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. 2019 Nov 25;9:17447. doi: 10.1038/s41598-019-53941-5

Characterization of the mitochondrial genome of the pathogenic fungus Scytalidium auriculariicola (Leotiomycetes) and insights into its phylogenetics

Cheng Chen 1,2,#, Qiang Li 3,#, Rongtao Fu 1, Jian Wang 1, Chuan Xiong 4, Zhonghan Fan 1, Rongping Hu 1, Hong Zhang 1, Daihua Lu 1,5,✉
PMCID: PMC6877775  PMID: 31768013

Abstract

Scytalidium auriculariicola is the causative pathogen of slippery scar disease in the cultivated cloud ear fungus, Auricularia polytricha. In the present study, the mitogenome of S. auriculariicola was sequenced and assembled by next-generation sequencing technology. The circular mitogenome is 96,857 bp long and contains 56 protein-coding genes, 2 ribosomal RNA genes, and 30 transfer RNA genes (tRNAs). The high frequency of A and T used in codons contributed to the high AT content (73.70%) of the S. auriculariicola mitogenome. Comparative analysis indicated that the base composition and the number of introns and protein-coding genes in the S. auriculariicola mitogenome varied from that of other Leotiomycetes mitogenomes, including a uniquely positive AT skew. Five distinct groups were found in the gene arrangements of Leotiomycetes. Phylogenetic analyses based on combined gene datasets (15 protein-coding genes) yielded well-supported (BPP = 1) topologies. A single-gene phylogenetic tree indicated that the nad4 gene may be useful as a molecular marker to analyze the phylogenetic relationships of Leotiomycetes species. This study is the first report on the mitochondrial genome of the genus Scytalidium, and it will contribute to our understanding of the population genetics and evolution of S. auriculariicola and related species.

Subject terms: Evolution, Microbiology

Introduction

Scytalidium auriculariicola is the causative pathogen of slippery scar on the cloud ear fungus Auricularia polytricha (Mont.) Sacc1. The pathogen only infects the mycelia of A. polytricha and not the fruiting body2. Slippery scar first appeared in cultivated A. polytricha in Sichuan Province in the 1990s, with the infection rate being over 40%2. The identity of the pathogen of slippery scar has been controversial and has undergone a process of re-identification and re-establishment. Sun et al.2 initially identified the pathogen as the Ascomycete S. lignicola according to Koch’s postulates, morphological observations, rDNA-internal transcribed spacer (ITS), and 18S sequence analysis. Peng et al.1 further investigated the causative pathogen of this disease by morphological observations, in vivo pathogenicity tests, and molecular evidence from rRNA ITS and RNA polymerase II subunit (RPB2) sequences. Their results showed that the pathogen is a new species in the Scytalidium genus differing from S. lignicola, which they named S. auriculariicola1. Peng et al.1 also pointed out that S. auriculariicola strains from diseased A. polytricha mycelium in China consist of two clonal groups. Previously, ITS rDNA sequences, 18S rDNA sequences, RPB2 genes, and ribosomal large subunit (LSU) genes have been used as molecular markers to determine species relationships between Scytalidium and other species within the Leotiomycetes1,3–5. However, limited genetic information has prevented a comprehensive understanding of phylogenetic relationships between Scytalidium and its related species6. Thus, more available molecular markers are needed to assess the relationships between Scytalidium and other taxa within the Leotiomycetes, especially between the important S. auriculariicola and its related species.

Mitochondria are organelles necessary for the life of eukaryotic cells, and their dysfunction is associated with disease, the aging process, development, and various biological traits7,8. Mitochondria are thought to originate from symbiotic bacteria and supply most of the energy for eukaryotes9. Mitochondrial genomes are independent from nuclear genomes and have maternal inheritance, a high copy number, larger sequence length than the rRNA gene, which has made them widely used as a tool for studying evolution, phylogenetics, population genetics, and comparative or evolutionary genomics10,11. Mitochondrial gene rearrangements and the secondary structure of tRNAs are also widely used for deep-level phylogenetic studies in eukaryotes12–14. However, the mitogenomes of fungi are not as well studied as those of animals and plants15. The limited available studies have shown that most fungal mitochondrial genomes are circular, with the exception of very few species with linear mitogenomes16,17. The size of fungal mitogenomes varies greatly, ranging from 18.84 kb (Hanseniaspora uvarum) to 235.85 kb18. Fungal mitochondrial DNA usually contains 14 conserved protein-coding genes (atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), 1 ribosomal protein S3 gene (rps3), 2 ribosomal RNA genes (rnl and rns), and a relatively constant set of tRNA genes19. Fungal mitogenomes sometimes include homing endonuclease genes, plasmid-derived genes, genes transferred from the nuclear genome, and genes of unknown function. The number and variation of mitochondrial genes, genome rearrangement, and the presence or absence of large intronic and intergenic sequences all contribute to the considerable variation in gene content, structure, and size of fungal mitogenomes. To date, no mitochondrial genomes are available in the Scytalidium, and only 16 species from the Leotiomycetes class, including Cairneyella variabilis, Marssonina brunnea, Phialocephala subalpina, 2 Glarea lozoyensis subspecies, 4 Pseudogymnoascus species, 4 Rhynchosporium species, 2 Sclerotinia species, and Botrytis cinera (teleomorph Botryotinia fuckeliana), have been sequenced20 (https://www.ncbi.nlm.nih.gov/genome/browse#!/organelles/Leotiomycetes). More mitogenomes are needed, especially from the Scytalidium genus, which contains multiple pathogens, to reveal species and genus-level phylogenetic relationships in Leotiomycetes.

