Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules

Comparative analysis of mitochondrial genomes of Chaetoceros species

Chaetoceros is one of the most diverse genera of marine planktonic diatoms. Chaetoceros species are common and may become dominant in coastal ecosystems. Many Chaetoceros species can develop harmful algal blooms with negative effects on the aquaculture industry. In this study, we constructed full-length mitochondrial genomes (mtDNAs) for 12 Chaetoceros species, including eight known species and four undescribed species. The sizes of these mtDNAs are generally similar, varying from 34,174 to 39,411 bp. Despite extensive synteny conservation, discrete regions showed high variations, and based on these regions, a specific primer chaetomt1 for Chaetoceros species was designed. The availability of mtDNAs from various Chaetoceros species is not only valuable as a super-barcode for phylogenetic analysis but also important for functional and evolutionary analysis of diatoms.

Description and characterization of the small mitochondrial genome of Trichoderma cerinum (Hypocreales, Hypocreaceae) and its evolutionary perspectives

Trichoderma Persoon (1794) is a genus of fungus found in soils and decaying wood all over the world. We present the assembly and annotation of the mitochondrial genome of Trichoderma cerinum Bissett, Kubicek & Szakacs (2003) and an assessment of the phylogeny of the group, discussing the loss and gain of shared genes in the evolutionary history of fungi. We downloaded the raw data of T. cerinum from the NCBI database and exported it to the Galaxy Europe platform, where we performed the mitogenome assembly using the NOVOplasty tool. We used three tools for annotation. The phylogeny was conducted with 12 Trichoderma species and the T. cerinum. Fusarium oxysporum was used as an outgroup. We got a circularized mitochondrial genome of 26,696 bp, with 15 protein-coding genes, 25 tRNAs, two rRNAs, two endonuclease sequences, and an orf40. This species contains only one intron in the cob gene. In our phylogenetic reconstruction, T. cerinum was recovered as a sister group of a clade containing Trichoderma lixii, Trichoderma afroharzianum, Trichoderma simmonsii, and Trichoderma harzianum.

An expanded phylogenomic analysis of Heterolobosea reveals the deep relationships, non-canonical genetic codes, and cryptic flagellate stages in the group

The phylum Heterolobosea Page and Blanton, 1985 is a group of eukaryotes that contains heterotrophic flagellates, amoebae, and amoeboflagellates, including the infamous brain-eating amoeba Naegleria fowleri. In this study, we investigate the deep evolutionary history of Heterolobosea by generating and analyzing transcriptome data from 16 diverse isolates and combine this with previously published data in a comprehensive phylogenomic analysis. This dataset has representation of all but one of the major lineages classified here as orders. Our phylogenomic analyses recovered a robustly supported phylogeny of Heterolobosea providing a phylogenetic framework for understanding their evolutionary history. Based on the newly recovered relationships, we revised the classification of Heterolobosea to the family level. We describe two new classes (Eutetramitea cl. nov. and Selenaionea cl. nov) and one new order (Naegleriida ord. nov.), and provide a new delimitation of the largest family of Heterolobosea, Vahlkampfiidae Jollos, 1917. Unexpectedly, we unveiled the first two cases of genetic code alterations in the group: UAG as a glutamine codon in the nuclear genome of Dactylomonas venusta and UGA encoding tryptophan in the mitochondrial genome of Neovahlkampfia damariscottae. In addition, analysis of the genome of the latter species confirmed its inability to make flagella, whereas we identified hallmark flagellum-specific genes in most other heteroloboseans not previously observed to form flagellates, suggesting that the loss of flagella in Heterolobosea is much rarer than generally thought. Finally, we define the first autapomorphy of the subphylum Pharyngomonada, represented by a fusion of two key genes for peroxisomal β-oxidation enzymes.

Mitochondrial Genomes from Fungal the Entomopathogenic Moelleriella Genus Reveals Evolutionary History, Intron Dynamics and Phylogeny

Members of the genus Moelleriella (Hypocreales, Clavicipitaceae) are insect pathogens with specificity for scale insects and whiteflies. However, no mitochondrial genomes are available for these fungi. Here, we assembled seven mitogenomes from M. zhongdongii, M. libera, M. raciborskii, M. gracilispora, M. oxystoma, Moelleriella sp. CGMCC 3.18909, and Moelleriella sp. CGMCC 3.18913, which varied in size from 40.8 to 95.7 Kb. Synteny and codon usage bias was relatively conserved, with the mitochondrial gene arrangement being completely homologous to the gene order of 21 other species within the Hypocreales. Nevertheless, significant intron polymorphism was observed between Moelleriella species. Evolutionary analyses revealed that all 15 core protein-coding genes had ka/ks < 1, indicating purifying selection pressure. Sequence variation within the mitochondrial ATP synthase F0 subunit 6 (atp6) gene showed the largest genetic distance, with the ATP synthase F0 subunit 9 (atp9) gene showing the smallest. Comparative analyses of mitogenomes revealed that introns were the primary factor contributing to the size variation in Moelleriella and, more broadly, within Hypocreales mitogenomes. Phylogenetic analyses indicated that the seven Moelleriella species examined form a well-supported clade, most closely related to Metarhizium. These data present the first mitogenomes from Moelleriella and further advance research into the taxonomy, origin, evolution, and genomics of Moelleriella.

