Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex

Characterization of the complete mitochondrial genome of Paecilomyces variotii and comparative evolutionary mitochondriomics of 36 fungi

BACKGROUD

Paecilomyces variotii has important economic value in stimulating crop growth, biodegradation, and other aspects. Up to now, there are no research reports on its mitochondrial genome.

METHODS AND RESULTS

The mitochondrial genome of Paecilomyces variotii was determined with the next-generation sequencing method (Illumina, NovaSeq), and its characteristics were analyzed using various bioinformatics approaches. The length of complete mitochondrial genome sequence of P. variotii is 40,965 bp and consists of 14 protein-coding genes, 2 ribosomal RNA genes, 1 ribosomal protein S3 gene, 26 transport RNA genes. The results of phylogenetics analysis using Bayesian inference and Maximum likelihood methods showed that P. variotii belongs to the Eurotiales order in the Thermoascaceae family, and 9 genera within the Eurotiomycetes class were effectively distinguished with high support rates (bootstrap value > 92% and posterior probabilities > 99%). The analysis of synonymous substitution rates and nonsynonymous substitution rates indicated that the Ka/Ks values of the 14 PCGs in the mitochondrial genomes of the two orders in the Eurotiomycetes class ranged from 0 to 0.4333.

CONCLUSIONS

This study revealed the structural and sequence information characteristics of the mitochondrial genome of P. variotii, and the phylogenetic results strongly support its classification within the family Thermoascaceae, consistent with traditional morphological taxonomy studies. The 14 PCGs in the mitochondrial genomes of the two orders in the Eurotiomycetes class are subject to strong purifying (negative) selection. The results of this research provides an important molecular basis for the development of genomics, evolutionary genetics and molecular markers of P. variotii in the future.

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.

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.

Mitogenomics and mitochondrial gene phylogeny decipher the evolution of Saccharomycotina yeasts

Saccharomycotina yeasts belong to diverse clades within the kingdom of fungi and are important to human everyday life. This work investigates the evolutionary relationships among these yeasts from a mitochondrial (mt) genomic perspective. A comparative study of 155 yeast mt genomes representing all major phylogenetic lineages of Saccharomycotina was performed, including genome size and content variability, intron and intergenic regions’ diversity, genetic code alterations, and syntenic variation. Findings from this study suggest that mt genome size diversity is the result of a ceaseless random process, mainly based on genetic recombination and intron mobility. Gene order analysis revealed conserved syntenic units and many occurring rearrangements, which can be correlated with major evolutionary events as shown by the phylogenetic analysis of the concatenated mt protein matrix. For the first time, molecular dating indicated a slower mt genome divergence rate in the early stages of yeast evolution, in contrast with a faster rate in the late evolutionary stages, compared to their nuclear time divergence. Genetic code reassignments of mt genomes are a perpetual process happening in many different parallel evolutionary steps throughout the evolution of Saccharomycotina. Overall, this work shows that phylogenetic studies based on the mt genome of yeasts highlight major evolutionary events.

Characterization and phylogenetic analysis of the complete mitochondrial genome of the pathogenic fungus Ilyonectria destructans

Ilyonectria destructans is a pathogenic fungus causing root rot and other symptoms on trees and many crops. This paper analyses the mitochondrial genome of I. destructans and compares it with other published Nectriaceae mitogenomes. The I. destructans mitogenome appears as a circular DNA molecule of 42,895 bp and an overall GC content of 28.23%. It contains 28 protein-coding genes (15 core protein genes and 13 free-standing ORFs), two rRNAs and 27 tRNAs. The gene content and order were found to be conserved in the mitogenome of I. destructans and other Nectriaceae, although the genome size varies because of the variation in the number and length of intergenic regions and introns. For most core protein-coding genes in Nectriaceae species, Ka/Ks < 1 indicates purifying selection. Among some Nectriaceae representatives, only the rps3 gene was found under positive selection. Phylogenetic analyses based on nucleotide sequences of 15 protein-coding genes divided 45 Hypocreales species into six major clades matching the families Bionectriaceae, Cordycipitaceae, Clavicipitaceae, Ophiocordycipitaceae, Hypocreaceae and Nectriaceae. I. destructans appeared as a sister species to unidentified Ilyonectia sp., closely related to C. ilicicola, N. cinnabarina and a clad of ten Fusarium species and G. moniliformis. The complete mitogenome of I. destructans reported in the current paper will facilitate the study of epidemiology, biology, genetic diversity of the species and the evolution of family Nectriace and the Hypocreales order.

