The 203 kbp mitochondrial genome of the phytopathogenic fungus Sclerotinia borealis reveals multiple invasions of introns and genomic duplications

An Alternative Self-Splicing Intron Lifecycle Revealed by Dynamic Intron Turnover in Epichloë Endophyte Mitochondrial Genomes

Self-splicing group I and II introns are selfish genetic elements that are widely yet patchily distributed across the tree of life. Their selfish behavior comes from super-Mendelian inheritance behaviors, collectively called "homing", which allow them to rapidly spread within populations to the specific genomic sites they home into. Observations of self-splicing intron evolutionary dynamics have led to the formulation of an intron "lifecycle" model where, once fixed in a population, the introns lose selection for homing and undergo an extensive period of degradation until their eventual loss. Here, we find that self-splicing introns are common in the mitochondrial genomes of Epichloë species, endophytic fungi that live in symbioses with grasses. However, these introns show substantial intron presence-absence polymorphism, with our analyses suggesting that these result from a combination of vertical intron inheritance coupled with multiple invasion and loss events over the course of Epichloë evolution. Surprisingly, we find little evidence for the extensive intron degradation expected under the existing intron lifecycle model. Instead, these introns in Epichloë appear to be lost soon after fixation, suggesting that Epichloë self-splicing introns have a different lifecycle. However, rapid intron loss alone cannot explain our results, indicating that additional factors, such as the evolution of homing suppressors, also contribute to Epichloë self-splicing intron dynamics. This work shows that self-splicing introns have more diverse evolutionary dynamics than previously appreciated.

Assembly and comparative analysis of the complete mitochondrial genome of Daedaleopsissinensis (Polyporaceae, Basidiomycota), contributing to understanding fungal evolution and ecological functions

Daedaleopsissinensis is a crucial wood-decaying fungus with significant lignocellulose-degrading ability, which plays a vital role in the material cycle and energy flow of forest ecosystems. However, the mitochondrial genome of D.sinensis has not yet been revealed. In the present study, the complete mitochondrial genome of D.sinensis was assembled and compared with related species. The mitochondrial genome spans 69,155 bp and has a GC content of 25.0%. It comprises 15 protein-coding genes (PCGs), 26 transfer RNA genes, two ribosomal RNA genes and one DNA polymerase gene (dpo). Herein, we characterised and analysed the codon preferences, variation and evolution of PCGs, repeats, intron dynamics, as well as RNA editing events in the D.sinensis mitochondrial genome. Further, a phylogenetic analysis of D.sinensis and the other 86 Basidiomycota species was performed using mitochondrial genome data. The results revealed that four species, D.confragosa, D.sinensis, D.nitida and Fomesfomentarius, were grouped in a closely-related cluster with high support values, indicating that a close phylogenetic relationship existed between Daedaleopsis and Fomes. This study reported on the initial assembly and annotation of the mitochondrial genome of D.sinensis, which greatly improved the knowledge of the fungus. These results contribute to the limited understanding of the mitochondrial repository of wood-decaying fungi, thereby laying the foundation for subsequent research on fungal evolution and ecological functions.

Complete mitochondrial genome sequence of the white root rot pathogen Dematophora necatrix (Xylariaceae: Xylariales)

The mitochondrial genome of Dematophora necatrix is 121,350 base pairs in length with a G + C content of 30.19%. Phylogenetic analysis showed that D. necatrix grouped with other members of the Xylariaceae, with which its mitogenome also shares a broadly similar architecture and gene content. The D. necatrix mitogenome contains 14 protein-coding and 26 tRNA-encoding genes, as well as one copy each of the rnl, rns, rps3 and nat1 genes. However, as much as 80% of this genome is intronic or non-coding. This is likely due to expansions and rearrangements caused by the large number of group I introns and the homing endonucleases and reverse-transcriptases they encode. Our study thus provides a valuable foundation from which to explore the mitochondrion's role in the biology of D. necatrix, and also serves as a resource for investigating the pathogen's population biology and general ecology.

Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics

Limited exploration in fungal mitochondrial genetics has uncovered diverse inheritance modes. The mitochondrial genomes are inherited uniparentally in the majority of sexual eukaryotes, our discovery of persistent mitochondrial heterogeneity within the natural population of the basidiomycete fungus Thelephora ganbajun represents a significant advance in understanding mitochondrial inheritance and evolution in eukaryotes. Here, we present a comprehensive analysis by sequencing and assembling the complete mitogenomes of 40 samples exhibiting diverse cox1 heterogeneity patterns from various geographical origins. Additionally, we identified heterogeneous variants in the nad5 gene, which, similar to cox1, displayed variability across multiple copies. Notably, our study reveals a distinct prevalence of introns and homing endonucleases in these heterogeneous genes. Furthermore, we detected potential instances of horizontal gene transfer involving homing endonucleases. Population genomic analyses underscore regional variations in mitochondrial genome composition among natural samples exhibiting heterogeneity. Thus, polymorphisms in heterogeneous genes, introns, and homing endonucleases significantly influence mitochondrial structure, structural variation, and evolutionary dynamics in this species. This study contributes valuable insights into mitochondrial genome architecture, population dynamics, and the evolutionary implications of mitochondrial heterogeneity in sexual eukaryotes.

Comparative Analysis of the Mitochondrial Genome Sequences of Diaporthe longicolla (syn. Phomopsis longicolla) Isolates Causing Phomopsis Seed Decay in Soybean

Diaporthe longicolla (syn. Phomopsis longicolla) is an important seed-borne fungal pathogen and the primary cause of Phomopsis seed decay (PSD) in soybean. PSD is one of the most devastating seed diseases, reducing soybean seed quality and yield worldwide. As part of a genome sequencing project on the fungal Diaporthe-Phomopsis complex, draft genomes of eight D. longicolla isolates were sequenced and assembled. Sequences of mitochondrial genomes were extracted and analyzed. The circular mitochondrial genomes ranged from 52,534 bp to 58,280 bp long, with a mean GC content of 34%. A total of 14 core protein-coding genes, 23 tRNA, and 2 rRNA genes were identified. Introns were detected in the genes of atp6, cob, cox1, cox2, cox3, nad1, nad2, nad5, and rnl. Three isolates (PL7, PL10, and PL185E) had more introns than other isolates. Approximately 6.4% of the mitochondrial genomes consist of repetitive elements. Moreover, 48 single-nucleotide polymorphisms (SNPs) and were identified. The mitochondrial genome sequences of D. longicolla will be useful to further study the molecular basis of seed-borne pathogens causing seed diseases, investigate genetic variation among isolates, and develop improved control strategies for Phomopsis seed decay of soybean.

The complete mitochondrial genomes of five critical phytopathogenic Bipolaris species: features, evolution, and phylogeny

In the present study, three mitogenomes from the Bipolaris genus (Bipolaris maydis, B. zeicola, and B. oryzae) were assembled and compared with the other two reported Bipolaris mitogenomes (B. oryzae and B. sorokiniana). The five mitogenomes were all circular DNA molecules, with lengths ranging from 106,403 bp to 135,790 bp. The mitogenomes of the five Bipolaris species mainly comprised the same set of 13 core protein-coding genes (PCGs), two rRNAs, and a certain number of tRNAs and unidentified open reading frames (ORFs). The PCG length, AT skew and GC skew showed large variability among the 13 PCGs in the five mitogenomes. Across the 13 core PCGs tested, nad6 had the least genetic distance among the 16 Pleosporales species we investigated, indicating that this gene was highly conserved. In addition, the Ka/Ks values for all 12 core PCGs (excluding rps3) were < 1, suggesting that these genes were subject to purifying selection. Comparative mitogenomic analyses indicate that introns were the main factor contributing to the size variation of Bipolaris mitogenomes. The introns of the cox1 gene experienced frequent gain/loss events in Pleosporales species. The gene arrangement and collinearity in the mitogenomes of the five Bipolaris species were almost highly conserved within the genus. Phylogenetic analysis based on combined mitochondrial gene datasets showed that the five Bipolaris species formed well-supported topologies. This study is the first report on the mitogenomes of B. maydis and B. zeicola, as well as the first comparison of mitogenomes among Bipolaris species. The findings of this study will further advance investigations into the population genetics, evolution, and genomics of Bipolaris species.