The first complete mitochondrial genome of Phellinus pomaceus var. prunastri (Pers.) Pat. 1926 (Hymenochaetales: Hymenochaetaceae) and phylogenetic analysis

Phellinus pomaceus var. prunastri (Pers.) Pat. 1926 is a famous medicinal fungus that has attracted considerable interest in biotechnology because of its diverse biologically active ingredients. Here, we provide the full mitochondrial genome sequence of P. pomaceus, which spans 122,850 bp and has a GC content of 26.04%. The genome comprises 15 essential protein-coding genes, 26 distinct ORFs, 24 intronic ORFs, 25 tRNAs, and 2 rRNA genes. Bayesian inference (BI) was employed for phylogenetic analysis, revealing the evolutionary relationships among 17 Basidiomycota fungi. The results strongly supported distinct clades and indicated that P. pomaceus is closely related to Fomitiporia mediterranea.

Assembly, Annotation, and Comparative Analysis of Mitochondrial Genomes in Trichoderma

Trichoderma is a widely studied ascomycete fungal genus, including more than 400 species. However, genetic information on Trichoderma is limited, with most species reporting only DNA barcodes. Mitochondria possess their own distinct DNA that plays a pivotal role in molecular function and evolution. Here, we report 42 novel mitochondrial genomes (mitogenomes) combined with 18 published mitogenomes of Trichoderma. These circular mitogenomes exhibit sizes of 26,276-94,608 bp, typically comprising 15 core protein-coding genes (PCGs), 2 rRNAs, and 16-30 tRNAs; however, the number of endonucleases and hypothetical proteins encoded in the introns of PCGs increases with genome size enlargement. According to the result of phylogenetic analysis of the whole mitogenome, these strains diverged into six distinct evolutionary branches, supported by the phylogeny based on 2830 single-copy nuclear genes. Comparative analysis revealed that dynamic Trichoderma mitogenomes exhibited variations in genome size, gene number, GC content, tRNA copy, and intron across different branches. We identified three mutation hotspots near the regions encoding nad3, cox2, and nad5 that caused major changes in the mitogenomes. Evolutionary analysis revealed that atp9, cob, nad4L, nad5, and rps3 have been influenced by positive selection during evolution. This study provides a valuable resource for exploring the important roles of the genetic and evolutionary dynamics of Trichoderma mitogenome in the adaptive evolution of biocontrol fungi.

ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment

Non-coding RNAs play a major role in diverse processes in living cells with their sequence and spatial structure serving as the principal determinants of their function. Superposition of RNA 3D structures is the most accurate method for comparative analysis of RNA molecules and for inferring structure-based sequence alignments. Topology-independent superposition is particularly relevant, as evidenced by structurally similar RNAs with sequence permutations such as tRNA and Y RNA. To date, state-of-the-art methods for RNA 3D structure superposition rely on intricate heuristics, and the potential for topology-independent superposition has not been exhausted. Recently, we introduced the ARTEM method for unrestrained pairwise superposition of RNA 3D modules and now we developed it further to solve the global RNA 3D structure alignment problem. Our new tool ARTEMIS significantly outperforms state-of-the-art tools in both sequentially-ordered and topology-independent RNA 3D structure superposition. Using ARTEMIS we discovered a helical packing motif to be preserved within different backbone topology contexts across various non-coding RNAs, including multiple ribozymes and riboswitches. We anticipate that ARTEMIS will be essential for elucidating the landscape of RNA 3D folds and motifs featuring sequence permutations that thus far remained unexplored due to limitations in previous computational approaches.

Comparative Mitogenomics Analysis Revealed Evolutionary Divergence among Purpureocillium Species and Gene Arrangement and Intron Dynamics of Ophiocordycipitaceae

The species of Purpureocillium are cosmopolitan and multitrophic fungi that can infect a wide range of invertebrate hosts. This study reports the mitogenome of P. atypicola, a specialized spider pathogenic fungus. The 112,465 bp mitogenome encoded genes typically found in fungal mitogenomes, and a total of 52 introns inserted into seven genes. A comparison with three other Purpureocillium species revealed significant differences in length and intron number, primarily due to intron variation; however, there was no dynamic variation in the introns of the cox1 gene within the same species of the Purpureocillium genus. Different mitochondrial protein-coding genes showed variable degrees of genetic differentiation among these species, but they were all under purifying selection. Additionally, frequent intron loss or gain events were detected to have occurred during the evolution of the Ophiocordycipitaceae mitogenomes, yet the gene arrangement remains conserved. A phylogenetic analysis of the combined mitochondrial gene set gave identical and well-supported tree topologies. The estimated age of the crown of Ophiocordycipitaceae and Purpureocillium were around the Early Cretaceous period (127 Mya) and Late Cretaceous period (83 Mya), respectively. The results of this study advance our understanding of the genomics, evolution, and taxonomy of this important fungal group.

A cryptic plastid and a novel mitochondrial plasmid in Leucomyxa plasmidifera gen. and sp. nov. (Ochrophyta) push the frontiers of organellar biology

Complete plastid loss seems to be very rare among secondarily non-photosynthetic eukaryotes. Leukarachnion sp. PRA-24, an amoeboid colourless protist related to the photosynthetic algal class Synchromophyceae (Ochrophyta), is a candidate for such a case based on a previous investigation by transmission electron microscopy. Here, we characterize this organism in further detail and describe it as Leucomyxa plasmidifera gen. et sp. nov., additionally demonstrating it is the first known representative of a broader clade of non-photosynthetic ochrophytes. We recovered its complete plastid genome, exhibiting a reduced gene set similar to plastomes of other non-photosynthetic ochrophytes, yet being even more extreme in sequence divergence. Identification of components of the plastid protein import machinery in the L. plasmidifera transcriptome assembly corroborated that the organism possesses a cryptic plastid organelle. According to our bioinformatic reconstruction, the plastid contains a unique combination of biosynthetic pathways producing haem, a folate precursor and tocotrienols. As another twist to its organellar biology, L. plasmidifera turned out to contain an unusual long insertion in its mitogenome related to a newly discovered mitochondrial plasmid exhibiting unprecedented features in terms of its size and coding capacity. Combined, our work uncovered further striking outcomes of the evolutionary course of semiautonomous organelles in protists.