In the present study, the pathogen S. auriculariicola was isolated, identified, and sequenced. We assembled and annotated the complete mitochondrial genome of S. auriculariicola and assessed its gene content, tRNA structure, and genome organization. The mitochondrial genome size, base composition, number of protein-coding genes, tRNA genes, and gene arrangement of S. auriculariicola and previously sequenced species within Leotiomycetes were compared. We then analyzed the phylogenetic relationships among various Leotiomycetes species based on mitochondrial genes. The mitochondrial genome of S. auriculariicola will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.

Results

Protein coding genes, rRNA genes, tRNA genes, intergenic regions, and codon analyses

The mitogenome of S. auriculariicola is composed of a circular DNA molecule of 96,857 bp (Fig. 1). The GC content of the S. auriculariicola mitogenome is 26.30%. The AT skew and GC skew were both positive in the S. auriculariicola mitogenome (Table 1). A total of 56 protein-coding genes were identified in the mitogenome of S. auriculariicola, including 15 core mitochondrial genes (atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, and rps3) and 41 ORFs (Table S1). Among these ORFs, we found 32 ORFs located in introns and the remaining 9 ORFs were regarded as free-standing. Twenty-one out of the 32 intronic ORFs were predicted to encode proteins that exhibit similarities to the homing endonucleases from the LAGLIDADG family. Eight ORFs are similar to homing endonucleases in the family GIY-YIG, and 3 ORFs were predicted to encode hypothetical proteins. We also found seven free-standing ORFs that were predicted to encode proteins that exhibit similarities to homing endonucleases in the LAGLIDADG (four ORFs) and GIY-YIG (three ORFs) families. In addition, two free-standing ORFs were predicted to encode hypothetical proteins (Table S1). All of the 56 detected mitochondrial genes were located on the sense strand.

Figure 1.

Figure 1

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Circular map of the Scytalidium auriculariicola mitochondrial genome. Various genes are represented with different color blocks. The mitochondrial circular map was drawn using the OGDRAW software58.

Table 1.

Comparison of Leotiomycetes mitogenomes.

Item Accession number Genome size (bp) GC content (%) AT skew GC skew conserved PCGs free-standing ORFs No. of introns Intronic ORFs No. of tRNAs
Scytalidium auriculariicola MK111108 96,857 26.30 0.030 0.127 14 9 27 32 30
Cairneyella variabilis NC_029759 27,186 26.27 −0.043 0.133 14 1 1 1 29
Glarea lozoyensis NC_031375 45,501 29.76 −0.041 0.081 14 4 5 2 30
Marssonina brunnea NC_015991 70,379 29.34 −0.009 0.068 14 8 18 13 28
Phialocephala subalpina NC_015789 43,742 27.95 −0.029 0.091 14 9 0 0 27
Pseudogymnoascus destructans NC_033907 32,181 28.53 −0.048 0.116 13 3 2 2 28
Pseudogymnoascus pannorum NC_027422 26,918 28.10 −0.063 0.113 13 1 1 1 27
Pseudogymnoascus_sp._04NY16 CM004376 32,146 28.66 −0.050 0.118 13 4 2 2 28
Pseudogymnoascus_sp._BL308 CM004375 32148 28.55 −0.045 0.112 13 4 2 2 29
Rhynchosporium agropyri NC_023125 68,904 29.36 −0.006 0.066 14 9 19 25 29
Rhynchosporium commune NC_023126 69,581 29.40 −0.006 0.068 14 9 18 25 29
Rhynchosporium orthosporum NC_023127 49,539 28.80 −0.028 0.086 14 9 3 2 32
Rhynchosporium secalis NC_023128 68,729 29.33 −0.007 0.069 14 8 18 25 29
Sclerotinia borealis NC_025200 203,051 32.01 −0.001 0.084 15 18 61 62 31
Sclerotinia sclerotiorum NC_035155 128,852 30.90 −0.007 0.103 14 21 36 32 35
Botrytis cinerea Broad Institute 82,212 29.90 −0.008 0.100 14 7 22 20 33
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The mitogenome of S. auriculariicola contains two rRNA genes, a large subunit ribosomal RNA gene (rnl), and a small subunit ribosomal RNA gene (rns). A total of 30 tRNA genes were detected. The length of individual tRNAs ranges from 71 to 86 bp, mainly due to the different sizes of the extra arms (Fig. 2). The main cluster of tRNA genes (16 tRNAs) is located around the rnl gene. The other two clusters, including ten and two tRNA genes, are located around the nad6 and atp9 genes, respectively. In addition, there are two other tRNA genes located between the nad4L and cox2 genes (Fig. 1). There are mispairings of bases in 27 out of the 30 tRNAs, with a total of 45 base mispairings, all of which are G-U mispairings (Table S2). The S. auriculariicola mitogenome contains two tRNAs that code for asparagine with the same anticodons, three tRNAs coding for methionine with the same anticodons, and three tRNAs that code for histidine with the same anticodons. In addition, there are four amino acids that have more than one anticodon coding for them (Table S3).