The complete mitochondrial genome of Pseudofabraea citricarpa (Dermateaceae: Helotiales) causing Citrus target spot

Pseudofabraea citricarpa (Dermateaceae: Helotiales) is known as a significant pathogen causing Citrus target spot disease and results in profound yield loss. In the present study, the complete mitochondrial genome (mitogenome) determined based on next-generation sequencing technology. The circular mitogenome (56,935 bp) comprised 14 conserved protein-coding genes (PCGs), 16 ORFs, two ribosomal RNA genes (rns and rnl), one non-coding RNA gene (rnpB), one ribosomal protein S3 (rps3) and 28 transfer RNA (tRNA) genes. The overall base composition is as follows: 36.08% A, 35.25% T, 13.04% C, and 15.63% G, with a GC content of 28.70%. The phylogenetic analysis shows that P. citricarpa, belonging to Dermateaceae, forms a separate clade and is sister to Sclerotiniaceae. The mitogenome of P. citricarpa reported in this study provides more molecular data for further research on the evolutionary relationships of Helotiales.

Trichoderma koningiopsis (Hypocreaceae) has the smallest mitogenome of the genus Trichoderma

Introduction

Fungal mitogenomes exhibit remarkable variation in conformation, size, gene content, arrangement and expression, including their intergenic spacers and introns.

Methods

The complete mitochondrial genome sequence of the mycoparasitic fungus Trichoderma koningiopsis was determined using the Illumina next-generation sequencing technology. We used data from our recent Illumina NGS-based project of T. koningiopsis genome sequencing to study its mitochondrial genome. The mitogenome was assembled, annotated, and compared with other fungal mitogenomes.

Results

T. koningiopsis strain POS7 mitogenome is a circular molecule of 27,560 bp long with a GC content of 27.80%. It harbors the whole complement of the 14 conserved mitochondrial protein-coding genes (PCG) such as atp6, atp8, atp9, cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6, also found in the same gene order to other Hypocreales. The mitogenome also contains 26 transfer RNA genes (tRNAs), 5 of them with more than one copy. Other genes also present in the assembled mitochondrial genome are a small rRNA subunit and a large rRNA subunit containing ribosomal protein S3 gene. Despite the small genome size, two introns were detected in the T. koningiopsis POS7 mitogenome, one of them in cox3 gene and the other in rnl gene, accounting 7.34% of this mitogenome with a total size of 2,024 bp. A phylogenetic analysis was done using the 14 PCGs genes of T. koningiopsis strain POS7 mitogenome to compare them with those from other fungi of the Subphyla Pezizomycotina and Saccharomycotina. T. koningiopsis strain POS7 was clustered together with other representatives of Trichoderma lineage, within the Hypocreales group, which is also supported by previous phylogenetic studies based on nuclear markers.

Discussion

The mitochondrial genome of T. koningiopsis POS7 will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.

Functional annotation and comparative analysis of four Botrytis cinerea mitogenomes reported from Punjab, Pakistan

Botrytis cinerea is one of the top phytopathogenic fungus which ubiquitously cause grey mold on a variety of horticultural plants. The mechanism of respiration in the fungus occurs within the mitochondria. Mitogenomes serve as a key molecular marker for the investigation of fungal evolutionary patterns. This study aimed at the complete assembly, characterization, and comparative relationship of four mitogenomes of Botrytis cinerea strains including Kst5C, Kst14A, Kst32B, Kst33A, respectively. High throughput sequencing of four mitogenomes allowed the full assembly and annotation of these sequences. The total genome length of these 4 isolates Kst5C Kst14A, Kst32B, Kst33A was 69,986 bp, 77,303 bp, 76,204 bp and 55, 226 bp respectively. The distribution of features represented 2 ribosomal RNA genes,14 respiration encoding proteins, 1 mitochondrial ribosomal protein-encoding gene, along with varying numbers of transfer RNA genes, protein-coding genes, mobile intronic regions and homing endonuclease genes including LAGLIDADG and GIY-YIG domains were found in all four mitogenomes. The comparative analyses performed also decipher significant results for four mitogenomes among fungal isolates included in the study. This is the first report on the detailed annotation of mitogenomes as a proof for investigation of variation patterns present with in the B. cinerea causing grey mold on strawberries in Pakistan. This study will also contribute to the rapid evolutionary analysis and population patterns present among Botrytis cinerea.

Comparative structural analysis on the mitochondrial DNAs from various strains of Lentinula edodes

The evolution of mitochondria through variations in mitochondrial DNA (mtDNA) is one of the intriguing questions in eukaryotic cells. In order to assess the causes of the variations in mitochondria, the mtDNAs of the 21 strains of Lentinula edodes were assembled for this study, and analyzed together with four published mtDNA sequences. The mtDNAs were within the sizes of 117 kb ~ 122 kb. The gene number was observed consistent except for two mtDNAs, which carry a duplicated trnG1-trnG2 unit or a putative gene deletion. The size variation was largely attributed to the number of introns, repeated sequences, transposable elements (TEs), and plasmid-related sequences. Intron loss and gain were found from cox1, rnl, and rns of three mtDNAs. Loss of two introns in cox1 of KY217797.1 reduced its size by 2.7 kb, making it the smallest cox1 gene (8.4 kb) among the cox1s of the 25 mtDNAs, whereas gain of a Group II intron (2.65 kb) and loss of a Group I intron (1.7 kb) in cox1 of MF774813.1 resulted in the longest cox1 (12 kb). In rnl of L. edodes, we discovered four intron insertion consensus sequences which were unique to basidiomycetes but not ascomycetes. Differential incorporation of introns was the primary cause of the rnl size polymorphism. Homing endonucleases (HEGs) were suggestively involved in the mobilization of the introns because all of the introns have HEG genes of the LAGRIDADG or GIY-YIG families with the conserved HEG cleavage sites. TEs contributed to 11.04% of the mtDNA size in average, of which 7.08% was LTR-retrotransposon and 3.96% was DNA transposon, whereas the repeated sequences covered 4.6% of the mtDNA. The repeat numbers were variable in a strain-dependent manner. Both the TEs and repeated sequences were mostly found in the intronic and intergenic regions. Lastly, two major deletions were found in the plasmid-related sequence regions (pol2-pol3 and pol1-atp8) in the five mtDNAs. Particularly, the 6.8 kb-long deletion at pol2-pol3 region made MF774813.1 the shortest mtDNA of all. Our results demonstrate that mtDNA is a dynamic molecule that persistently evolves over a short period of time by insertion/deletion and repetition of DNA segments at the strain level.

Comparative analysis of the complete mitochondrial genomes of four cordyceps fungi

Cordyceps is a large group of entomogenous, medicinally important fungi. In this study, we sequenced, assembled, and annotated the entire mitochondrial genome of Ophiocordyceps xuefengensis, in addition to comparing it against other three complete cordyceps mitogenomes that were previously published. Comparative analysis indicated that the four complete mitogenomes are all composed of circular DNA molecules, although their sizes significantly differ due to high variability in intron and intergenic region sizes in the Ophiocordyceps sinensis and O. xuefengensis mitogenomes. All mitogenomes contain 14 conserved genes and two ribosomal RNA genes, but varying numbers of tRNA introns. The Ka/Ks ratios for all 14 PCGs and rps3 were all less than 1, indicating that these genes have been subject to purifying selection. Phylogenetic analysis was conducted using concatenated amino acid and nucleotide sequences of the 14 PCGs and rps3 using two different methods (Maximum Likelihood and Bayesian analysis), revealing highly supported relationships between O. xuefengensis and other Ophiocordyceps species, in addition to a close relationship with O. sinensis. Further, the analyses indicated that cox1 and rps3 play important roles in population differentiation. These mitogenomes will allow further study of the population genetics, taxonomy, and evolutionary biology of medicinally important cordyceps species.