The Mitogenomes of Ophiostoma minus and Ophiostoma piliferum and Comparisons With Other Members of the Ophiostomatales

Fungi assigned to the Ophiostomatales are of economic concern as many are blue-stain fungi and some are plant pathogens. The mitogenomes of two blue-stain fungi, Ophiostoma minus and Ophiostoma piliferum, were sequenced and compared with currently available mitogenomes for other members of the Ophiostomatales. Species representing various genera within the Ophiostomatales have been examined for gene content, gene order, phylogenetic relationships, and the distribution of mobile elements. Gene synteny is conserved among the Ophiostomatales but some members were missing the atp9 gene. A genome wide intron landscape has been prepared to demonstrate the distribution of the mobile genetic elements (group I and II introns and homing endonucleases) and to provide insight into the evolutionary dynamics of introns among members of this group of fungi. Examples of complex introns or nested introns composed of two or three intron modules have been observed in some species. The size variation among the mitogenomes (from 23.7 kb to about 150 kb) is mostly due to the presence and absence of introns. Members of the genus Sporothrix sensu stricto appear to have the smallest mitogenomes due to loss of introns. The taxonomy of the Ophiostomatales has recently undergone considerable revisions; however, some lineages remain unresolved. The data showed that genera such as Raffaelea appear to be polyphyletic and the separation of Sporothrix sensu stricto from Ophiostoma is justified.

Mitogenomes of Two Phallus Mushroom Species Reveal Gene Rearrangement, Intron Dynamics, and Basidiomycete Phylogeny

Phallus indusiatus and Phallus echinovolvatus are edible bamboo mushrooms with pharmacological properties. We sequenced, assembled, annotated, and compared the mitogenomes of these species. Both mitogenomes were composed of circular DNA molecules, with sizes of 89,139 and 50,098 bp, respectively. Introns were the most important factor in mitogenome size variation within the genus Phallus. Phallus indusiatus, P. echinovolvatus, and Turbinellus floccosus in the subclass Phallomycetidae have conservative gene arrangements. Large-scale gene rearrangements were observed in species representing 42 different genera of Basidiomycetes. A variety of intron position classes were found in the 44 Basidiomycete species analyzed. A novel group II intron from the P. indusiatus mitogenome was compared with other fungus species containing the same intron, and we demonstrated that the insertion sites of the intron had a base preference. Phylogenetic analyses based on combined gene datasets yielded well-supported Bayesian posterior probability (BPP = 1) topologies. This indicated that mitochondrial genes are reliable molecular markers for analyzing the phylogenetic relationships of the Basidiomycetes. This is the first study of the mitogenome of the genus Phallus, and it increases our understanding of the population genetics and evolution of bamboo mushrooms and related species.

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.

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.

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.

Mollisiaceae: An overlooked lineage of diverse endophytes

Mollisia is a taxonomically neglected discomycete genus (Helotiales, Leotiomycetes) of commonly encountered saprotrophs on decaying plant tissues throughout temperate regions. The combination of indistinct morphological characters, more than 700 names in the literature, and lack of reference DNA sequences presents a major challenge when working with Mollisia. Unidentified endophytes, including strains that produced antifungal or antiinsectan secondary metabolites, were isolated from conifer needles in New Brunswick and placed with uncertainty in Phialocephala and Mollisia, necessitating a more comprehensive treatment of these genera. In this study, morphology and multigene phylogenetic analyses were used to explore the taxonomy of Mollisiaceae, including Mollisia, Phialocephala, and related genera, using new field collections, herbarium specimens, and accessioned cultures and sequences. The phylogeny of Mollisiaceae was reconstructed and compared using the nuc internal transcribed spacer rDNA (ITS) barcode and partial sequences of the 28S nuc rDNA (LSU) gene, largest subunit of RNA polymerase II (RPB1), DNA topoisomerase I (TOP1), and the hypothetical protein Lipin/Ned1/Smp2 (LNS2). The results show that endophytism is common throughout the Mollisiaceae lineage in a diverse range of hosts but is infrequently attributed to Mollisia because of a paucity of reference sequences. Generic boundaries within Mollisiaceae are poorly resolved and based on phylogenetic evidence the family included species placed in Acephala, Acidomelania, Barrenia, Bispora, Cheirospora, Cystodendron, Fuscosclera, Hysteronaevia, Loramyces, Mollisia, Neopyrenopeziza, Obtectodiscus, Ombrophila, Patellariopsis, Phialocephala, Pulvinata, Tapesia (=Mollisia), and Trimmatostroma. Taxonomic novelties included the description of five novel Mollisia species and five novel Phialocephala species and the synonymy of Fuscosclera with Phialocephala, Acidomelania with Mollisia, and Loramycetaceae with Mollisiaceae.