Figure 2.

Figure 2

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Codon usage in the Scytalidium auriculariicola mitochondrial genome. Codon families are plotted on the X axis and represented by different color patches. Frequency of codon usage is plotted on the Y axis.

The mitogenome of S. auriculariicola contains three pairs of overlapping genes: orf196/orf118 overlap by 23 nucleotides, nad4L/nad5 and nad2/orf447 overlap by 1 bp. In addition, the S. auriculariicola mitogenome contains 55 intergenic regions with lengths ranging from 5 to 1986 bp, with a total length of 20,534 bp (Table S1). Intergenic nucleotides account for 21.20% of the mitogenome.

All of the 15 conserved protein-coding genes start with the canonical translation initiation codon ATG except for cox1 and nad4, which start with TTG (Table S4). Five genes (atp9, cox3, nad3, cox2, and rps3) use TAG as the stop codon while the others use TAA. Codon usage analysis indicated that the most frequently used codons in the S. auriculariicola mitogenome are AAA (6.53%, for lysine; Lys), TTA (6.23%, leucine; Leu), ATA (5.68%, for isoleucine; Ile), AAT (5.34%, for asparagine; Asn), TTT (5.31%, for phenylalanine; Phe), and TAT (5.02%, for tyrosine; Tyr) (Fig. 3; Table S5). The high frequency of A and T use in codons contributes to the high AT content (73.70%) of the S. auriculariicola mitochondrial genome.

Figure 3.

Figure 3

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Putative secondary structures of the 30 tRNA genes from Scytalidium auriculariicola mitochondrial genome. The tRNAs are labeled with the abbreviations of their corresponding amino acids. The tRNA arms are illustrated as for trnM3. The map of tRNA structures was drawn using the mitos software69.

Repetitive elements analysis

There are 33 repeat regions that were identified by a BLASTn search of the S. auriculariicola mitogenome against itself. The size of the repeats ranges from 39 to 610 bp; 19 repeat regions are over 100 bp, and 10 are over 200 bp. The similarities of these repeated sequences are between 74.81% and 100%. The longest repeat regions are located in the intergenic region between nad2 and orf173. The repeat sequences account for 5.65% of the entire S. auriculariicola mitogenome (Table S6).

We detected 26 tandem repeats in the mitogenome of S. auriculariicola. The length of the tandem repeats ranges from 6 to 77 bp. Copy numbers of each tandem repeat were between 2.0 and 16.5. The longest tandem sequence occurs with two copies. The tandem sequences account for 1.58% of the entire mitogenome (Table S7). We identified 47 forward, 1 palindromic, and 2 reverse repeats in the mitogenome of S. auriculariicola, accounting for 3.70% of the entire mitogenome (Table S8).

Comparative genome analysis

The size of S. auriculariicola mitogenome is the third largest genome among the 16 mitogenomes in the Leotiomycetes (Table 1), being only smaller than those of Sclerotinia borealis and Sclerotinia sclerotiorum, which belong to the family Sclerotiniaceae, order Helotiales. The GC content of the S. auriculariicola mitogenome is very low (26.30%) and is only higher than that of C. variabilis (26.27%). Both the AT skew and GC skew of the S. auriculariicola mitogenome are positive, while the AT skew is negative and GC skew positive in the other mitogenomes from the Leotiomycetes. The number of protein-coding genes and introns is closely related to the size of mitogenomes. The S. borealis with the largest mitogenome has 95 protein-coding genes and 61 introns, while the P. pannorum with the smallest mitogenome has only 15 protein-coding genes and one intron. The number of tRNA genes in the mitogenomes of Leotiomycetes varies from 27 to 35 (Table 1).

The composition of Leotiomycetes mitogenomes is shown in Table 2. The size of RNA genes and conserved protein-coding genes is relatively conservative between different species. The size of introns and intergenic regions is found closely related to the size variations of mitogenomes. Free-standing ORFs also contribute to the size variation of Leotiomycetes mitogenomes, which varies greatly between different species. The mitogenome of S. sclerotiorum contained the largest size of free-standing ORFs, followed by S. borealis, R. orthosporum and P. subalpina. The mitogenome of S. borealis contains the largest repeated sequences (exceeding 20 kb), while C. variabilis mitogenome contains the smallest (only 30 bp).