The First Mitochondrial Genome of Ciborinia camelliae and Its Position in the Sclerotiniaceae Family

Ciborinia camelliae is the causal agent of camellia flower blight (CFB). It is a hemibiotrophic pathogen, inoperculate Discomycete of the family Sclerotiniaceae. It shows host and organ specificity infecting only flowers of species belonging to the genus Camellia, causing serious damage to the ornamental component of the plant. In this work, the first mitochondrial genome of Ciborinia camellia is reported. The mitogenome was obtained by combining Illumina short read and Nanopore long read technology. To resolve repetitive elements, specific primers were designed and used for Sanger sequencing. The manually curated mitochondrial DNA (mtDNA) of the Italian strain DSM 112729 is a circular sequence of 114,660 bp, with 29.6% of GC content. It contains two ribosomal RNA genes, 33 transfer RNAs, one RNase P gene, and 62 protein-coding genes. The latter include one gene coding for a ribosomal protein (rps3) and the 14 typical proteins involved in the oxidative metabolism. Moreover, a partial mtDNA assembled from a contig list was obtained from the deposited genome assembly of a New Zealand strain of C. camelliae. The present study contributes to understanding the mitogenome arrangement and the evolution of this phytopathogenic fungus in comparison to other Sclerotiniaceae species and confirms the usefulness of mitochondrial analysis to define phylogenetic positioning of this newly sequenced species.

Characterization of the mitochondrial genomes of three powdery mildew pathogens reveals remarkable variation in size and nucleotide composition

Powdery mildews comprise a large group of economically important phytopathogenic fungi. However, limited information exists on their mitochondrial genomes. Here, we assembled and compared the mitochondrial genomes of the powdery mildew pathogens Blumeria graminis f. sp. tritici, Erysiphe pisi, and Golovinomyces cichoracearum. Included in the comparative analysis was also the mitochondrial genome of Erysiphe necator that was previously analysed. The mitochondrial genomes of the four Erysiphales exhibit a similar gene content and organization but a large variation in size, with sizes ranging from 109800 bp in B. graminis f. sp. tritici to 332165 bp in G. cichoracearum, which is the largest mitochondrial genome of a fungal pathogen reported to date. Further comparative analysis revealed an unusual bimodal GC distribution in the mitochondrial genomes of B. graminis f. sp. tritici and G. cichoracearum that was not previously observed in fungi. The cytochrome b (cob) genes of E. necator, E. pisi, and G. cichoracearum were also exceptionally rich in introns, which in turn harboured rare open reading frames encoding reverse transcriptases that were likely acquired horizontally. Golovinomyces cichoracearum had also the longest cob gene (45 kb) among 703 fungal cob genes analysed. Collectively, these results provide novel insights into the organization of mitochondrial genomes of powdery mildew pathogens and represent valuable resources for population genetics and evolutionary studies.

Gcorn fungi: A Web Tool for Detecting Biases between Gene Evolution and Speciation in Fungi

(1) Background: Fungi contain several millions of species, and the diversification of fungal genes has been achieved by speciation, gene duplication, and horizontal gene transfer. Although several databases provide information on orthologous and paralogous events, these databases show no information on biases between gene mutation and speciation. Here, we designed the Gcorn fungi database to better understand such biases. (2) Methods: Amino acid sequences of fungal genes in 249 species, which contain 2,345,743 sequences, were used for this database. Homologous genes were grouped at various thresholds of the homology index, which was based on the percentages of gene mutations. By grouping genes that showed highly similar homology indices to each other, we showed functional and evolutionary traits in the phylogenetic tree depicted for the gene of interest. (3) Results: Gcorn fungi provides well-summarized information on the evolution of a gene lineage and on the biases between gene evolution and speciation, which are quantitatively identified by the Robinson–Foulds metric. The database helps users visualize these traits using various depictions. (4) Conclusions: Gcorn fungi is an open access database that provides a variety of information with which to understand gene function and evolution.

Revisiting the Neurospora crassa mitochondrial genome

The mitochondrial genome of Neurospora crassa has been less studied than its nuclear counterpart, yet it holds great potential for understanding the diversity and evolution of this important fungus. Here we describe a new mitochondrial DNA (mtDNA) complete sequence of a N. crassa wild type strain. The genome with 64 839 bp revealed 21 protein-coding genes and several hypothetical open reading frames with no significant homology to any described gene. Five large repetitive regions were identified across the genome, including partial or complete genes. The largest repeated region holds a partial nd2 section that was also detected in Neurospora intermedia, suggesting a rearrangement that occurred before the N. crassa speciation. Interestingly, N. crassa has a palindrome adjacent to the partial nd2 repeated region possibly related to the genomic rearrangement, which is absent in N. intermedia. Finally, we compared the sequences of the three available N. crassa complete mtDNAs and found low levels of intraspecific variability. Most differences among strains were due to small indels in noncoding regions. The revisiting of the N. crassa mtDNA forms the basis for future studies on mitochondrial genome organization and variability.

The Coevolution of Fungal Mitochondrial Introns and Their Homing Endonucleases (GIY-YIG and LAGLIDADG)

Fungal mitochondrial (mt) genomes exhibit great diversity in size which is partially attributed to their variable intergenic regions and most importantly to the inclusion of introns within their genes. These introns belong to group I or II, and both of them are self-splicing. The majority of them carry genes encoding homing endonucleases, either LAGLIDADG or GIY-YIG. In this study, it was found that these intronic homing endonucleases genes (HEGs) may originate from mt free-standing open reading frames which can be found nowadays in species belonging to Early Diverging Fungi as “living fossils.” A total of 487 introns carrying HEGs which were located in the publicly available mt genomes of representative species belonging to orders from all fungal phyla was analyzed. Their distribution in the mt genes, their insertion target sequence, and the phylogenetic analyses of the HEGs showed that these introns along with their HEGs form a composite structure in which both selfish elements coevolved. The invasion of the ancestral free-standing HEGs in the introns occurred through a perpetual mechanism, called in this study as “aenaon” hypothesis. It is based on recombination, transpositions, and horizontal gene transfer events throughout evolution. HEGs phylogenetically clustered primarily according to their intron hosts and secondarily to the mt genes carrying the introns and their HEGs. The evolutionary models created revealed an “intron-early” evolution which was enriched by “intron-late” events through many different independent recombinational events which resulted from both vertical and horizontal gene transfers.

The mitochondrial genome of the grape powdery mildew pathogen Erysiphe necator is intron rich and exhibits a distinct gene organization

Powdery mildews are notorious fungal plant pathogens but only limited information exists on their genomes. Here we present the mitochondrial genome of the grape powdery mildew fungus Erysiphe necator and a high-quality mitochondrial gene annotation generated through cloning and Sanger sequencing of full-length cDNA clones. The E. necator mitochondrial genome consists of a circular DNA sequence of 188,577 bp that harbors a core set of 14 protein-coding genes that are typically present in fungal mitochondrial genomes, along with genes encoding the small and large ribosomal subunits, a ribosomal protein S3, and 25 mitochondrial-encoded transfer RNAs (mt-tRNAs). Interestingly, it also exhibits a distinct gene organization with atypical bicistronic-like expression of the nad4L/nad5 and atp6/nad3 gene pairs, and contains a large number of 70 introns, making it one of the richest in introns mitochondrial genomes among fungi. Sixty-four intronic ORFs were also found, most of which encoded homing endonucleases of the LAGLIDADG or GIY-YIG families. Further comparative analysis of five E. necator isolates revealed 203 polymorphic sites, but only five were located within exons of the core mitochondrial genes. These results provide insights into the organization of mitochondrial genomes of powdery mildews and represent valuable resources for population genetic and evolutionary studies.