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.

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.

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 complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class

BACKGROUND

Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallanina suborder (Dracunculoidea superfamily) exhibited a unique gene order, the other objective of this research was to study the evolution of mitochondrial architecture in the Spirurida order. Thus, we sequenced the complete mitogenome of the Camallanus cotti fish parasite and conducted structural and phylogenomic comparative analyses with all available Spirurida mitogenomes.

RESULTS

The mitogenome is exceptionally large (17,901 bp) among the Chromadorea and, with 46 (pseudo-) genes, exhibits a unique architecture among nematodes. Six protein-coding genes (PCGs) and six tRNAs are duplicated. An additional (seventh) tRNA (Trp) was probably duplicated by the remolding of tRNA-Ser2 (missing). Two pairs of these duplicated PCGs might be functional; three were incomplete and one contained stop codons. Apart from Ala and Asp, all other duplicated tRNAs are conserved and probably functional. Only 19 unique tRNAs were found. Phylogenomic analysis included Gnathostomatidae (Spirurina) in the Camallanina suborder.

CONCLUSIONS

Within the Nematoda, comparable PCG duplications were observed only in the enoplean Mermithidae family, but those result from mitochondrial recombination, whereas characteristics of the studied mitogenome suggest that likely rearrangement mechanisms are either a series of duplications, transpositions and random loss events, or duplication, fragmentation and subsequent reassembly of the mitogenome. We put forward a hypothesis that the evolution of mitogenomic architecture is extremely discontinuous, and that once a long period of stasis in gene order and content has been punctuated by a rearrangement event, such a destabilised mitogenome is much more likely to undergo subsequent rearrangement events, resulting in an exponentially accelerated evolutionary rate of mitogenomic rearrangements. Implications of this model are particularly important for the application of gene order similarity as an additive source of phylogenetic information. Chromadorean nematodes, and particularly Camallanina clade (with C. cotti as an example of extremely accelerated rate of rearrangements), might be a good model to further study this discontinuity in the dynamics of mitogenomic evolution.

Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles

BACKGROUND

Whereas an increasing number of pathogenic and mutualistic ascomycetous species were sequenced in the past decade, species showing a seemingly neutral association such as root endophytes received less attention. In the present study, the genome of Phialocephala subalpina, the most frequent species of the Phialocephala fortinii s.l. - Acephala applanata species complex, was sequenced for insight in the genome structure and gene inventory of these wide-spread root endophytes.

RESULTS

The genome of P. subalpina was sequenced using Roche/454 GS FLX technology and a whole genome shotgun strategy. The assembly resulted in 205 scaffolds and a genome size of 69.7 Mb. The expanded genome size in P. subalpina was not due to the proliferation of transposable elements or other repeats, as is the case with other ascomycetous genomes. Instead, P. subalpina revealed an expanded gene inventory that includes 20,173 gene models. Comparative genome analysis of P. subalpina with 13 ascomycetes shows that P. subalpina uses a versatile gene inventory including genes specific for pathogens and saprophytes. Moreover, the gene inventory for carbohydrate active enzymes (CAZymes) was expanded including genes involved in degradation of biopolymers, such as pectin, hemicellulose, cellulose and lignin.

CONCLUSIONS

The analysis of a globally distributed root endophyte allowed detailed insights in the gene inventory and genome organization of a yet largely neglected group of organisms. We showed that the ubiquitous root endophyte P. subalpina has a broad gene inventory that links pathogenic and saprophytic lifestyles.