Characterization of the complete mitochondrial genome of the medical fungus Ganoderma resinaceum Boud., 1889 (Polyporales: Ganodermataceae)

The medical mushroom Ganoderma resinaceum Boud., 1889, is of great interest in pharmacy due to its diverse functional active ingredients. However, the mitochondrial genome of G. resinaceum remains unexplored. Here, we present the complete mitochondrial genome of G. resinaceum, which spans 67,458 bp and has a GC content of 25.65%. This genome encompasses 15 core protein-coding genes, 8 independent ORFs, 15 intronic ORFs, 27 tRNAs, and 2 rRNA genes. Through phylogenetic analysis using Bayesian inference (BI), we elucidated the evolutionary relationships among 34 Basidiomycota fungi, revealing distinct clades and indicating a close relationship between G. resinaceum and G. subamboinense.

Mitogenomics, phylogeny and morphology reveal two new entomopathogenic species of Ophiocordyceps (Ophiocordycipitaceae, Hypocreales) from south-western China

Ophiocordyceps encompasses over 300 species, demonstrating a wide range of morphological features, hosts and habitats within its species diversity. In this study, two novel species in Ophiocordyceps were revealed parasitising Hepialidae larva buried in soil. Ophiocordycepsalbastroma was morphologically characterised by white stromata, solitary and cylindrical conidiogenous cells and smooth ovoid or ellipsoidal conidia. Ophiocordycepsnigristroma was characterised by woody and dark brown stromata, monophialidic, swollen base and lageniform conidiogenous cells and smooth fusiform or oval conidia. The two new species formed a separate clade, respectively, based on the phylogenetic analyses of a combined dataset including nrSSU, nrLSU, rpb1, rpb2, and tef-1α, as well as a dataset of mitochondrial 14 protein coding genes (PCGs). They were all closely grouped with O.sinensis. The mitochondrial genomes of them were first reported. Their mitogenomes were all typical of circular molecules, with positive AT and GC skew, similar GC content, similar genetic composition, similar codon usage and conservative gene positions. However, the length of the mitogenomes varied. Changes in the length of the genes were the leading cause of changes in the length of mitochondrial genome of Ophiocordyceps. The discovery and identification of new Ophiocordyceps species and analysis their mitochondrial genomes may serve as foundations for phylogeny and diversity research within the genus Ophiocordyceps.

Characterization and phylogenetic analysis of the Talaromyces liani (kamyschko) Yilmaz, Frisvad & Samson, 2014 (Eurotiales: trichocomaceae) mitochondrial genome

The filamentous fungus Talaromyces liani (Kamyschko) Yilmaz, Frisvad & Samson, 2014, has attracted considerable interest in biotechnology due to its diverse industrial applications and physiological characteristics. However, the mitochondrial genome of T. liani remains uncharacterized. Here, we present the complete mitochondrial genome of T. liani, comprising 38,000 bp with a GC content of 24.61%. This genome includes 15 core protein-coding genes, 4 independent ORFs, 6 intronic ORFs, 26 tRNAs, and 2 rRNA genes. Phylogenetic analysis using Bayesian inference (BI) revealed the evolutionary relationships among 15 fungi from Eurotiales, strongly supporting distinct clades and indicating that T. liani most closely related to T. pinophilus.

Complete genome of the Medicago anthracnose fungus, Colletotrichum destructivum, reveals a mini-chromosome-like region within a core chromosome

Colletotrichum destructivum (Cd) is a phytopathogenic fungus causing significant economic losses on forage legume crops (Medicago and Trifolium species) worldwide. To gain insights into the genetic basis of fungal virulence and host specificity, we sequenced the genome of an isolate from Medicago sativa using long-read (PacBio) technology. The resulting genome assembly has a total length of 51.7 Mb and comprises ten core chromosomes and two accessory chromosomes, all of which were sequenced from telomere to telomere. A total of 15, 631 gene models were predicted, including genes encoding potentially pathogenicity-related proteins such as candidate-secreted effectors (484), secondary metabolism key enzymes (110) and carbohydrate-active enzymes (619). Synteny analysis revealed extensive structural rearrangements in the genome of Cd relative to the closely related Brassicaceae pathogen, Colletotrichum higginsianum. In addition, a 1.2 Mb species-specific region was detected within the largest core chromosome of Cd that has all the characteristics of fungal accessory chromosomes (transposon-rich, gene-poor, distinct codon usage), providing evidence for exchange between these two genomic compartments. This region was also unique in having undergone extensive intra-chromosomal segmental duplications. Our findings provide insights into the evolution of accessory regions and possible mechanisms for generating genetic diversity in this asexual fungal pathogen.