Table 2.

The size of different mitochondrial regions and their proportion to the whole mitogenome.

ID Mitogenome RNA genes Introns Conserved PCGs Free-standing ORFs Intergenic regions Repeated sequences
size (bp) size (bp) Proportion size (bp) proportion size (bp) proportion size (bp) proportion size (bp) proportion size (bp) proportion
Sbo 203051 7000 3.45 125696 61.90 13935 6.86 10461 5.15 45959 22.63 23122 11.39
Ssc 128852 7016 5.45 53723 41.69 12757 9.90 12690 9.85 42666 33.11 12321 9.56
Sau 96857 6865 7.09 48702 50.28 13668 14.11 7113 7.34 20509 21.17 5470 5.65
Bci 82212 7343 8.93 31793 38.67 13242 16.11 6351 7.73 23483 28.56 4723 5.74
Mbr 70379 6916 9.83 19289 27.41 15098 21.45 6246 8.87 22830 32.44 6402 9.10
Rco 69581 7073 10.17 27385 39.36 14118 20.29 6633 9.53 14372 20.66 3551 5.10
Rag 68904 7074 10.27 28435 41.27 13529 19.63 6024 8.74 13842 20.09 2694 3.91
Rse 68729 7073 10.29 27385 39.84 15099 21.97 6255 9.10 12917 18.79 3466 5.04
Ror 49539 7310 14.76 4016 8.11 13419 27.09 9177 18.52 15617 31.52 7363 14.86
Glo 45501 7432 16.33 5525 12.14 15456 33.97 2886 6.34 14202 31.21 5726 12.58
Psu 43742 7411 16.94 0 0.00 13938 31.86 8217 18.79 14176 32.41 2838 6.49
Pde 32181 6495 20.18 3334 10.36 12681 39.41 3429 10.66 6242 19.40 1144 3.55
Psp.1 32148 6564 20.42 3332 10.36 12488 38.85 2967 9.23 6797 21.14 1112 3.46
Psp.2 32146 6493 20.20 3332 10.37 12359 38.45 2925 9.10 7037 21.89 1218 3.79
Cva 27186 7147 26.29 1905 7.01 13176 48.47 753 2.77 4205 15.47 30 0.11
Ppa 26918 6407 23.80 1999 7.43 12621 46.89 363 1.35 5528 20.54 742 2.76
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Species information in this table can be found in Supplementary Table S9.

Gene rearrangements

Five different groups of gene arrangement were detected in the 16 Leotiomycetes mitogenomes (Fig. 4). The results indicated that Leotiomycetes have undergone large-scale gene rearrangements in their mitogenomes over the course of evolution. The gene order of the S. auriculariicola mitogenome is identical to that of C. variabilis, which belongs to the Helotiaceae, order Helotiales. However, large-scale gene rearrangements were observed in the G. lozoyensis mitogenome, another species of the Helotiaceae. The mitochondrial gene order of four Rhynchosporium species, R. agropyri, R. commune, R. orthosporum, and R. secalis, is the same as that of S. auriculariicola. However, the atp9 genes of Rhynchosporium sp. are likely dysfunctional due to a premature stop codon in a conserved domain21. The mitochondrial gene order of S. auriculariicola is also similar to those of M. brunnea and P. subalpine, with the position of the rps3 gene in their mitogenomes differing. In the Pseudogymnoascus genus, we observed an identical mitochondrial gene order between the four Pseudogymnoascus species, P. destructans, P. pannorum, P. sp.04NY16, and P. sp.BL308. In the Sclerotiniaceae family, the order of mitochondrial genes of three Sclerotiniaceae species, S. sclerotiorum, S. borealia, and B. cinerea, is identical, except for minor differences (the location of atp9) in the S. borealia mitogenome due to replication events of atp9 genes. In addition, large-scale gene rearrangements were observed between the mitogenomes of S. auriculariicola, the Sclerotiniaceae, and Pseudogymnoascus.

Figure 4.

Figure 4

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Comparison of gene order across 16 Leotiomycetes mitogenomes. Cva, Cairneyella variabilis (NC_029759); Glo, Glarea lozoyensis (NC_031375); Mbr, Marssonina brunnea f. sp. Multigermtubi (NC_015991); Psu, Phialocephala subalpine (NC_015789); Pde, Pseudogymnoascus destructans (NC_033907); Ppa, Pseudogymnoascus pannorum (NC_027422); Psp1, Pseudogymnoascus_sp._04NY16 (CM004376); Psp2, Pseudogymnoascus_sp._BL308 (CM004375); Rag, Rhynchosporium agropyri (NC_023125); Rco, Rhynchosporium commune (NC_023126); Ror, Rhynchosporium orthosporum (NC_023127); Rse, Rhynchosporium secalis (NC_023128); Sbo, Sclerotinia borealis (NC_025200); Ssc, Sclerotinia sclerotiorum 1980 UF-70 (NC_035155); Bci, Botrytis cinerea (Broad Institute); Sau, Scytalidium auriculariicola (MK111108). The # symbol indicates the rps3 gene is located in the intron of the rnl gene.