The complete mitochondrial genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 confirms evolutionary division within the fungal Phialocephala fortinii s.l. - Acephala appalanata species complex

Despite the recent surge in mitochondrial (mt) genome sequencing, Kingdom Fungi remains underrepresented with respect to mtDNA. We describe the mt genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 (Helotiales, Ascomycota). This strain is of interest to the Canadian forestry industry as it produces the anti-insectan compound rugulosin. Sequence was obtained from whole genome shotgun sequencing. Comparison to the only other published Phialocephala mt genome, Phialocephala subalpina, indicates that the suite of common mt genes - cox1-3, cob, nad1-6 and 4L, atp6, 8 and 9, as well as rrnL and rrnS - has retained an identical order. Nad4L remains one of the most conserved mitochondrial genes within Phialocephala. Members of the closely related Phialocephala fortinii s.l. - Acephala appalanata species complex (PAC) share too much sequence similarity to properly resolve lineages using ITS barcoding alone. Using P. scopiformis sequence as an outgroup, we determined ancestral gene states that help confirm clades within Phialocephala. Our results show: (1) the complete mt genome of P. scopiformis, representing the 10th complete mt genome for the order Helotiales (containing >3800 species), and (2) how large-scale genomic patterns, such as mitochondrial gene order, can be used to confirm lineages within fungal species complexes.

Complete mitochondrial genome sequence of the phytopathogenic fungi Sclerotinia sclerotiorum JX-21

Sclerotinia sclerotiorum is one of the most devastating necrotrophic fungal plant pathogens in agriculture causing diseases in over 400 species of plants including important crops and numerous weeds. In this work, the mitochondrial sequence of S. sclerotiorum with different strain obtained from the infected stems of Brassica campestris L. in Wangjiang County, Anhui Province, China is presented. The mt DNA codes for 14 proteins of the respiratory chain, 1 ribosomal protein, 2 homing endonucleases, 2 rRNAs, 25 tRNAs, and 5 hypothetical proteins ORFs. Phylogenetic analysis with protein-coding gene sequences of reported Ascomycota mt genomes revealed the close relationship of JX-21 with the family of Sclerotiniaceae.

Analysis of the Mitochondrial Genome in Hypomyces aurantius Reveals a Novel Twintron Complex in Fungi

Hypomyces aurantius is a mycoparasite that causes cobweb disease, a most serious disease of cultivated mushrooms. Intra-species identification is vital for disease control, however the lack of genomic data makes development of molecular markers challenging. Small size, high copy number, and high mutation rate of fungal mitochondrial genome makes it a good candidate for intra and inter species differentiation. In this study, the mitochondrial genome of H. H.a0001 was determined from genomic DNA using Illumina sequencing. The roughly 72 kb genome shows all major features found in other Hypocreales: 14 common protein genes, large and small subunit rRNAs genes and 27 tRNAs genes. Gene arrangement comparison showed conserved gene orders in Hypocreales mitochondria are relatively conserved, with the exception of Acremonium chrysogenum and Acremonium implicatum. Mitochondrial genome comparison also revealed that intron length primarily contributes to mitogenome size variation. Seventeen introns were detected in six conserved genes: five in cox1, four in rnl, three in cob, two each in atp6 and cox3, and one in cox2. Four introns were found to contain two introns or open reading frames: cox3-i2 is a twintron containing two group IA type introns; cox2-i1 is a group IB intron encoding two homing endonucleases; and cox1-i4 and cox1-i3 both contain two open reading frame (ORFs). Analyses combining secondary intronic structures, insertion sites, and similarities of homing endonuclease genes reveal two group IA introns arranged side by side within cox3-i2. Mitochondrial data for H. aurantius provides the basis for further studies relating to population genetics and species identification.