Characterization of the complete mitochondrial genome of Mucor indicus Lendn. 1930 (Mucorales: Mucoraceae), isolated from the wine fermentation system

Mucor indicus Lendn. 1930 has been widely used in food fermentation; however, its mitochondrial genome characteristics are not well understood. In this study, the complete mitochondrial genome of M. indicus was obtained, which was 61,400 bp in length with a GC content of 33%. The M. indicus mitochondrial genome was found to contain 14 core protein-coding genes, four free-standing ORFs, 18 intronic ORFs, 26 tRNAs, and two rRNA genes. Phylogenetic trees were generated for 25 early-differentiated fungi using the Bayesian inference (BI) method, which demonstrated that M. indicus is closely related to Mucor piriformis. This study provides useful information for the classification and evolution of Mucor species or other early-differentiated fungi.

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 Penicillium expansum: Insights into the fungal evolution and phylogeny

Penicillium expansum is an important phytopathogenic fungus that causes blue mold disease. In this study, the novel mitochondrial genome of P. expansum was sequenced, assembled, annotated, and compared with the previously published Penicillium mitogenomes. P. expansum mitogenome is composed of circular DNA molecules with a genome size of 25,496 bp. It encodes 16 protein-encoding genes (PCGs), two rRNA genes, and 25 tRNA genes. Comparative analysis with six other Penicillium species revealed that gene length, GC content, AT skew, and GC skew were variable among the core protein-coding genes. The Penicillium species' gene synteny analysis identified several gene rearrangements. Among the core 15 PCGs, atp8 had the lowest K2P genetic distance, which shows that this gene is highly conserved. The Ka/Ks value of most PCGs was less than 1, which shows that these genes have undergone purifying selection. Phylogenetic analysis based on 14 concatenated core mitochondrial genes revealed that P. expansum shares a close relationship with P. solitum. This study served as a first report on the complete mitochondrial genome of P. expansum and its comparative analysis that will contribute to population genetics and rapid evolutionary studies among Penicillium species.

Mitochondrial genomic characteristics and phylogenetic analysis of a brewing fungus, Rhizopus microsporus Tiegh. 1875 (Mucorales: Rhizopodaceae)

Rhizopus microsporus Tiegh. 1875 is widely used in a variety of industries, such as brewing, wine making, baking, and medicine production, as it has the capability to break down proteins and generate surface-active agents. To date, the mitochondrial genome features of early evolved fungi from the Rhizopus genus have not been extensively studied. Our research obtained a full mitochondrial genome of R. microsporus species, which was 43,837 bp in size and had a GC content of 24.93%. This genome contained 14 core protein-coding genes, 3 independent ORFs, 7 intronic ORFs, 24 tRNAs, and 2 rRNA genes. Through the use of the BI phylogenetic inference method, we were able to create phylogenetic trees for 25 early differentiation fungi which strongly supported the major clades; this indicated that R. microsporus is most closely related to Rhizopus oryzae.

Mitogenome evolution in Trichoderma afroharzianum strains: for a better understanding of distinguishing genus

Trichoderma afroharzianum (Hypocreales) is known as an important mycoparasite and biocontrol fungus and feeds on fungal material by parasitizing other fungi. Recent studies indicate that this species is also an ear rot pathogen in Europe. Here, the complete mitochondrial genome of three T. afroharzianum strains was sequenced using next-generation sequencing and comparatively characterized by the reported Trichoderma mitogenomes. T. afroharzianum mitogenomes were varying between 29 511 bp and 29 517 bp in length, with an average A + T content of 72.32%. These mitogenomes contain 14 core protein coding genes (PCGs), 22 tRNAs, two rRNAs, one gene encoding the ribosomal protein S3, and three or four genes including conserved domains for the homing endonucleases (HEGs; GIY-YIG type and LAGLIDADG type). All PCGs are initiated by ATG codons, except for atp8, and all are terminated with TAA. A significant correlation was observed between nucleotide composition and codon preference. Four introns belonging to the group I intron class were predicted, accounting for about 14.54% of the size of the mitogenomes. Phylogenetic analyses confirmed the positions of T. afroharzianum strains within the genus of Trichoderma and supported a sister group relationship between T. afroharzianum and T. simmonsii. The recovered trees also supported the monophyly of all included families and of the genus of Acremonium. The characterization of mitochondrial genome of T. afroharzianum contributes to the understanding of phylogeny and evolution of Hypocreales.

First telomere-to-telomere gapless assembly of the rice blast fungus Pyricularia oryzae

Rice blast caused by Pyricularia oryzae (syn., Magnaporthe oryzae) was one of the most destructive diseases of rice throughout the world. Genome assembly was fundamental to genetic variation identification and critically impacted the understanding of its ability to overcome host resistance. Here, we report a gapless genome assembly of rice blast fungus P. oryzae strain P131 using PacBio, Illumina and high throughput chromatin conformation capture (Hi-C) sequencing data. This assembly contained seven complete chromosomes (43,237,743 bp) and a circular mitochondrial genome (34,866 bp). Approximately 14.31% of this assembly carried repeat sequences, significantly greater than its previous assembled version. This assembly had a 99.9% complement in BUSCO evaluation. A total of 14,982 genes protein-coding genes were predicted. In summary, we assembled the first telomere-to-telomere gapless genome of P. oryzae, which would be a valuable genome resource for future research on the genome evolution and host adaptation.

