Characterization of the complete mitochondrial genome of Peniophora lycii (Russulales: Peniophoraceae) with its phylogenetic analysis

Abstract Peniophora lycii is a resupinate lichen-like species distributed all over the world. In the present study, we sequenced and assembled the complete mitochondrial genome of Peniophora lycii. The size of the mitochondrial genome of P. lycii was 38,296 bp, with a GC content of 25.89%. Twenty protein-coding genes, 2 ribosomal RNA genes, and 24 transfer RNA genes were identified in the mitochondrial genome of P. lycii. Phylogenetic analysis based on combined mitochondrial gene dataset indicated that the mitochondrial genome of P. lycii exhibited a close relationship with that of Heterobasidion irregulare.

The species Peniophora lycii (Pers.) Hohn. & Litsch. 1907 belongs to the Peniophoraceae family of the Russulales order. P. lycii is a resupinate lichen-like species that usually colonizes dead branches of deciduous and coniferous trees all over the world (Pontoppidan et al. 2007;Glazunova et al. 2020). The Russulales is a well-known order that contained morphologically diverse mushrooms (Miller et al. 2006). Species from this order have diverse lifestyles, including saprotrophic, ectomycorrhizal, root-parasitic, and insect-symbiotic (Geml et al. 2010;Zhou and Dai 2013). The family Peniophoraceae is primarily saprotrophic fungi. Mitochondrial genome has been widely used to understand the phylogeny, life pattern evolution and genetics of fungal species (Li et al. 2020a(Li et al. , 2020cWang et al. 2020a;Wu et al. 2021). However, up to now, no complete mitochondrial genome from the genus Peniophora has been reported. The mitochondrial genome of P. lycii will promote the understanding of the phylogeny, origin, and taxonomy of this important fungal genus.
The specimen (P. lycii) was collected from Sichuan, China (101.23 E;27.56 N). A specimen was deposited in Collection Center of Chengdu University under the voucher number Ply_s93. The complete mitochondrial genome of P. lycii was sequenced and de novo assembled according to previous described methods (Li et al. 2019b;Cheng et al. 2021). Briefly, the total genomic DNA of P. lycii was extracted using a Fungal DNA Kit (D3390-00, Omega Bio-Tek, Norcross, GA). The extracted genomic DNA was purified using a Gel Extraction Kit (Omega Bio-Tek, Norcross, GA). We stored the purified DNA in Leshan Vocational and Technical College (No. DNA_ Ply_s93). Sequencing libraries were constructed for sequencing using a NEBNextV R Ultra TM II DNA Library Prep Kit (NEB, Beijing, China). Whole genomic sequencing (WGS) of P. lycii was conducted using Illumina HiSeq 2500 Platform (Illumina, San Diego, CA). Illumina PCR adapter reads and low-quality reads from the paired-end were filtered using custom scripts. About 1.5% of low quality sequences were excluded from downstream analysis. The mitochondrial genome of P. lycii was assembled by NOVOPlasty v4.3.1 (Dierckxsens et al. 2017) using the rns gene of Lactarius hatsudake as the seed sequence (Li et al. 2019a). The average mitochondrial sequence coverage was 1357 Â. We annotated the complete mitochondrial genome of P. lycii according to previous described methods (Wang et al. 2020b;Ye et al. 2020). Briefly, the protein-coding genes, rRNA genes, tRNA genes, and introns of the P. lycii mitogenome were annotated using MITOS (Bernt et al. 2013) and MFannot (Valach et al. 2014), both based on the genetic code 4. The tRNA genes in the P. lycii mitochondrial genome were also predicted using tRNAscan-SE v1.3.1 (Lowe and Chan 2016). Different annotation results were verified and manual corrected according to the annotations of close related mitogenomes (Li et al. 2018).
The complete mitochondrial genome of P. lycii is 38,296 bp in length, which is the smallest mitochondrial genome in Russulales to date (Li et al. 2018(Li et al. , 2019a. The base composition of the P. lycii mitochondrial genome is as follows: A (36.80%), T (37.31%), G (12.87%) and C (13.01%). The complete mitochondrial genome of P. lycii contains 20 protein-coding genes, 2 ribosomal RNA genes (rns and rnl), and 24 transfer RNA genes. No intron was detected in the P. lycii mitochondrial genome (Zhang and Zhang 2019). We constructed a phylogenetic tree for 13 Russulales species to investigate the phylogenetic status of P. lycii. Bayesian analysis (BI) method was used to construct phylogenetic tree based on the combined 14 core protein-coding genes and 2 rRNA genes of mitochondrial genomes (atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, rns, and rnl) according to previous described methods (Li et al. 2019c;2020b;2021b). First, we aligned individual proteincoding genes of mitochondrial genomes using MAFFT v7.037 (Katoh et al. 2019), and then we concatenated these alignments into a combined gene dataset using SequenceMatrix v1.7.8 (Vaidya et al. 2011). Potential phylogenetic conflicts between different genes were detected by a partition homogeneity test (Li et al. 2021a); PartitionFinder 2.1.1 (Lanfear et al. 2017) was used to determine best-fit models of evolution and partitioning schemes. MrBayes v3.2.0 (Ronquist et al. 2012) was used to perform the BI analysis. Pleurotus cornucopiae from the order Agaricales was set as outgroup (Xu et al. 2018). As shown in the phylogenetic tree (Figure 1), the mitochondrial genome of P. lycii exhibited a close relationship with that of Heterobasidion irregular (Himmelstrand et al. 2014).

Disclosure statement
The authors have declared that no competing interests exist.

Funding
This study is supported by the Project of Leshan science and Technology Bureau (19NZD080).

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. MW752417. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA724896, SRR14320041, and SAMN18864199, respectively. The first eleven mitochondrial genomes from the ectomycorrhizal