The potential of Dark Septate Endophytes to form root symbioses with ectomycorrhizal and ericoid mycorrhizal middle European forest plants

The unresolved ecophysiological significance of Dark Septate Endophytes (DSE) may be in part due to existence of morphologically indistinguishable cryptic species in the most common Phialocephala fortinii s. l.--Acephala applanata species complex (PAC). We inoculated three middle European forest plants (European blueberry, Norway spruce and silver birch) with 16 strains of eight PAC cryptic species and other DSE and ectomycorrhizal/ericoid mycorrhizal fungi and focused on intraradical structures possibly representing interfaces for plant-fungus nutrient transfer and on host growth response. The PAC species Acephala applanata simultaneously formed structures resembling ericoid mycorrhiza (ErM) and DSE microsclerotia in blueberry. A. macrosclerotiorum, a close relative to PAC, formed ectomycorrhizae with spruce but not with birch, and structures resembling ErM in blueberry. Phialocephala glacialis, another close relative to PAC, formed structures resembling ErM in blueberry. In blueberry, six PAC strains significantly decreased dry shoot biomass compared to ErM control. In birch, one A. macrosclerotiorum strain increased root biomass and the other shoot biomass in comparison with non-inoculated control. The dual mycorrhizal ability of A. macrosclerotiorum suggested that it may form mycorrhizal links between Ericaceae and Pinaceae. However, we were unable to detect this species in Ericaceae roots growing in a forest with presence of A. macrosclerotiorum ectomycorrhizae. Nevertheless, the diversity of Ericaceae mycobionts was high (380 OTUs) with individual sites often dominated by hitherto unreported helotialean and chaetothyrialean/verrucarialean species; in contrast, typical ErM fungi were either absent or low in abundance. Some DSE apparently have a potential to form mycorrhizae with typical middle European forest plants. However, except A. applanata, the tested representatives of all hitherto described PAC cryptic species formed typical DSE colonization without specific structures necessary for mycorrhizal nutrient transport. A. macrosclerotiorum forms ectomycorrhiza with conifers but not with broadleaves and probably does not form common mycorrhizal networks between conifers with Ericaceae.

Analysis of the complete mitochondrial genome of Pochonia chlamydosporia suggests a close relationship to the invertebrate-pathogenic fungi in Hypocreales

Background

The fungus Pochonia chlamydosporia parasitizes nematode eggs and has become one of the most promising biological control agents (BCAs) for plant-parasitic nematodes, which are major agricultural pests that cause tremendous economic losses worldwide. The complete mitochondrial (mt) genome is expected to open new avenues for understanding the phylogenetic relationships and evolution of the invertebrate-pathogenic fungi in Hypocreales.

Results

The complete mitogenome sequence of P. chlamydosporia is 25,615 bp in size, containing the 14 typical protein-coding genes, two ribosomal RNA genes, an intronic ORF coding for a putative ribosomal protein (rps3) and a set of 23 transfer RNA genes (trn) which recognize codons for all amino acids. Sequence similarity studies and syntenic gene analyses show that 87.02% and 58.72% of P. chlamydosporia mitogenome sequences match 90.50% of Metarhizium anisopliae sequences and 61.33% of Lecanicillium muscarium sequences with 92.38% and 86.04% identities, respectively. A phylogenetic tree inferred from 14 mt proteins in Pezizomycotina fungi supports that P. chlamydosporia is most closely related to the entomopathogenic fungus M. anisopliae. The invertebrate-pathogenic fungi in Hypocreales cluster together and clearly separate from a cluster comprising plant-pathogenic fungi (Fusarium spp.) and Hypocrea jecorina. A comparison of mitogenome sizes shows that the length of the intergenic regions or the intronic regions is the major size contributor in most of mitogenomes in Sordariomycetes. Evolutionary analysis shows that rps3 is under positive selection, leading to the display of unique evolutionary characteristics in Hypocreales. Moreover, the variability of trn distribution has a clear impact on gene order in mitogenomes. Gene rearrangement analysis shows that operation of transposition drives the rearrangement events in Pezizomycotina, and most events involve in trn position changes, but no rearrangement was found in Clavicipitaceae.

Conclusions

We present the complete annotated mitogenome sequence of P. chlamydosporia. Based on evolutionary and phylogenetic analyses, we have determined the relationships between the invertebrate-pathogenic fungi in Hypocreales. The invertebrate-pathogenic fungi in Hypocreales referred to in this paper form a monophyletic group sharing a most recent common ancestor. Our rps3 and trn gene order results also establish a foundation for further exploration of the evolutionary trajectory of the fungi in Hypocreales.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0341-8) contains supplementary material, which is available to authorized users.