Compared with the arrangement of rps3 genes in type 1, the rps3 genes in the gene arrangement type 2 become free-standing ORFs, and are transferred to the downstream of the cox2 gene. The gene arrangement type 3 is characterized by the loss of atp9 gene, and the relocation of nad4, cox2, atp8, nad4L, nad5, cob, and nad1 genes. For the gene arrangement type 4, the rns, nad6, cox3, rnl and rps3 genes are transferred to the downstream of nad5 gene; nad4 and cob genes are transferred to the upstream of the atp9 gene. The type5 involves multiple gene repositions, including atp9, cox2, cox3, nad1, nad2, nad3, and nad4 genes.

Synteny analysis indicated that the six Leotiomycetes mitogenomes can be divided into fifteen homologous regions, where the sizes and relative positions of these regions are highly variable (Fig. 5). Nine of the fifteen homologous regions were detected in all six mitogenomes. The R. orthosporum mitogenome has all 15 homologous regions while the other mitogenomes lack one to three homologous regions. M. brunnea lacks the homologous region ‘A’, S. borealia lacks the homologous regions ‘N’ and ‘O’, and S. auriculariicola lacks the homologous regions ‘D’, ‘E’, and ‘O’.

Figure 5.

Figure 5

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Mitogenome synteny among six Leotiomycetes species. Synteny analyses were generated in Mauve 2.4.0. Fifteen homologous regions were identified among the six mitogenomes. The sizes and relative positions of the homologous fragments varied across the mitogenomes.

Phylogenetic analysis

We used the Bayesian inference method to establish the phylogenetic relationships of 16 species within Leotiomycetes, 8 species from Dothideomycetes, and 11 species from Eurotiomycetes based on the combined mitochondrial gene set (15 typical protein-coding genes) using three Acremonium species, A. chrysogenum, A. fuci, and A. implicatum, as outgroups. The best-fit evolutionary model for the phylogenetic analysis is “GTR + I + G”. We obtained a stable evolutionary tree topology (Fig. 6) with all of the recovered clades well supported (Bayesian posterior probability (BPP) = 1). Based on the phylogenetic analysis, the 38 Pezizomycotina species could be divided into four major clades corresponding to the classes Sordariomycetes, Eurotiomycetes, Dothideomycetes, and Leotiomycetes20. The 16 Leotiomycetes species were divided into three clades in the phylogenetic tree. The genus Pseudogymnoascus containing four species, P. pannorum, P. destructans, P. sp.04NY16, and P. sp.BL308, is the first clade. S. auriculariicola is the second single clade. The third clade contains 11 fungal species within the order Helotiales. In the order Helotiales, the relationships of the three families were consistently recovered as (Sclerotiniaceae + (Helotiaceae + (Dermateaceae)).

Figure 6.

Figure 6

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The phylogenetic tree was calculated from the multiple sequence alignment of the combined mitochondrial gene set (15 PCGs) of 38 fungal species. Topology was inferred using Bayesian method. Species analysed are shown in Table S9. The phylogenetic tree was drawn using the Figtree v1.4.3 software (https://mac.softpedia.com/get/Graphics/FigTree.shtml).

Single-gene tree topologies varied (Fig. S1), which indicates incongruent phylogenetic signals among different genes. However, the BI phylogenies based on the nad4 gene were consistent with the all-protein-coding genes phylogeny. Therefore, the nad4 gene may be a useful barcode sequence for species identification and phylogenetic analysis within the Leotiomycetes.

The phylogenetic analysis of nuclear multi-locus polygenes yielded evolutionary trees different from that of mitochondrial genes (Fig. S2). The BPP value of the nuclear multi-locus phylogenetic tree is between 0.43 and 1. Pseudocercospora mori, belonging to the Dothideomycetes class, is incorrectly clustered into the Eurotiomycetes class in the nuclear multi-locus phylogenetic tree. Exophiala dermatitidis and Cladophialophora bantiana,both belonging to the Eurotiomycetes class, are also incorrectly clustered into the Dothideomycetes class. In addition, M. brunnea, belonging to the order of Helotiales, forms an independent clade separated from other Helotiales species. The results further prove that mitochondrial genes are suitable as reliable tools for analyzing phylogenetic relationships of Leotiomycetes species.

