erinaceus, the main species in the genus of Hericium, also known as saprotrophic fungi, has round and thick basidiocarps, white to off-white flesh, and is slightly translucent and rubbery.It is often found hanging onto the trunks of trees.The surface of the pileus is full of needle-like thorns after maturity.It is shaped like a monkey's head, hence the Chinese name 'Hou tou jun' or 'Ci wei jun' (Wang et al. 2009).There is one H. erinaceus reference genome based on the strains CS-4 (Gong et al. 2020), and the mitochondrial sequence is still absent from the reference genome.Therefore, in this study, the complete mitochondrial sequence of H. erinaceus HE0021 was assembled and compared to other Agaricomycetes species.This result could be helpful for species identification and the genetics and evolutionary processes of Hericium and other Agaricomycetes species.

DNA sequencing and cleaning of raw reads
The mycelium of HE0021 was isolated from the fruiting body, which is collected from dead wood, grown in a potato dextrose agar (w/v: 2% potato boiled for potato extract broth, 2% glucose, and 2% agar) (PDA) medium.It was identified as H. erinaceus based on its morphological characteristics (Wang et al. 2009) and ITS gene sequence blast result in NCBI (100% similar to H. erinaceus MT448853, Figure S1) by the Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, People's Republic of China.The amplification of internal transcribed spacer (ITS) region of rDNA was carried out using universal primers ITS1 (5 0 -TCCGTAGGTGAACCT GCGG-3 0 ) and ITS4 (5 0 -TCCTCCGCTTA TTGATATC-3 0 ).Genomic DNA was extracted from the mycelium using a DNAsecure Plant Kit (Tiangen Biotech Co. Ltd., Beijing, China).An aliquot of purified DNA (0.2 lg) was then fragmented by sonication to a size of 350 bp.Subsequently, a short-insert (350 bp) library was constructed using the Nextera XT DNA library preparation kit (Illumina, San Diego, CA).The DNA libraries were sequenced on the Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads.The raw data were edited using next-generation sequencing (NGS) QC Tool Kit v2.3.3 (Patel and Jain 2012).Finally, a total of 16,868,580 clean reads were obtained from the library of H. erinaceus.

Assembly, annotation, and visualization
High-quality sequence data (5.1 G) were selected for the assembly of the complete mitochondrial genome using CLC Assembly Cell Packages v4.2.1 (Qiagen, Aarhus, Denmark) with default parameters.The online MITOS server was used to annotate other genomic elements (Bernt et al. 2013), and the assembly process utilized the H. coralloides mitochondrial genome sequence as a reference (GenBank accession  number: KY007042) after predicting the coding genes using fgenesB (Solovyev and Salamov 2011).All predicted genes were blasted against the NCBI nr nucleotide with 10 −5 as the cut-off e-value to check their validity.A circular map of its complete mitochondrial genome was visualized using SnapGene (GSL Biotech LLC, San Diego, CA).

Results
The average read mapping depth of the assembled mitochondrial genome was above �7000 (Figure S2).The complete mitochondrial genome of H. erinaceus HE0021 is 83,518 base pairs long, possessing a double-stranded molecular weight of 51.579 MDa.The mitochondrial genome contains 49 genes consisting of 15 PCGs, 27 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs) (Figure 2).The genome has an obviously biased A þ T content of 81.7%, and the slightly positive AT-skew (0.006) and GC-skew (0.024).There is one PCG (Cox1) uses TTA as the start codon, and the rest of the 15 PCGs start with the ATG initiation codon.The lengths of tRNAs range from 69 to 86 bp.The rrnS and rrnL lengths are 1874 bp and 3488 bp, respectively.
The GTR þ F þ I þ G4 model was used to reconstruct the ML tree.The phylogenetic analysis revealed that H. erinaceus and H. coralloides belong to the same clade, although discernible genetic diversity exists between the two species (Figure 3).

Discussion and conclusions
In this study, we reported the complete mitogenome sequence of H. erinaceus for the first time.The assembly circular mitochondrion was 83,518 bp in length.The phylogenetic analysis results indicate that H. erinaceus and H. coralloides are in one clade, but genetic diversity exists between the two species.The complete mitochondrial genome of H. erinaceus presented here provides valuable genomic information for further species identification and phylogenetic study of Hericiaceae.

Figure 1 .
Figure 1.The fruit body of 2017-HE0021 strains (the photograph is courtesy of Xiaoya Song).

Figure 2 .
Figure 2. Schematic circular map of the assembled mitochondrial genome of H. erinaceus HE0021.