The Mitogenomic Characterization and Phylogenetic Analysis of the Plant Pathogen Phyllosticta yuccae

Phyllosticta yuccae is an important plant pathogen causing leaf spot disease in Yucca gigantea Lem. It is imperative to note that the amount of information available about the mitogenome of this subject is severely limited. This must be addressed immediately, as it is crucial to our understanding and progress in this field. To better understand the mitogenomic characteristics of P. yuccae, we conducted its sequencing by MGISEQ. Afterwards, the mitogenome was assembled and annotated. The mitogenomic characteristics and phylogenetic placement of the P. yuccae strain KUMCC 6213 were analyzed. The study revealed that the mitogenome of P. yuccae is a circular DNA molecule, consisting of 178,540 base pairs. It contains a total of 64 genes, including 14 protein-coding genes (PCGs), 26 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 22 open reading frame genes (ORF), accounting for 80.98% of the total size. Repetitive sequences accounted for 15.42% of the mitogenome. The analysis of codon usage indicated that the codon UUA was the most commonly utilized, whereas the amino acid Leu was the most frequently employed. A comparative analysis of mitogenomes between P. yuccae and Macrophomina phaseolina (Tassi) Goid. showed notable variations in the position and size of gene clusters, with cox1, nad4, and nad4L genes exhibiting relatively low conservation. Phylogenetic analysis based on the 14 PCGs revealed that P. yuccae has the closest genetic relationship with M. phaseolina (Botryosphaeriaceae, Botryosphaeriales). This study first reports the mitogenome of P. yuccae and validates its phylogenetic placement. The findings enhance the knowledge of mitogenomes in Botryosphaeriales, offering novel perspectives on the genetics and evolution of the plant pathogen P. yuccae. This is crucial for the accurate prevention and management of leaf spot disease in Y. gigantea.

Characterization of Complete Mitochondrial Genomes of the Five Peltigera and Comparative Analysis with Relative Species

In the present study, the complete mitochondrial genomes of five Peltigera species (Peltigera elisabethae, Peltigera neocanina, Peltigera canina, Peltigera ponojensis, Peltigera neckeri) were sequenced, assembled and compared with relative species. The five mitogenomes were all composed of circular DNA molecules, and their ranged from 58,132 bp to 69,325 bp. The mitochondrial genomes of the five Peltigera species contain 15 protein-coding genes (PCGs), 2 rRNAs, 26-27 tRNAs and an unidentified open reading frame (ORF). The PCG length, AT skew and GC skew varied among the 15 PCGs in the five mitogenomes. Among the 15 PCGs, cox2 had the least K2P genetic distance, indicating that the gene was highly conserved. The synteny analysis revealed that the coding regions were highly conserved in the Peltigera mitochondrial genomes, but gene rearrangement occurred in the intergenic regions. The phylogenetic analysis based on the 14 PCGs showed that the 11 Peltigera species formed well-supported topologies, indicating that the protein-coding genes in the mitochondrial genome may be used as a reliable molecular tool in the study of the phylogenetic relationship of Peltigera.

Miniature RNAs are embedded in an exceptionally protein-rich mitoribosome via an elaborate assembly pathway

The mitochondrial ribosome (mitoribosome) has diverged drastically from its evolutionary progenitor, the bacterial ribosome. Structural and compositional diversity is particularly striking in the phylum Euglenozoa, with an extraordinary protein gain in the mitoribosome of kinetoplastid protists. Here we report an even more complex mitoribosome in diplonemids, the sister-group of kinetoplastids. Affinity pulldown of mitoribosomal complexes from Diplonema papillatum, the diplonemid type species, demonstrates that they have a mass of > 5 MDa, contain as many as 130 integral proteins, and exhibit a protein-to-RNA ratio of 11:1. This unusual composition reflects unprecedented structural reduction of ribosomal RNAs, increased size of canonical mitoribosomal proteins, and accretion of three dozen lineage-specific components. In addition, we identified >50 candidate assembly factors, around half of which contribute to early mitoribosome maturation steps. Because little is known about early assembly stages even in model organisms, our investigation of the diplonemid mitoribosome illuminates this process. Together, our results provide a foundation for understanding how runaway evolutionary divergence shapes both biogenesis and function of a complex molecular machine.

Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction

Compared to nuclear genomes, mitochondrial genomes (mitogenomes) are small and usually code for only a few dozen genes. Still, identifying genes and their structure can be challenging and time-consuming. Even automated tools for mitochondrial genome annotation often require manual analysis and curation by skilled experts. The most difficult steps are (i) the structural modelling of intron-containing genes; (ii) the identification and delineation of Group I and II introns; and (iii) the identification of moderately conserved, non-coding RNA (ncRNA) genes specifying 5S rRNAs, tmRNAs and RNase P RNAs. Additional challenges arise through genetic code evolution which can redefine the translational identity of both start and stop codons, thus obscuring protein-coding genes. Further, RNA editing can render gene identification difficult, if not impossible, without additional RNA sequence data. Current automated mito- and plastid-genome annotators are limited as they are typically tailored to specific eukaryotic groups. The MFannot annotator we developed is unique in its applicability to a broad taxonomic scope, its accuracy in gene model inference, and its capabilities in intron identification and classification. The pipeline leverages curated profile Hidden Markov Models (HMMs), covariance (CMs) and ERPIN models to better capture evolutionarily conserved signatures in the primary sequence (HMMs and CMs) as well as secondary structure (CMs and ERPIN). Here we formally describe MFannot, which has been available as a web-accessible service (https://megasun.bch.umontreal.ca/apps/mfannot/) to the research community for nearly 16 years. Further, we report its performance on particularly intron-rich mitogenomes and describe ongoing and future developments.