Is it an ant or a butterfly? Convergent evolution in the mitochondrial gene order of Hymenoptera and Lepidoptera

Insect mitochondrial genomes (mtDNA) are usually double helical and circular molecules containing 37 genes that are encoded on both strands. The arrangement of the genes is not constant for all species, and produces distinct gene orders (GOs) that have proven to be diagnostic in defining clades at different taxonomic levels. In general, it is believed that distinct taxa have a very low chance of sharing identically arranged GOs. However, examples of identical, homoplastic local rearrangements occurring in distinct taxa do exist. In this study, we sequenced the complete mtDNAs of the ants Formica fusca and Myrmica scabrinodis (Formicidae, Hymenoptera) and compared their GOs with those of other Insecta. The GO of F. fusca was found to be identical to the GO of Dytrisia (the largest clade of Lepidoptera). This finding is the first documented case of an identical GO shared by distinct groups of Insecta, and it is the oldest known event of GO convergent evolution in animals. Both Hymenoptera and Lepidoptera acquired this GO early in their evolution. Using a phylogenetic approach combined with new bioinformatic tools, the chronological order of the evolutionary events that produced the diversity of the hymenopteran GOs was determined. Additionally, new local homoplastic rearrangements shared by distinct groups of insects were identified. Our study showed that local and global homoplasies affecting the insect GOs are more widespread than previously thought. Homoplastic GOs can still be useful for characterizing the various clades, provided that they are appropriately considered in a phylogenetic and taxonomic context.

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

Here we report the complete sequence of the mitochondrial (mt) genome of the necrotrophic phytopathogenic fungus Sclerotinia borealis, a member of the order Helotiales of Ascomycetes. The 203,051 bp long mtDNA of S. borealis represents one of the largest sequenced fungal mt genomes. The large size is mostly determined by the presence of mobile genetic elements, which include 61 introns. Introns contain a total of 125,394 bp, are scattered throughout the genome, and are found in 12 protein-coding genes and in the ribosomal RNA genes. Most introns contain complete or truncated ORFs that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Integrations of mobile elements are also evidenced by the presence of two regions similar to fragments of inverton-like plasmids. Although duplications of some short genome regions, resulting in the appearance of truncated extra copies of genes, did occur, we found no evidences of extensive accumulation of repeat sequences accounting for mitochondrial genome size expansion in some other fungi. Comparisons of mtDNA of S. borealis with other members of the order Helotiales reveal considerable gene order conservation and a dynamic pattern of intron acquisition and loss during evolution. Our data are consistent with the hypothesis that horizontal DNA transfer has played a significant role in the evolution and size expansion of the S. borealis mt genome.

Characterization and phylogenetic analysis of the mitochondrial genome of Glarea lozoyensis indicates high diversity within the order Helotiales

BACKGROUND

Glarea lozoyensis is a filamentous fungus used for the industrial production of non-ribosomal peptide pneumocandin B0. In the scope of a whole genome sequencing the complete mitochondrial genome of the fungus has been assembled and annotated. It is the first one of the large polyphyletic Helotiaceae family. A phylogenetic analysis was performed based on conserved proteins of the oxidative phosphorylation system in mitochondrial genomes.

RESULTS

The total size of the mitochondrial genome is 45,038 bp. It contains the expected 14 genes coding for proteins related to oxidative phosphorylation,two rRNA genes, six hypothetical proteins, three intronic genes of which two are homing endonucleases and a ribosomal protein rps3. Additionally there is a set of 33 tRNA genes. All genes are located on the same strand. Phylogenetic analyses based on concatenated mitochondrial protein sequences confirmed that G. lozoyensis belongs to the order of Helotiales and that it is most closely related to Phialocephala subalpina. However, a comparison with the three other mitochondrial genomes known from Helotialean species revealed remarkable differences in size, gene content and sequence. Moreover, it was found that the gene order found in P. subalpina and Sclerotinia sclerotiorum is not conserved in G. lozoyensis.

CONCLUSION

The arrangement of genes and other differences found between the mitochondrial genome of G. lozoyensis and those of other Helotiales indicates a broad genetic diversity within this large order. Further mitochondrial genomes are required in order to determine whether there is a continuous transition between the different forms of mitochondrial genomes or G. lozoyensis belongs to a distinct subgroup within Helotiales.