Discussion

Mitochondrial markers have been successfully applied in phylogenetic taxonomy and evolutionary biology due to the advantage of their faster evolution22,23. The advent of next-generation sequencing technology has promoted the sequencing of fungal mitochondrial genomes. However, the mitogenomes of fungi are still less well-understood than those of animals and plants24. As of July 2019, only 612 mitogenomes of fungi have been reported in the NCBI database, 488 of which belong to the Ascomycetes. However, most species from the Ascomycetes belong to the Saccharomycetes and Sordariomycetes, which account for more than 78%, while the Leotiomycetes account for less than 4%. More mitogenomes belonging to Leotiomycetes are needed to facilitate our understanding of the mitochondrial characteristics and evolution of this group. In the present study, we first sequenced and analyzed the S. auriculariicola mitogenome, which is the first reported sequencing of a mitogenome of the Scytalidium genus. The mitogenome size of S. auriculariicola is larger than that of other Leotiomycetes, with the exception of S. borealis and S. sclerotiorum20. Variability in the length of mitogenomes has been frequently observed in the Leotiomycetes class, which is consistent with the variable mitogenomes in many eukaryotes25,26. The largest mitogenome in Leotiomycetes fungi is 203.05 kb20, while P. pannorum contains the smallest mitogenome at 26.92 kb (Table 1). The S. borealis mitogenome has the largest number of introns (61) in the Leotiomycetes, while only one intron was detected in the P. pannorum mitogenome. Another species, C. variabilis, which contained a mitogenome of less than 30 kb, also had only one intron. Therefore, the number of introns was considered one of the main factors contributing to the mitogenome size variation27,28. Interestingly, the intron-free species, P. subalpina, has a mitogenome size of 43.74 kb, higher than that of P. destructans, P. sp.04NY16, and P. sp.BL308, which have two introns each. Similarly, the number of introns in the R. orthosporum mitogenome is less than that of G. lozoyensis, which contains a much smaller mitogenome. Previous studies have shown that the size of fungal mitogenomes is related to the number of introns, intergenic regions, repetitive elements, plasmid-derived regions, and gene transfer events29,30. In the present study, we found that the number of free-standing ORFs of the P. subalpina mitogenome is higher than that of P. destructans, Pseudogymnoascus sp.04NY16, and Pseudogymnoascus sp.BL308. Furthermore, the number of free-standing ORFs of the R. orthosporum mitogenome is more than that of G. lozoyensis. The size of free-standing ORFs in P. subalpina and R. orthosporum mitogenomes accounts for 18.79% and 18.52% of their total mitogenomes, respectively (Table 2). The results reveal that free-standing ORFs are also an important factor affecting the mitogenome sizes of the Leotiomycetes.

Mitogenomes have an independent evolutionary origin relative to nuclear genomes31 and are widely believed to originate from endosymbiotic bacteria9. In the course of evolution, most mitochondrial genes of eukaryotes have been transferred to the nuclear genome32,33, a process that has been frequent, sporadic, and episodic32. The transfer of nucleic acids from the mitochondrion to the nucleus is an ongoing process in most eukaryotes, resulting in the transfer of functional genes32,34. The presence of genes in mitochondria has its advantages, such as the production of hydrophobic proteins in mitochondria to avoid long-distance transport from the nucleus, and the maintenance of mitochondrial structure35,36. The mitogenome of S. auriculariicola retains all 15 typical protein-coding genes (atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, and rps3) for energy metabolism and transcriptional regulation. However, four species of Pseudogymnoascus have lost the mitochondrial atp9 gene. In addition, the S. auriculariicola mitogenome has 31 intronic ORFs and 10 independent ORFs. Most of these ORFs are homing endonuclease genes (25 LAGLIDADG, 11 GIY-YIG), but there are five ORFs with unknown functions. ORFs have been widely found in fungal mitogenomes, though their origin and function have not been elucidated37. More studies on the mitogenomes of S. auriculariicola and related species are needed to recover the exact functions of these ORF genes.

tRNA genes are important nexus molecules between mRNAs and protein, and are essential for translation38. The S. auriculariicola mitogenome contains 30 tRNAs, most of which are clustered around rnl, nad6, and atp9. This is similar to S. borealis, P. subalpina, and G. lozoyensis, which also belong to the Leotiomycetes. The number of mitochondrial tRNAs of Leotiomycetes ranges from 27 to 35, which is higher than that of most fungi with 22–26 tRNAs19,39,40. These tRNA genes can adequately satisfy the need to decode and predict all of the codons in mitochondrial ORFs, thus reducing the need for tRNAs to enter mitochondria from the cytoplasm41. All of the tRNAs in the mitogenome of S. auriculariicola have distinctive primary and secondary structures, of which 27 have base mutations and mismatches, with all of them being G-U mismatches. In addition to G-U mismatches, C-U and A-C mismatches also exist in other eukaryotic mitogenomes42. Mitochondrial tRNA mutations have been demonstrated to be associated with metabolism and various diseases43,44. However, little research has been done on tRNA mutations in fungal mitogenomes. Further studies are needed to investigate the effects of mitochondrial tRNA mutations on the growth and pathogenicity of pathogenic fungi.