The first two mitochondrial genomes from Apiotrichum reveal mitochondrial evolution and different taxonomic assignment of Trichosporonales

Apiotrichum is a diverse anamorphic basidiomycetous yeast genus, and its mitogenome characterization has not been revealed. In this study, we assembled two Apiotrichum mitogenomes and compared them with mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. The mitogenomes of Apiotrichum gracile and A. gamsii comprised circular DNA molecules, with sizes of 34,648 bp and 38,096 bp, respectively. Intronic regions were found contributed the most to the size expansion of A. gamsii mitogenome. Comparative mitogenomic analysis revealed that 6.85-38.89% of nucleotides varied between tRNAs shared by the two Apiotrichum mitogenomes. The GC content of all core PCGs in A. gamsii was lower than that of A. gracile, with an average low value of 4.97%. The rps3 gene differentiated the most among Agaricomycotina, Pucciniomycotina and Ustilaginomycotina species, while nad4L gene was the most conserved in evolution. The Ka/Ks values for cob and rps3 genes were > 1, indicating the two genes may be subjected to positive selection in Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. Frequent intron loss/gain events and potential intron transfer events have been detected in evolution of Agaricomycotina, Pucciniomycotina and Ustilaginomycotina. We further detected large-scale gene rearrangements between the 19 mitogenomes from Agaricomycotina, Pucciniomycotina and Ustilaginomycotina, and fifteen of the 17 mitochondrial genes shared by Apiotrichum varied in gene arrangements. Phylogenetic analyses based on maximum likelihood and Bayesian inference methods using a combined mitochondrial gene dataset revealed different taxonomic assignment of two Apiotrichum species, wherein A. gamsii had a more closely relationship with Trichosporon asahii. This study served as the first report on mitogenomes from the genus Apiotrichum, which promotes the understanding of evolution, genomics, and phylogeny of Apiotrichum.

Phylogenomics and taxon-rich phylogenies of new and historical specimens shed light on the systematics of Hypnea (Cystocloniaceae, Rhodophyta)

Cystocloniacae is a highly diverse family of Rhodophyta, including species of ecological and economic importance, whose phylogeny remains largely unresolved. Species delimitation is unclear, particularly in the most speciose genus, Hypnea, and cryptic diversity has been revealed by recent molecular assessments, especially in the tropics. Here, we carried out the first phylogenomic investigation of Cystocloniaceae, focused on the genus Hypnea, inferred from chloroplast and mitochondrial genomes including taxa sampled from new and historical collections. In this work, molecular synapomorphies (gene losses, InDels and gene inversions) were identified to better characterize clades in our congruent organellar phylogenies. We also present taxon-rich phylogenies based on plastid and mitochondrial markers. Molecular and morphological comparisons of historic collections with contemporary specimens revealed the need for taxonomic updates in Hypnea, the synonymization of H. marchantae to a later heterotypic synonym of H. cervicornis and the description of three new species: H. davisiana sp. nov., H. djamilae sp. nov. and H. evaristoae sp. nov.

Mitochondrial characteristics of the powdery mildew genus Erysiphe revealed an extraordinary evolution in protein-coding genes

The genus Erysiphe was an obligate parasite causing powdery mildew disease on a wide range of higher plants. However, the knowledge of their mitogenome architecture for lifestyle adaptability was scarce. Here, we assembled the first complete mitogenome (190,559 bp in size) for rubber tree powdery mildew pathogen Erysiphe quercicola. Comparable analysis of the Erysiphe mitogenomes exhibited conserved gene content, genome organization and codon usage bias, but extensive dynamic intron gain/loss events were presented between Erysiphe species. The phylogeny of the Ascomycota species constructed in the phylogenetic analysis showed genetic divergences of the Erysiphe species. Compared with other distant saprophytic and plant pathogenic fungi, Erysiphe had a flat distribution of evolutionary pressures on fungal standard protein-coding genes (PCGs). The Erysiphe PCGs had the highest mean selection pressure. In particular, Erysiphe's cox1, nad1, cob and rps3 genes had the most elevated selection pressures among corresponding PCGs across fungal genera. Altogether, the investigations provided a novel insight into the potential evolutionary pattern of the genus Erysiphe to adapt obligate biotrophic lifestyle and promoted the understanding of the high plasticity and population evolution of fungal mitogenomes.

Morphology, phylogeny, mitogenomics and metagenomics reveal a new entomopathogenic fungus Ophiocordycepsnujiangensis (Hypocreales, Ophiocordycipitaceae) from Southwestern China

Ophiocordyceps contains the largest number of Cordyceps sensu lato, various species of which are of great medicinal value. In this study, a new entomopathogenic fungus, Ophiocordycepsnujiangensis, from Yunnan in southwestern China, was described using morphological, phylogenetic, and mitogenomic evidence, and its fungal community composition was identified. It was morphologically characterized by a solitary, woody, and dark brown stromata, smooth-walled and septate hyphae, solitary and gradually tapering conidiogenous cells with plenty of warty protrusions, and oval or fusiform conidia (6.4-11.2 × 3.7-6.4 µm) with mucinous sheath. The phylogenetic location of O.nujiangensis was determined based on the Bayesian inference (BI) and the maximum likelihood (ML) analyses by concatenating nrSSU, nrLSU, tef-1a, rpb1, and rpb2 datasets, and ten mitochondrial protein-coding genes (PCGs) datasets (atp6, atp9, cob, cox2, nad1, nad2, nad3, nad4, nad4L, and nad5). Phylogenetic analyses revealed that O.nujiangensis belonged to the Hirsutellasinensis subclade within the Hirsutella clade of Ophiocordyceps. And O.nujiangensis was phylogenetically clustered with O.karstii, O.liangshanensis, and O.sinensis. Simultaneously, five fungal phyla and 151 fungal genera were recognized in the analysis of the fungal community of O.nujiangensis. The fungal community composition differed from that of O.sinensis, and differences in the microbial community composition of closely related species might be appropriate as further evidence for taxonomy.