Recent and Ongoing Horizontal Transfer of Mitochondrial Introns Between Two Fungal Tree Pathogens

Two recently introduced fungal plant pathogens (Ceratocystis lukuohia and Ceratocystis huliohia) are responsible for Rapid ‘ōhi‘a Death (ROD) in Hawai‘i. Despite being sexually incompatible, the two pathogens often co-occur in diseased ‘ōhi‘a sapwood, where genetic interaction is possible. We sequenced and annotated 33 mitochondrial genomes of the two pathogens and related species, and investigated 35 total Ceratocystis mitogenomes. Ten mtDNA regions [one group I intron, seven group II introns, and two autonomous homing endonuclease (HE) genes] were heterogeneously present in C. lukuohia mitogenomes, which were otherwise identical. Molecular surveys with specific primers showed that the 10 regions had uneven geographic distribution amongst populations of C. lukuohia. Conversely, identical orthologs of each region were present in every studied isolate of C. huliohia regardless of geographical origin. Close relatives of C. lukuohia lacked or, rarely, had few and dissimilar orthologs of the 10 regions, whereas most relatives of C. huliohia had identical or nearly identical orthologs. Each region included or worked in tandem with HE genes or reverse transcriptase/maturases that could facilitate interspecific horizontal transfers from intron-minus to intron-plus alleles. These results suggest that the 10 regions originated in C. huliohia and are actively moving to populations of C. lukuohia, perhaps through transient cytoplasmic contact of hyphal tips (anastomosis) in the wound surface of ‘ōhi‘a trees. Such contact would allow for the transfer of mitochondria followed by mitochondrial fusion or cytoplasmic exchange of intron intermediaries, which suggests that further genomic interaction may also exist between the two pathogens.

Pan-Mitogenomics Approach Discovers Diversity and Dynamism in the Prominent Brown Rot Fungal Pathogens

Monilinia fructicola and Monilinia laxa species are the most destructive and economically devastating fungal plant pathogens causing brown rot disease on stone and pome fruits worldwide. Mitochondrial genomes (mitogenomes) play critical roles influencing the mechanisms and directions of the evolution of fungal pathogens. The pan-mitogenomics approach predicts core and accessory regions of the mitochondrial genomes and explains the gain or loss of variation within and between species. The present study is a fungal pan-mitogenome of M. fructicola (N = 8) and M. laxa (N = 8) species. The completely sequenced and annotated mitogenomes showed high variability in size within and between the species. The mitogenomes of M. laxa were larger, ranging from 178,351 to 179,780bp, than the mitogenomes of M. fructicola, ranging from 158,607 to 167,838bp. However, size variation within the species showed that M. fructicola isolates were more variable in the size range than M. laxa isolates. All the mitogenomes included conserved mitochondrial genes, as well as variable regions including different mobile introns encoding homing endonucleases or maturase, non-coding introns, and repetitive elements. The linear model analysis supported the hypothesis that the mitogenome size expansion is due to presence of variable (accessory) regions. Gene synteny was mostly conserved among all samples, with the exception for order of the rps3 in the mitogenome of one isolate. The mitogenomes presented AT richness; however, A/T and G/C skew varied among the mitochondrial genes. The purifying selection was detected in almost all the protein-coding genes (PCGs) between the species. However, cytochrome b was the only gene showing a positive selection signal among the total samples. Combined datasets of amino acid sequences of 14 core mitochondrial PCGs and rps3 obtained from this study together with published mitochondrial genome sequences from some other species from Heliotales were used to infer a maximum likelihood (ML) phylogenetic tree. ML tree indicated that both Monilinia species highly diverged from each other as well as some other fungal species from the same order. Mitogenomes harbor much information about the evolution of fungal plant pathogens, which could be useful to predict pathogenic life strategies.

The Mitochondrial Genome of a Plant Fungal Pathogen Pseudocercospora fijiensis (Mycosphaerellaceae), Comparative Analysis and Diversification Times of the Sigatoka Disease Complex Using Fossil Calibrated Phylogenies

Mycosphaerellaceae is a highly diverse fungal family containing a variety of pathogens affecting many economically important crops. Mitochondria play a crucial role in fungal metabolism and in the study of fungal evolution. This study aims to: (i) describe the mitochondrial genome of Pseudocercospora fijiensis, and (ii) compare it with closely related species (Sphaerulina musiva, S. populicola, P. musae and P. eumusae) available online, paying particular attention to the Sigatoka disease’s complex causal agents. The mitochondrial genome of P. fijiensis is a circular molecule of 74,089 bp containing typical genes coding for the 14 proteins related to oxidative phosphorylation, 2 rRNA genes and a set of 38 tRNAs. P. fijiensis mitogenome has two truncated cox1 copies, and bicistronic transcription of nad2-nad3 and atp6-atp8 confirmed experimentally. Comparative analysis revealed high variability in size and gene order among selected Mycosphaerellaceae mitogenomes likely to be due to rearrangements caused by mobile intron invasion. Using fossil calibrated Bayesian phylogenies, we found later diversification times for Mycosphaerellaceae (66.6 MYA) and the Sigatoka disease complex causal agents, compared to previous strict molecular clock studies. An early divergent Pseudocercospora fijiensis split from the sister species P. musae + P. eumusae 13.31 MYA while their sister group, the sister species P. eumusae and P. musae, split from their shared common ancestor in the late Miocene 8.22 MYA. This newly dated phylogeny suggests that species belonging to the Sigatoka disease complex originated after wild relatives of domesticated bananas (section Eumusae; 27.9 MYA). During this time frame, mitochondrial genomes expanded significantly, possibly due to invasions of introns into different electron transport chain genes.

Comparative mitogenomics of Agaricomycetes: Diversity, abundance, impact and coding potential of putative open-reading frames

The mitochondrion is an organelle found in eukaryote organisms, and it is vital for different cellular pathways. The mitochondrion has its own DNA molecule and, because its genetic content is relatively conserved, despite the variation of size and structure, mitogenome sequences have been widely used as a promising molecular biomarker for taxonomy and evolution in fungi. In this study, the mitogenomes of two fungal species of Agaricomycetes class, Phellinotus piptadeniae and Trametes villosa, were assembled and annotated for the first time. We used these newly sequenced mitogenomes for comparative analyses with other 55 mitogenomes of Agaricomycetes available in public databases. Mitochondrial DNA (mtDNA) size and content are highly variable and non-coding and intronic regions, homing endonucleases (HEGs), and unidentified ORFs (uORFs) significantly contribute to the total size of the mitogenome. Furthermore, accessory genes (most of them as HEGs) are shared between distantly related species, most likely as a consequence of horizontal gene transfer events. Conversely, uORFs are only shared between taxonomically related species, most probably as a result of vertical evolutionary inheritance. Additionally, codon usage varies among mitogenomes and the GC content of mitochondrial features may be used to distinguish coding from non-coding sequences. Our results also indicated that transposition events of mitochondrial genes to the nuclear genome are not common. Despite the variation of size and content of the mitogenomes, mitochondrial genes seemed to be reliable molecular markers in our time-divergence analysis, even though the nucleotide substitution rates of mitochondrial and nuclear genomes of fungi are quite different. We also showed that many events of mitochondrial gene shuffling probably happened amongst the Agaricomycetes during evolution, which created differences in the gene order among species, even those of the same genus. Altogether, our study revealed new information regarding evolutionary dynamics in Agaricomycetes.

The mitogenomes of two saprophytic Boletales species (Coniophora) reveals intron dynamics and accumulation of plasmid-derived and non-conserved genes

The order Boletales is a group of fungi with complex life styles, which include saprophytic and ectomycorrhizal mushroom-forming fungi. In the present study, the complete mitogenomes of two saprophytic Boletales species, Coniophora olivacea, and C. puteana, were assembled and compared with mitogenomes of ectomycorrhizal Boletales. Both mitogenomes comprised circular DNA molecules with sizes of 78,350 bp and 79,655 bp, respectively. Comparative mitogenomic analysis indicated that the two saprophytic Boletales species contained more plasmid-derived (7 on average) and unknown functional genes (12 on average) than the four ectomycorrhizal Boletales species previously reported. In addition, the core protein coding genes, nad2 and rps3, were found to be subjected to positive selection pressure between some Boletales species. Frequent intron gain/loss events were detected in Boletales and Basidiomycetes, and several novel intron classes were found in two Coniophora species. A total of 33 introns were detected in C. olivacea, and most were found to have undergone contraction in the C. olivacea mitogenome. Mitochondrial genes of Coniophora species were found to have undergone large-scale gene rearrangements, and the accumulation of intra-genomic repeats in the mitogenome was considered as one of the main contributing factors. Based on combined mitochondrial gene sets, we obtained a well-supported phylogenetic tree for 76 Basidiomycetes, demonstrating the utility of mitochondrial gene analysis for inferring Basidiomycetes phylogeny. The study served as the first report on the mitogenomes of the family Coniophorineae, which will help to understand the origin and evolution patterns of Boletales species with complex lifestyles.