The GC content of mitogenomes varies among organisms and is thought to be influenced by mutation bias, selection, and reconstruction-related DNA repair bias45. The GC content of the S. auriculariicola mitogenome is lower than that of all of the Leotiomycetes except C. variabilis, suggesting that the S. auriculariicola mitogenome has undergone a large number of variations during its evolution. In addition, the S. auriculariicola mitogenome has a uniquely positive AT skew, while the AT skews are negative in the mitogenomes of other Leotiomycetes. According to the second parity rule, as long as there is no mutation or selection bias, each base in the complementary DNA strand exists at approximately equal frequencies46. The presence of AT or GC skews on the same DNA strand from different species indicated that mitogenomes of different species underwent different mutations or environmental selection. Compared with other Leotiomycetes, the S. auriculariicola mitogenome has a unique A-over-T situation, indicating that it had undergone a unique genetic mutations or evolutionary selection.

Because all of the mitochondria originate from common ancestors, mitochondrial gene rearrangements have been widely used to study the origin and evolution of eukaryotes. Plant and animal mitogenomes have been extensively studied with regard to gene rearrangement, and several models have been established to explain its causes47,48. In recent years, there have been many studies on mitochondrial gene rearrangement in fungi39,49, which exists even within the same genus6. Andrey et al.20 compared the mitochondrial gene recombination of seven fungi in the Helotiales order and found that the mitochondrial genes can be divided into two main groups. In the present study, we analyzed the mitochondrial gene rearrangement in 16 Leotiomycetes fungi, including S. auriculariicola, and divided them into 5 distinct groups. Further, large-scale rearrangements of mitochondrial genes in the Leotiomycetes were confirmed by synteny analysis, indicating that the mitochondrial genes of Leotiomycetes have undergone different evolutionary patterns.

Mitochondrial genomes are widely used in fungal phylogenetic analysis due to their useful and informative markers50. Because many fungi are very similar in morphology and difficult to distinguish, fungal classification is easily confused. Phylogenetic and taxonomic analyses of fungi therefore need to be combined with molecular markers, and those of the mitochondrial genome could to be a good complement. In the present study, we constructed phylogenetic trees with 15 protein-coding genes genes. The high support rate indicated that these mitochondrial gene data can be used as reliable molecular markers. However, most single-gene phylogenetic trees exhibited different branches of evolution, and some even failed to distinguish fungi of different classes. This is due to insufficient evolutionary signals provided by individual genes51. However, the single-gene evolutionary tree of the nad4 gene is consistent with that of combined mitochondrial gene set, suggesting that the nad4 gene can be used as a potential molecular marker for evaluating the taxonomy of Leotiomycetes fungi. The nad4 gene had relatively conserved gene length (ranging from 1464 bp to 1485 bp) and intron number (zero or one) between different Leotiomycete species. In addition, the nad4 gene may be subjected to low oxidative stress in mitochondria compared with other mitochondrial genes, which leads to different selective pressures on nad4 gene. All of these promote nad4 to become a potential molecular marker to analyze phylogenetic relationships of Leotiomycete species.

In conclusion, this study enriches the mitochondrial database of Leotiomycetes fungi and fills in a gap for the mitogenomes of the Scytalidium genus. The gene content, structure, gene rearrangement, and phylogenetic analysis of the S. auriculariicola mitogenome will provide a basis for population genetics, taxonomy, and evolutionary biology of the Leotiomycetes and related groups.

Materials and Methods

Sampling and DNA extraction

The symptomatic mycelium of the pathogen of slippery scar from A. polytricha was collected from Jintang, Sichuan Province, China. The isolation of the causative pathogen was conducted according to Peng et al.1. Suspected fungi were first cultured on PDA medium for 3 days, and then inoculated into cultivation bags with healthy A. polytricha mycelia. The inoculated cultivation bags were cultured at 25 °C for 20 days. Then the pathogenic fungi were re-isolated from the cultivation bags with infected A. polytricha, which showed the symptoms of slippery scar. The strain was identified as S. auriculariicola based on the Koch’s postulates, morphology, and ITS sequences. The mycelium of S. auriculariicola was cultured in liquid potato dextrose medium for 4 days and then collected for DNA extraction. Total DNA was extracted from the mycelia using the fungal DNA Kit D3390-00 (Omega Bio-Tek, Norcross, GA, USA) according to the manufacturer’s instructions. The quality of extracted DNA was checked by electrophoresis, and DNA was stored at −20 °C until sequencing. The S. auriculariicola strain was stored in Sichuan Academy of Agricultural Sciences (No. SAAS_Sau), and is available from Cheng Chen and Daihua Lu of the Sichuan Academy of Agricultural Sciences, China.

Sequencing, assembly, and annotation of the mitochondrial genome

Purified DNA was used to construct sequencing libraries following the instructions of the NEBNext Ultra II DNA Library Prep Kit (NEB, Beijing, China). Whole genome shotgun sequencing was performed using an Illumina HiSeq 2500 Platform (Illumina, San Diego, CA, USA). We performed quality control and de novo assembly of the mitogenome according to Bi52. SPAdes 3.9.0 software53 was used for de novo assembly of the mitogenome, and the MITObim V1.9 program54 was used to fill in the gaps between contigs.