Mechanisms and players of mitoribosomal biogenesis revealed in trypanosomatids

Translation in mitochondria is mediated by mitochondrial ribosomes, or mitoribosomes, complex ribonucleoprotein machines with dual genetic origin. Mitoribosomes in trypanosomatid parasites diverged markedly from their bacterial ancestors and other eukaryotic lineages in terms of protein composition, rRNA content, and overall architecture, yet their core functional elements remained conserved. Recent cryo-electron microscopy studies provided atomic models of trypanosomatid large and small mitoribosomal subunits and their precursors, making these parasites the organisms with the best-understood biogenesis of mitoribosomes. The structures revealed molecular mechanisms and players involved in the assembly of mitoribosomes not only in the parasites, but also in eukaryotes in general.

Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements

Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 Å resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway. Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3' rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria.

The first two mitochondrial genomes for the genus Ramaria reveal mitochondrial genome evolution of Ramaria and phylogeny of Basidiomycota

In the present study, we assembled and analyzed the mitogenomes of two Ramaria species. The assembled mitogenomes of Ramaria cfr. rubripermanens and R. rubella were circularized, with sizes of 126,497 bp and 143,271 bp, respectively. Comparative mitogenome analysis showed that intron region contributed the most (contribution rate, 43.74%) to the size variations of Ramaria mitogenomes. The genetic contents, gene length, tRNAs, and codon usages of the two Ramaria mitogenomes varied greatly. In addition, the evolutionary rates of different core protein coding genes (PCGs) in Phallomycetidae mitogenomes varied. We detected large-scale gene rearrangements between Phallomycetidae mitogenomes, including gene displacement and tRNA doubling. A total of 4499 bp and 7746 bp aligned fragments were detected between the mitochondrial and nuclear genomes of R. cfr. rubripermanens and R. rubella, respectively, indicating possible gene transferring events. We further found frequent intron loss/gain and potential intron transfer events in Phallomycetidae mitogenomes during the evolution, and the mitogenomes of R. rubella contained a novel intron P44. Phylogenetic analyses using both Bayesian inference (BI) and Maximum Likelihood (ML) methods based on a combined mitochondrial gene dataset obtained an identical and well-supported phylogenetic tree for Basidiomycota, wherein R. cfr. rubripermanens and Turbinellus floccosus are sister species. This study served as the first report on mitogenomes from the genus Ramaria, which provides a basis for understanding the evolution, genetics, and taxonomy of this important fungal group.

Comparative Mitogenomic Analysis Reveals Intraspecific, Interspecific Variations and Genetic Diversity of Medical Fungus Ganoderma

Ganoderma species are widely distributed in the world with high diversity. Some species are considered to be pathogenic fungi while others are used as traditional medicine in Asia. In this study, we sequenced and assembled four Ganoderma complete mitogenomes, including G. subamboinense s118, G. lucidum s37, G. lingzhi s62, and G. lingzhi s74. The sizes of the four mitogenomes ranged from 50,603 to 73,416 bp. All Ganoderma specimens had a full set of core protein-coding genes (PCGs), and the rps3 gene of Ganoderma species was detected to be under positive or relaxed selection. We found that the non-conserved PCGs, which encode RNA polymerases, DNA polymerases, homing endonucleases, and unknown functional proteins, are dynamic within and between Ganoderma species. Introns were thought to be the main contributing factor in Ganoderma mitogenome size variation (p < 0.01). Frequent intron loss/gain events were detected within and between Ganoderma species. The mitogenome of G. lucidum s26 gained intron P637 in the cox3 gene compared with the other two G. lucidum mitogenomes. In addition, some rare introns in Ganoderma were detected in distinct Basidiomycetes, indicating potential gene transfer events. Comparative mitogenomic analysis revealed that gene arrangements also varied within and between Ganoderma mitogenomes. Using maximum likelihood and Bayesian inference methods with a combined mitochondrial gene dataset, phylogenetic analyses generated identical, well-supported tree topologies for 71 Agaricomycetes species. This study reveals intraspecific and interspecific variations of the Ganoderma mitogenomes, which promotes the understanding of the origin, evolution, and genetic diversity of Ganoderma species.

Draft Genome Sequence of Purpureocillium takamizusanense, a Potential Bioinsecticide

To investigate the biocontrol capability of the entomopathogenic fungus Purpureocillium takamizusanense , the genome of the wild-type strain isolated from synnemata on Meimuna opalifera , was sequenced using a combination of HiSeq and Nanopore technologies, and annotated using evidence from RNA sequences and protein sequences from its sister species Purpureocillium lilacinum .

The mitochondrial genome of a wild edible mushroom, Russula rosea

Russula rosea is a common wild edible ectomycorrhizal fungus, which is widely distributed all over the world. We assembled the complete mitochondrial genome of R. rosea with the total length was 54177 bp and the GC content of 22.34%. It contains a total of 57 genes, including 14 standard protein-coding genes, one conserved ribosomal protein S3 gene (rps3), two rRNA genes, 24 tRNA genes, 15 free-standing open reading frames (ORFs) and one DNA polymerase gene (dpo). Mitochondrial genome found a close evolutionary relationship between Russula rosea and Russula lepida, which was helpful to study the genetic evolutionary relationship of edible fungi.