The 287,403 bp Mitochondrial Genome of Ectomycorrhizal Fungus Tuber calosporum Reveals Intron Expansion, tRNA Loss, and Gene Rearrangement

In the present study, the mitogenome of Tuber calosporum was assembled and analyzed. The mitogenome of T. calosporum comprises 15 conserved protein-coding genes, two rRNA genes, and 14 tRNAs, with a total size of 287,403 bp. Fifty-eight introns with 170 intronic open reading frames were detected in the T. calosporum mitogenome. The intronic region occupied 69.41% of the T. calosporum mitogenome, which contributed to the T. calosporum mitogenome significantly expand relative to most fungal species. Comparative mitogenomic analysis revealed large-scale gene rearrangements occurred in the mitogenome of T. calosporum, involving gene relocations and position exchanges. The mitogenome of T. calosporum was found to have lost several tRNA genes encoding for cysteine, aspartate, histidine, etc. In addition, a pair of fragments with a total length of 32.91 kb in both the nuclear and mitochondrial genomes of T. calosporum was detected, indicating possible gene transfer events. A total of 12.83% intragenomic duplications were detected in the T. calosporum mitogenome. Phylogenetic analysis based on mitochondrial gene datasets obtained well-supported tree topologies, indicating that mitochondrial genes could be reliable molecular markers for phylogenetic analyses of Ascomycota. This study served as the first report on mitogenome in the family Tuberaceae, thereby laying the groundwork for our understanding of the evolution, phylogeny, and population genetics of these important ectomycorrhizal fungi.

First characterization of the complete mitochondrial genome of fungal plant-pathogen Monilinia laxa which represents the mobile intron rich structure

Monilinia laxa is an important fungal plant pathogen causing brown rot on many stone and pome fruits worldwide. Mitochondrial genome (mitogenome) plays a critical role in evolutionary biology of the organisms. This study aimed to characterize the complete mitogenome of M. laxa by using next-generation sequencing and approaches of de novo assembly and annotation. The total length of the mitogenome of M. laxa was 178,357 bp, and its structure was circular. GC content of the mitogenome was 30.1%. Annotation of the mitogenome presented 2 ribosomal RNA (rRNA) genes, 32 transfer RNA genes (tRNA), 1 gene encoding mitochondrial ribosomal protein S3, 14 protein-coding genes and 15 open reading frame encoding hypothetical proteins. Moreover, the group I mobile introns encoding homing endonucleases including LAGLIDADG and GIY-YIG families were found both within coding regions (genic) and intergenic regions of the mitogenome, indicating an enlarged size and a dynamic structure of the mitogenome. Furthermore, a comparative mitogenomic analysis was performed between M. laxa and the three closely related fungal phytopathogen species (Botryotinia fuckeliana, Sclerotinia sclerotiorum and, S. borealis). Due to the number and distribution of introns, the large extent of structural rearrangements and diverse mitogenome sizes were detected among the species investigated. Monilinia laxa presented the highest number of homing endonucleases among the fungal species considered in the analyses. This study is the first to report a detailed annotation of the mitogenome of an isolate of M. laxa, providing a solid basis for further investigations of mitogenome variations for the other Monilinia pathogens causing brown rot disease.

The First Mitochondrial Genome for Geastrales (Sphaerobolus stellatus) Reveals Intron Dynamics and Large-Scale Gene Rearrangements of Basidiomycota

In this study, the mitogenome of artillery fungus, Sphaerobolus stellatus, was assembled and compared with other Basidiomycota mitogenomes. The Sphaerobolus stellatus mitogenome was composed of circular DNA molecules, with a total size of 152,722 bp. Accumulation of intergenic and intronic sequences contributed to the Sphaerobolus stellatus mitogenome becoming the fourth largest mitogenome among Basidiomycota. We detected large-scale gene rearrangements in Basidiomycota mitogenomes, and the Sphaerobolus stellatus mitogenome contains a unique gene order. The quantity and position classes of intron varied between 75 Basidiomycota species we tested, indicating frequent intron loss/gain events occurred in the evolution of Basidiomycota. A novel intron position classes (P1281) was detected in the Sphaerobolus stellatus mitogenome, without any homologous introns from other Basidiomycota species. A pair of fragments with a total length of 9.12 kb in both the nuclear and mitochondrial genomes of Sphaerobolus stellatus was detected, indicating possible gene transferring events. Phylogenetic analysis based on the combined mitochondrial gene set obtained well-supported tree topologies (Bayesian posterior probabilities ≥ 0.99; bootstrap values ≥98). This study served as the first report on the mitogenome from the order Geastrales, which will promote the understanding of the phylogeny, population genetics, and evolution of the artillery fungus, Sphaerobolus stellatus.

Intra-specific comparison of mitochondrial genomes reveals host gene fragment exchange via intron mobility in Tremella fuciformis

Background

Mitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation.

Results

Draft mitochondrial genomes of 16 Tremella fuciformis isolates (TF01-TF16) were assembled from Illumina and PacBio sequencing data. Mitochondrial DNA contigs were extracted and assembled into complete circular molecules, ranging from 35,104 bp to 49,044 bp in size. All mtDNAs contained the same set of 41 conserved genes with identical gene order. Comparative analyses revealed that introns and intergenic regions were variable, whereas genic regions (including coding sequences, tRNA, and rRNA genes) were conserved. Among 24 introns detected, 11 were in protein-coding genes, 3 in tRNA genes, and the other 10 in rRNA genes. In addition, two mobile fragments were found in intergenic regions. Interestingly, six introns containing N-terminal duplication of the host genes were found in five conserved protein-coding gene sequences. Comparison of genes with and without these introns gave rise to the following proposed model: gene fragment exchange with other species can occur via gain or loss of introns with N-terminal duplication of the host genes.

Conclusions

Our findings suggest a novel mechanism of fungal mitochondrial gene evolution: partial foreign gene replacement though intron mobility.

Genome Sequence of the Chestnut Blight Fungus Cryphonectria parasitica EP155: A Fundamental Resource for an Archetypical Invasive Plant Pathogen

Cryphonectria parasitica is the causal agent of chestnut blight, a fungal disease that almost entirely eliminated mature American chestnut from North America over a 50-year period. Here, we formally report the genome of C. parasitica EP155 using a Sanger shotgun sequencing approach. After finishing and integration with simple-sequence repeat markers, the assembly was 43.8 Mb in 26 scaffolds (L₅₀ = 5; N₅₀ = 4.0Mb). Eight chromosomes are predicted: five scaffolds have two telomeres and six scaffolds have one telomere sequence. In total, 11,609 gene models were predicted, of which 85% show similarities to other proteins. This genome resource has already increased the utility of a fundamental plant pathogen experimental system through new understanding of the fungal vegetative incompatibility system, with significant implications for enhancing mycovirus-based biological control.

The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes

A number of species in Bipolaris are important plant pathogens. Due to a limited number of synapomorphic characters, it is difficult to perform species identification and to estimate phylogeny of Bipolaris based solely on morphology. In this study, we sequenced the complete mitochondrial genome of Bipolaris sorokiniana, and presented the detailed annotation of the genome. The B. sorokiniana mitochondrial genome is 137,775 bp long, and contains two ribosomal RNA genes, 12 core protein-coding genes, 38 tRNA genes. In addition, two ribosomal protein genes (rps3 gene and rps5 gene) and the fungal mitochondrial RNase P gene (rnpB) are identified. The large genome size is mostly determined by the presence of numerous intronic and intergenic regions. A total of 28 introns are inserted in eight core protein-coding genes. Together with the published mitochondrial genome sequences, we conducted a preliminary phylogenetic inference of Dothideomycetes under various datasets and substitution models. The monophyly of Capnodiales, Botryosphaeriales and Pleosporales are consistently supported in all analyses. The Venturiaceae forms an independent lineage, with a distant phylogenetic relationship to Pleosporales. At the family level, the Mycosphaerellaceae, Botryosphaeriaceae. Phaeosphaeriaceae, and Pleosporaceae are recognized in the majority of trees.

Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes

The order Hypocreales (Ascomycota) is composed of ubiquitous and ecologically diverse fungi such as saprobes, biotrophs, and pathogens. Despite their phylogenetic relationship, these species exhibit high variability in biomolecules production, lifestyle, and fitness. The mitochondria play an important role in the fungal biology, providing energy to the cells and regulating diverse processes, such as immune response. In spite of its importance, the mechanisms that shape fungal mitogenomes are still poorly understood. Herein, we investigated the variability and evolution of mitogenomes and its relationship with the divergence time using the order Hypocreales as a study model. We sequenced and annotated for the first time Trichoderma harzianum mitochondrial genome (mtDNA), which was compared to other 34 mtDNAs species that were publicly available. Comparative analysis revealed a substantial structural and size variation on non-coding mtDNA regions, despite the conservation of copy number, length, and structure of protein-coding elements. Interestingly, we observed a highly significant correlation between mitogenome length, and the number and size of non-coding sequences in mitochondrial genome. Among the non-coding elements, group I and II introns and homing endonucleases genes (HEGs) were the main contributors to discrepancies in mitogenomes structure and length. Several intronic sequences displayed sequence similarity among species, and some of them are conserved even at gene position, and were present in the majority of mitogenomes, indicating its origin in a common ancestor. On the other hand, we also identified species-specific introns that advocate for the origin by different mechanisms. Investigation of mitochondrial gene transfer to the nuclear genome revealed that nuclear copies of the nad5 are the most frequent while atp8, atp9, and cox3 could not be identified in any of the nuclear genomes analyzed. Moreover, we also estimated the divergence time of each species and investigated its relationship with coding and non-coding elements as well as with the length of mitogenomes. Altogether, our results demonstrated that introns and HEGs are key elements on mitogenome shaping and its presence on fast-evolving mtDNAs could be mostly explained by its divergence time, although the intron sharing profile suggests the involvement of other mechanisms on the mitochondrial genome evolution, such as horizontal transference.

Comparative Analyses of Mitochondrial Genomes Provide Evolutionary Insights Into Nematode-Trapping Fungi

Predatory fungi in Orbiliaceae (Ascomycota) have evolved a diversity of trapping devices that enable them to trap and kill nematodes, other small animals, and protozoans. These trapping devices include adhesive hyphae, adhesive knobs, adhesive networks, constricting rings, and non-constricting rings. Their diversity and practical importance have attracted significant attention from biologists, making them excellent model organisms for studying adaptative evolution and as biological control agents against parasitic nematodes. The putative origins and evolutionary relationships among these carnivorous fungi have been investigated using nuclear protein-encoding genes, but their patterns of mitogenome relationships and divergences remain unknown. Here we analyze and compare the mitogenomes of 12 fungal strains belonging to eight species, including six species representing all four types of nematode trapping devices and two from related but non-predatory fungi. All 12 analyzed mitogenomes were of circular DNA molecules, with lengths ranging from 146,101 bp to 280,699 bp. Gene synteny analysis revealed several gene rearrangements and intron transfers among the mitogenomes. In addition, the number of protein coding genes (PCGs), GC content, AT skew, and GC skew varied among these mitogenomes. The increased number and total size of introns were the main contributors to the length differences among the mitogenomes. Phylogenetic analyses of the protein-coding genes indicated that mitochondrial and nuclear genomes evolved at different rates, and signals of positive selection were found in several genes involved in energy metabolism. Our study provides novel insights into the evolution of nematode-trapping fungi and shall facilitate further investigations of this ecologically and agriculturally important group of fungi.

Promising Perspectives for Detection, Identification, and Quantification of Plant Pathogenic Fungi and Oomycetes through Targeting Mitochondrial DNA

Fungi and oomycetes encompass many pathogens affecting crops worldwide. Their effective control requires screening pathogens across the local and international trade networks along with the monitoring of pathogen inocula in the field. Fundamentals to all of these concerns are their efficient detection, identification, and quantification. The use of molecular markers showed the best promise in the field of plant pathogen diagnostics. However, despite the unquestionable benefits of DNA-based methods, two significant limitations are associated with their use. The first limitation concerns the insufficient level of sensitivity due to the very low and uneven distribution of pathogens in plant material. The second limitation pertains to the inability of widely used diagnostic assays to detect cryptic species. Targeting mtDNA appears to provide a solution to these challenges. Its high copy number in microbial cells makes mtDNA an attractive target for developing highly sensitive assays. In addition, previous studies on different pathogen taxa indicated that mitogenome sequence variation could improve cryptic species delimitation accuracy. This review sheds light on the potential application of mtDNA for pathogen diagnostics. This paper covers a brief description of qPCR and DNA barcoding as two major strategies enabling the diagnostics of plant pathogenic fungi and oomycetes. Both strategies are discussed along with the potential use of mtDNA, including their strengths and weaknesses.

Evidence of Extensive Intraspecific Noncoding Reshuffling in a 169-kb Mitochondrial Genome of a Basidiomycetous Fungus

Comparative genomics of fungal mitochondrial genomes (mitogenomes) have revealed a remarkable pattern of rearrangement between and within major phyla owing to horizontal gene transfer and recombination. The role of recombination was exemplified at a finer evolutionary time scale in basidiomycetes group of fungi as they display a diversity of mitochondrial DNA inheritance patterns. Here, we assembled mitogenomes of six species from the Hymenochaetales order of basidiomycetes and examined 59 mitogenomes from 2 genetic lineages of Phellinus noxius. Gene order is largely collinear, while intergene regions are major determinants of mitogenome size variation. Substantial sequence divergence was found in shared introns consistent with high horizontal gene transfer frequency observed in yeasts, but we also identified a rare case where an intron was retained in five species since speciation. In contrast to the hyperdiversity observed in nuclear genomes of Phellinus noxius, mitogenomes’ intraspecific polymorphisms at protein-coding sequences are extremely low. Phylogeny network based on introns revealed turnover as well as exchange of introns between two lineages. Strikingly, some strains harbor a mosaic origin of introns from both lineages. Analysis of intergenic sequence indicated substantial differences between and within lineages, and an expansion may be ongoing as a result of exchange between distal intergenes. These findings suggest that the evolution in mitochondrial DNAs is usually lineage specific but chimeric mitotypes are frequently observed, thus capturing the possible evolutionary processes shaping mitogenomes in a basidiomycete. The large mitogenome sizes reported in various basidiomycetes appear to be a result of interspecific reshuffling of intergenes.

Mitochondrial genome and diverse inheritance patterns in Pleurotus pulmonarius

Pleurotus pulmonarius, a member of the Pleurotaceae family in Basidiomycota, is an edible, economically important mushroom in most Asian countries. In this study, the complete mitochondrial genomes (mtDNA) of three P. pulmonarius strains - two monokaryotic commercial (J1-13 and ZA3) and one wild (X1-15) - were sequenced and analyzed. In ZA3 and X1-15, the mtDNA molecule was found to be a single circle of 68,305 bp and 73,435 bp, respectively. Both strains contain 14 core protein-coding genes and two ribosomal RNA (rRNA) subunit genes. The ZA3 strain has 22 transfer RNA (tRNA) genes and nine introns: eight in cytochrome c oxidase subunit 1 (coxl), and one in the rRNA large subunit (rnl). Monokaryotic J1-13 and ZA3 mtDNAs were found to be similar in their structure. However, the wild strain X1-15 contains 25 tRNA genes and only seven introns in coxl. Open reading frames (ORFs) of ZA3/J1-13 and X1-15 encode LAGLIDADG, ribosomal protein S3, and DNA polymerase II. In addition, mtDNA inheritance in J1-13, ZA3, and X1-15 was also studied. Results showed that the mtDNA inheritance pattern was uniparental and closely related to dikaryotic hyphal location with respect to the parent. Results also show that mtDNA inheritance is influenced by both the parental nuclear genome and mitogenome in the zone of contact between two compatible parents. In summary, this analysis provides valuable information and a basis for further studies to improve our understanding of the inheritance of fungal mtDNA.

Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes

Morchella crassipes (Vent.) Pers., a typical yellow morel species with high economic value, is mainly distributed in the low altitude plains of Eurasia. However, rare research has been performed on its genomics and polarity, thus limiting its research and development. Here, we reported a fine physical map of the nuclear genome at the subchromosomal-scale and the complete mitochondrial genome of M. crassipes. The complete size of the nuclear genome was 56.7 Mb, and 23 scaffolds were assembled, with eight of them being complete chromosomes. A total of 11,565 encoding proteins were predicted. The divergence time analysis showed that M. crassipes representing yellow morels differentiated with black morels at ~33.98 Mya (million years), with 150 gene families contracted and expanded in M. crassipes versus the two black morels (M. snyderi and M. importuna). Furthermore, 409 CAZYme genes were annotated in M. crassipes, containing almost all plant cell wall degrading enzymes compared with the mycorrhizal fungi (truffles). Genomic annotation of mating type loci and amplification of the mating genes in the monospore population was conducted, the results indicated that M. crassipes is a heterothallic fungus. Additionally, a complete circular mitochondrial genome of M. crassipes was assembled, the size reached as large as 531,195 bp. It can be observed that the strikingly large size was the biggest up till now, coupled with 14 core conserved mitochondrial protein-coding genes, two rRNAs, 31 tRNAs, 51 introns, and 412 ncORFs. The total length of intron sequences accounted for 53.67% of the mitochondrial genome, with 19 introns having a length over 5 kb. Particularly, 221 of 412 ncORFs were distributed within 51 introns, and the total length of the ncORFs sequence accounted for 40.83% of the mitochondrial genome, and 297 ncORFs had expression activity in the mycelium stage, suggesting their potential functions in M. crassipes. Meanwhile, there was a high degree of repetition (51.31%) in the mitochondria of M. crassipes. Thus, the large number of introns, ncORFs and internal repeat sequences may contribute jointly to the largest fungal mitochondrial genome to date. The fine physical maps of nuclear genome and mitochondrial genome obtained in this study will open a new door for better understanding of the mysterious species of M. crassipes.

The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences

The complete mitochondrial genome of Morchella importuna, the famous edible and medicinal mushroom, was assembled as a 272,238 bp single circular dsDNA. As the largest mitogenome among fungi, it exhibits several distinct characteristics. The mitogenome of M. importuna encoded 14 core conserved mitochondrial protein-coding genes and 151 mitochondrial non-conserved open reading frames (ncORFs) were predicted, of which 61 were annotated as homing endonuclease genes, and 108 were confirmed to be expressed during the vegetative growth stages of M. importuna. In addition, 34 introns were identified in seven core genes (cob, cox1, cox2, cox3, nad1, nad4 and nad5) and two rRNA genes (rrnS and rrnL) with a length from 383 bp to 7453 bp, and eight large introns with a length range of 2340 bp to 7453 bp contained multiple intronic mtORFs. Moreover, 34 group I (IA, IB, IC1, IC2, ID and derived group I introns) and four group II intron domains were identified for the 34 introns, including five hybrid ones. Furthermore, the M. importuna mitogenome showed the presence of about 18.7% mitogenomic interspersed repeats. These and the aforementioned ncORFs and introns, contributed to the enlarged size of the mitogenome.

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

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.

The complete mitochondrial genomes of two model ectomycorrhizal fungi (Laccaria): features, intron dynamics and phylogenetic implications

Laccaria amethystine and L. bicolor have served as model species for studying the life history and genetics of ectomycorrhizal fungi. However, the characterizations and variations of their mitogenomes are still unknown. In the present study, the mitogenomes of the two Laccaria species were assembled, annotated, and compared. The two mitogenomes of L. amethystine and L. bicolor comprised circular DNA molecules, with the sizes of 65,156 bp and 95,304 bp, respectively. Genome collinearity analysis revealed large-scale gene rearrangements between the two Laccaria species. Comparative mitogenome analysis indicated the introns of cox1 genes in Agaricales experienced frequent lost/gain eveants, which promoted the organization and size variations in Agaricales mitogenomes. Evolutionary analysis indicated the core protein-coding genes in the two mitogenomes were subject to strong pressure of purifying selection. Phylogenetic analysis using the Bayesian inference (BI) and Maximum likelihood (ML) methods based on a combined mitochondrial gene set resulted in identical and well-supported tree topologies, wherein the two Laccaria species were most closely related to Coprinopsis cinerea. This study severed as the first study on the mitogenomes of Laccaria species, which promoted a comprehensive understanding of the genetics and evolution of the model ectomycorrhizal fungi.

Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya

BACKGROUND

Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mitochondria are vital organelles, and play various essential roles in eukaryotic cells.

RESULTS

In this study, we provide the Hypsizygus marmoreus mitochondrial (mt) genome assembly: the circular sequence is 102,752 bp in size and contains 15 putative protein-coding genes, 2 ribosomal RNAs subunits and 28 tRNAs. We compared the mt genomes of the 27 fungal species in the Pezizomycotina and Basidiomycotina subphyla, with the results revealing that H. marmoreus is a sister to Tricholoma matsutake and the phylogenetic distribution of this fungus based on the mt genome. Phylogenetic analysis shows that Ascomycetes mitochondria started to diverge earlier than that of Basidiomycetes and supported the robustness of the hyper metric tree. The fungal sequences are highly polymorphic and gene order varies significantly in the dikarya data set, suggesting a correlation between the gene order and divergence time in the fungi mt genome. To detect the mt genome variations in H. marmoreus, we analyzed the mtDNA sequences of 48 strains. The phylogeny and variation sited type statistics of H. marmoreus provide clear-cut evidence for the existence of four well-defined cultivations isolated lineages, suggesting female ancestor origin of H. marmoreus. Furthermore, variations on two loci were further identified to be molecular markers for distinguishing the subgroup containing 32 strains of other strains. Fifteen conserved protein-coding genes of mtDNAs were analyzed, with fourteen revealed to be under purifying selection in the examined fungal species, suggesting the rapid evolution was caused by positive selection of this gene.

CONCLUSIONS

Our studies have provided new reference mt genomes and comparisons between species and intraspecies with other strains, and provided future perspectives for assessing diversity and origin of H. marmoreus.

Comparative Mitochondrial Genome Analysis of Two Ectomycorrhizal Fungi (Rhizopogon) Reveals Dynamic Changes of Intron and Phylogenetic Relationships of the Subphylum Agaricomycotina

In the present study, we assembled and compared two mitogenomes from the Rhizopogon genus. The two mitogenomes of R. salebrosus and R. vinicolor comprised circular DNA molecules, with the sizes of 66,704 bp and 77,109 bp, respectively. Comparative mitogenome analysis indicated that the length and base composition of protein coding genes (PCGs), rRNA genes and tRNA genes varied between the two species. Large fragments aligned between the mitochondrial and nuclear genomes of both R. salebrosus (43.41 kb) and R. vinicolor (12.83 kb) indicated that genetic transfer between mitochondrial and nuclear genomes has occurred over evolutionary time of Rhizopogon species. Intronic regions were found to be the main factors contributing to mitogenome expansion in R. vinicolor. Variations in the number and type of introns in the two mitogenomes indicated that frequent intron loss/gain events occurred during the evolution of Rhizopogon species. Phylogenetic analyses based on Bayesian inference (BI) and Maximum likelihood (ML) methods using a combined mitochondrial gene set yielded identical and well-supported tree topologies, wherein Rhizopogon species showed close relationships with Agaricales species. This is the first study of mitogenomes within the genus Rhizopogon, and it provides a basis for understanding the evolution and differentiation of mitogenomes from the ectomycorrhizal fungal genus.

Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species

Background

Species in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Many of them cause white-rot root disease in diverse woody plants worldwide. Mitochondrial genomes (mitogenomes) are widely used in evolutionary and population studies, but despite the importance and wide distribution of Armillaria, the complete mitogenomes have not previously been reported for this genus. Meanwhile, the well-supported phylogeny of Armillaria species provides an excellent framework in which to study variation in mitogenomes and how they have evolved over time.