MFannot (http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl) and MITOS55 tools were used for mitogenome annotation of S. auriculariicola, both of which are based on Genetic Code 4. Uncertain results were adjusted manually by sequence alignments with orthologous genes without intron from the closely related species. The initially annotated protein-coding genes, rRNA, or tRNA genes of S. auriculariicola were also modified by alignment with previously published Leotiomycetes mitogenomes. ORFs were functionally annotated by InterProScan software56. The tRNAscan-SE 2.0 program was used to predict tRNA genes57. Finally, we used the OrganellarGenomeDraw (OGDRAW) tool58 to draw a map of the S. auriculariicola complete mitogenome.

Analysis of the mitogenomic organization

We used the Lasergene v7.1 (DNASTAR; http://www.dnastar.com/) tool with default settings to analyze the base composition of the mitogenome of S. auriculariicola. Strand asymmetry of the mitogenome was assessed using the following formulas: AT skew = [A − T]/[A + T], and GC skew = [G − C]/[G + C]59. We calculated the codon usage using Sequence Manipulation Suite software60 based on genetic code 4. We compared the arrangement of genes in S. auriculariicola with those of other published Leotiomycetes species. Genomic synteny analysis of mitogenomes from six representative species within the Leotiomycetes was conducted with Mauve v2.4.061.

Repetitive elements analysis

We searched the entire mitogenome of S. auriculariicola by BLASTn searches against itself using Circoletto62 (http://tools.bat.infspire.org/circoletto/) with an E-value of <10−10, aiming to identify large intragenomic replications of sequences and interspersed repeats. The Tandem Repeats Finder63 (http://tandem.bu.edu/trf/trf.advanced.sub-mit.html) with default settings was used to analyze the tandem repeats. We searched for repeated sequences including forward, reverse, complementary, and reverse complementary sequences in S. auriculariicola using the REPuter64 tool with E-values <10−5.

Phylogenetic analysis

For the phylogenetic analysis, we constructed a phylogenetic tree based on 15 common mitochondrial genes from S. auriculariicola and other 15 species in Leotiomycetes, 8 species in Dothideomycetes, 11 species in Eurotiomycetes, and 3 species in Sordariomycetes (outgroup). The MAFFT algorithm within the TranslatorX online platform65 was used to align the 15 conserved protein-coding genes. The Sequence Matrix 1.7.8 program66 was used to combine the individual genes into a combined matrix. We used the Modelgenerator v85167 tool to determine the best-fit evolutionary model for the phylogenetic analysis.

The Bayesian inference (BI) method was used for phylogenetic analysis based on the combined gene dataset with the MrBayes 3.2.668 program. Two independent runs were performed for 2 × 106 generations sampling per 100 generations. Each run was sampled every 100 generations. Stationarity was assumed to have been reached when the estimated sample size (ESS) was >100, and the potential scale reduction factor (PSRF) approached 1.0. After the analysis was stable, the first 25% of the yielded trees were discarded as burn-in, and a 50% majority-rule consensus tree with posterior probability (PP) values was generated from the remaining trees. In order to compare mitochodrial phylogeny with nuclear multi-locus phylogeny, we downloaded internal transcribed spacer (ITS), RNA polymerase II second largest subunit (RPB2), translation elongation factor-1 alpha (EF1-α) and beta-tubulin (β-TUB) genes of 38 species from the NCBI database. Phylogenetic trees were constructed using the same method as mitochondrial genes. We also used the BI method to analyze the phylogenetic relationships of S. auriculariicola and related species using individual mitochondrial genes (15 core protein-coding genes); the purpose of which is to test whether these genes were useful as molecular markers for the phylogenetic analysis of Leotiomycetes species.

Supplementary information

Supplementary information (32.2MB, tif)
Supplementary information (23.2MB, tif)
Supplementary information (101.3KB, xlsx)

Acknowledgements

We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript. This research was funded by the Foundation Program of the Financial & Innovational Capacity Building Project of Sichuan (2019LWJJ-007& 2016GYSH-014) and Traction project of Chengdu industrial upgrading (2015-NY02-00063-NC).

Author contributions

Conceived and designed experiments: C.C., Q.L. and D.H.L. Performed the experiments: C.C., Q.L., J.W. and R.T.F. Analyzed the data: C.C., Q.L., C.X., and D.H.L. Contributed reagents/materials/analysis tools: C.C., Q.L., C.X., Z.H.F., H.Z., R.P.H. and D.H.L. Wrote the paper: C.C.

Data availability

The newly sequenced S. auriculariicola mitogenome was deposited to the GenBank database as accession number MK111108.

Competing interests

The authors declare no competing interests.

Footnotes

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

These authors contributed equally: Cheng Chen and Qiang Li.

Supplementary information

is available for this paper at 10.1038/s41598-019-53941-5.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplementary information (32.2MB, tif)
Supplementary information (23.2MB, tif)
Supplementary information (101.3KB, xlsx)

Data Availability Statement

The newly sequenced S. auriculariicola mitogenome was deposited to the GenBank database as accession number MK111108.

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