Results

Here we completely sequenced, assembled, and annotated the circular mitogenomes of four species: A. borealis, A. gallica, A. sinapina, and A. solidipes (116,443, 98,896, 103,563, and 122,167 bp, respectively). The variation in mitogenome size can be explained by variable numbers of mobile genetic elements, introns, and plasmid-related sequences. Most Armillaria introns contained open reading frames (ORFs) that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Insertions of mobile elements were also evident as fragments of plasmid-related sequences in Armillaria mitogenomes. We also found several truncated gene duplications in all four mitogenomes.

Conclusions

Our study showed that fungal mitogenomes have a high degree of variation in size, gene content, and genomic organization even among closely related species of Armillara. We suggest that mobile genetic elements invading introns and intergenic sequences in the Armillaria mitogenomes have played a significant role in shaping their genome structure. The mitogenome changes we describe here are consistent with widely accepted phylogenetic relationships among the four species.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5732-z) contains supplementary material, which is available to authorized users.

The mitochondrial genome of Endoconidiophora resinifera is intron rich

Endoconidiophora resinifera (=Ceratocystis resinifera) is a blue-stain fungus that occurs on conifers. The data showed that the Endoconidiophora resinifera mitochondrial genome is one of the largest mitochondrial genomes (>220 kb) so far reported among members of the Ascomycota. An exceptional large number of introns (81) were noted and differences among the four strains were restricted to minor variations in intron numbers and a few indels and single nucleotide polymorphisms. The major differences among the four strains examined are due to size polymorphisms generated by the absence or presence of mitochondrial introns. Also, these mitochondrial genomes encode the largest cytochrome oxidase subunit 1 gene (47.5 kb) reported so far among the fungi. The large size for this gene again can be attributed to the large number of intron insertions. This study reports the first mitochondrial genome for the genus Endoconidiophora, previously members of this genus were assigned to Ceratocystis. The latter genus has recently undergone extensive taxonomic revisions and the mitochondrial genome might provide loci that could be applied as molecular markers assisting in the identification of taxa within this group of economically important fungi. The large mitochondrial genome also may provide some insight on mechanisms that can lead to mitochondrial genome expansion.

Annotation and analysis of the mitochondrial genome of Coniothyrium glycines, causal agent of red leaf blotch of soybean, reveals an abundance of homing endonucleases

Coniothyrium glycines, the causal agent of soybean red leaf blotch, is a USDA APHIS-listed Plant Pathogen Select Agent and potential threat to US agriculture. Sequencing of the C. glycines mt genome revealed a circular 98,533-bp molecule with a mean GC content of 29.01%. It contains twelve of the mitochondrial genes typically involved in oxidative phosphorylation (atp6, cob, cox1-3, nad1-6, and nad4L), one for a ribosomal protein (rps3), four for hypothetical proteins, one for each of the small and large subunit ribosomal RNAs (rns and rnl) and a set of 30 tRNAs. Genes were encoded on both DNA strands with cox1 and cox2 occurring as adjacent genes having no intergenic spacers. Likewise, nad2 and nad3 are adjacent with no intergenic spacers and nad5 is immediately followed by nad4L with an overlap of one base. Thirty-two introns, comprising 54.1% of the total mt genome, were identified within eight protein-coding genes and the rnl. Eighteen of the introns contained putative intronic ORFs with either LAGLIDADG or GIY-YIG homing endonuclease motifs, and an additional eleven introns showed evidence of truncated or degenerate endonuclease motifs. One intron possessed a degenerate N-acetyl-transferase domain. C. glycines shares some conservation of gene order with other members of the Pleosporales, most notably nad6-rnl-atp6 and associated conserved tRNA clusters. Phylogenetic analysis of the twelve shared protein coding genes agrees with commonly accepted fungal taxonomy. C. glycines represents the second largest mt genome from a member of the Pleosporales sequenced to date. This research provides the first genomic information on C. glycines, which may provide targets for rapid diagnostic assays and population studies.

Comparison of the Mitochondrial Genome Sequences of Six Annulohypoxylon stygium Isolates Suggests Short Fragment Insertions as a Potential Factor Leading to Larger Genomic Size

Mitochondrial DNA (mtDNA) is a core non-nuclear genetic material found in all eukaryotic organisms, the size of which varies extensively in the eumycota, even within species. In this study, mitochondrial genomes of six isolates of Annulohypoxylon stygium (Lév.) were assembled from raw reads from PacBio and Illumina sequencing. The diversity of genomic structures, conserved genes, intergenic regions and introns were analyzed and compared. Genome sizes ranged from 132 to 147 kb and contained the same sets of conserved protein-coding, tRNA and rRNA genes and shared the same gene arrangements and orientation. In addition, most intergenic regions were homogeneous and had similar sizes except for the region between cytochrome b (cob) and cytochrome c oxidase I (cox1) genes which ranged from 2,998 to 8,039 bp among the six isolates. Sixty-five intron insertion sites and 99 different introns were detected in these genomes. Each genome contained 45 or more introns, which varied in distribution and content. Introns from homologous insertion sites also showed high diversity in size, type and content. Comparison of introns at the same loci showed some complex introns, such as twintrons and ORF-less introns. There were 44 short fragment insertions detected within introns, intergenic regions, or as introns, some of them located at conserved domain regions of homing endonuclease genes. Insertions of short fragments such as small inverted repeats might affect or hinder the movement of introns, and these allowed for intron accumulation in the mitochondrial genomes analyzed, and enlarged their size. This study showed that the evolution of fungal mitochondrial introns is complex, and the results suggest short fragment insertions as a potential factor leading to larger mitochondrial genomes in A. stygium.

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen

Background

Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare).

Results

The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes (SPs) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SPs nor the TEs reside preferentially in genomic regions with unique features. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs, but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome.

Conclusions

The characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of significant compartmentalization) are consistent with a “one-speed” genome that differs in its architecture and (co-)evolutionary pattern from the “two-speed” genomes reported for several other filamentous phytopathogens.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4750-6) contains supplementary material, which is available to authorized users.

The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi

Ophiostoma novo-ulmi, a member of the Ophiostomatales (Ascomycota), is the causal agent of the current Dutch elm disease pandemic in Europe and North America. The complete mitochondrial genome (mtDNA) of Ophiostoma novo-ulmi subsp. novo-ulmi, the European component of O. novo-ulmi, has been sequenced and annotated. Gene order (synteny) among the currently available members of the Ophiostomatales was examined and appears to be conserved, and mtDNA size variability among the Ophiostomatales is due in part to the presence of introns and their encoded open reading frames. Phylogenetic analysis of concatenated mitochondrial protein-coding genes yielded phylogenetic estimates for various members of the Ophiostomatales, with strong statistical support showing that mtDNA analysis may provide valuable insights into the evolution of the Ophiostomatales.

Comparative genomics of maize ear rot pathogens reveals expansion of carbohydrate-active enzymes and secondary metabolism backbone genes in Stenocarpella maydis

Stenocarpella maydis is a plant pathogenic fungus that causes Diplodia ear rot, one of the most destructive diseases of maize. To date, little information is available regarding the molecular basis of pathogenesis in this organism, in part due to limited genomic resources. In this study, a 54.8 Mb draft genome assembly of S. maydis was obtained with Illumina and PacBio sequencing technologies, and analyzed. Comparative genomic analyses with the predominant maize ear rot pathogens Aspergillus flavus, Fusarium verticillioides, and Fusarium graminearum revealed an expanded set of carbohydrate-active enzymes for cellulose and hemicellulose degradation in S. maydis. Analyses of predicted genes involved in starch degradation revealed six putative α-amylases, four extracellular and two intracellular, and two putative γ-amylases, one of which appears to have been acquired from bacteria via horizontal transfer. Additionally, 87 backbone genes involved in secondary metabolism were identified, which represents one of the largest known assemblages among Pezizomycotina species. Numerous secondary metabolite gene clusters were identified, including two clusters likely involved in the biosynthesis of diplodiatoxin and chaetoglobosins. The draft genome of S. maydis presented here will serve as a useful resource for molecular genetics, functional genomics, and analyses of population diversity in this organism.