First two mitochondrial genomes for the order Filobasidiales reveal novel gene rearrangements and intron dynamics of Tremellomycetes

In the present study, two mitogenomes from the Filobasidium genus were assembled and compared with other Tremellomycetes mitogenomes. The mitogenomes of F. wieringae and F. globisporum both comprised circular DNA molecules, with sizes of 27,861 bp and 71,783 bp, respectively. Comparative mitogenomic analysis revealed that the genetic contents, tRNAs, and codon usages of the two Filobasidium species differed greatly. The sizes of the two Filobasidium mitogenomes varied greatly with the introns being the main factor contributing to mitogenome expansion in F. globisporum. Positive selection was observed in several protein-coding genes (PCGs) in the Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina species, including cob, cox2, nad2, and rps3 genes. Frequent intron loss/gain events were detected to have occurred during the evolution of the Tremellomycetes mitogenomes, and the mitogenomes of 17 species from Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina have undergone large-scale gene rearrangements. Phylogenetic analyses based on Bayesian inference and the maximum likelihood methods using a combined mitochondrial gene set generated identical and well-supported phylogenetic trees, wherein Filobasidium species had close relationships with Trichosporonales species. This study, which is the first report on mitogenomes from the order Filobasidiales, provides a basis for understanding the genomics, evolution, and taxonomy of this important fungal group.

Comparative mitochondrial genome analyses reveal conserved gene arrangement but massive expansion/contraction in two closely related Exserohilum pathogens

Exserohilum turcicum and E. rostratum, two closely related fungal species, are both economically important pathogens but have quite different target hosts (specific to plants and cross-kingdom infection, respectively). In the present study, complete circular mitochondrial genomes of the two Exserohilum species were sequenced and de novo assembled, which 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). Comparative analyses indicated that these two fungi had significant mitogenomic collinearity and consistent mitochondrial gene arrangement, yet with vastly different mitogenome sizes, 264,948 bp and 64,620 bp, respectively. By contrast with the 17 introns containing 17 intronic ORFs (one-to-one) in the E. rostratum mitogenome, E. turcicum involved far more introns (70) and intronic ORFs (126), which was considered as the main contributing factors of their mitogenome expansion/contraction. Within the generally intron-rich gene cox1, a total of 18 and 10 intron position classes (Pcls) were identified separately in the two mitogenomes. Moreover, 16.16% and 10.85% ratios of intra-mitogenomic repetitive regions were detected in E. turcicum and E. rostratum, respectively. Based on the combined mitochondrial gene dataset, we established a well-supported topology of phylogeny tree of 98 ascomycetes, implying that mitogenomes may act as an effective molecular marker for fungal phylogenetic reconstruction. Our results served as the first report on mitogenomes in the genus Exserohilum, and would have significant implications in understanding the origin, evolution and pathogenic mechanisms of this fungal lineage.

Characterization of the complete mitochondrial genome of Aspergillus terricola (Aspergillaceae, Eurotiales), isolated from soy sauce fermentation system

In the present study, the complete mitochondrial genome of Aspergillus terricola É.J. Marchal 1893 was sequenced and assembled. The mitochondrial genome of A. terricola was composed of circular DNA molecules, with a total size of 28,689 bp. The GC content of the A. terricola mitochondrial genome was 26.34%. A total of 18 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, and 26 transfer RNA (tRNA) genes were detected in the A. terricola mitochondrial genome. Phylogenetic analysis based on the combined mitochondrial gene dataset indicated that the A. terricola exhibited a close relationship with A. parasiticus.

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.

Mitochondrial Genomics of Six Cacao Pathogens From the Basidiomycete Family Marasmiaceae

Thread blight disease has recently been described as an emerging disease on cacao (Theobroma cacao) in Ghana. In Ghana, thread blight disease is caused by multiple species of the Marasmiaceae family: Marasmius tenuissimus, M. crinis-equi, M. palmivorus, and Marasmiellus scandens. Interestingly, two additional members of the Marasmiaceae; Moniliophthora roreri (frosty pod rot) and Moniliophthora perniciosa (witches’ broom disease), are major pathogens of cacao in the Western hemisphere. It is important to accurately characterize the genetic relationships among these economically important species in support of their disease management. We used data from Illumina NGS-based genome sequencing efforts to study the mitochondrial genomes (mitogenomes) of the four cacao thread blight associated pathogens from Ghana and compared them with published mitogenomes of Mon. roreri and Mon. perniciosa. There is a remarkable interspecies variation in mitogenome size within the six cacao-associated Marasmiaceae species, ranging from 43,121 to 109,103 bp. The differences in genome lengths are primarily due to the number and lengths of introns, differences in intergenic space, and differences in the size and numbers of unidentified ORFs (uORF). Among seven M. tenuissimus mitogenomes sequenced, there is variation in size and sequence pointing to divergent evolution patterns within the species. The intronic regions show a high degree of sequence variation compared to the conserved sequences of the 14 core genes. The intronic ORFs identified, regardless of species, encode GIY-YIG or LAGLIDADG domain-containing homing endonuclease genes. Phylogenetic relationships using the 14 core proteins largely mimic the phylogenetic relationships observed in gene order patterns, grouping M. tenuissimus with M. crinis-equi, and M. palmivorus with Mon. roreri and Mon. perniciosa, leaving Mar. scandens as an outlier. The results from this study provide evidence of independent expansion/contraction events and sequence diversification in each species and establish a foundation for further exploration of the evolutionary trajectory of the fungi in Marasmiaceae family.

Mitogenome-wide comparison and phylogeny reveal group I intron dynamics and intraspecific diversification within the phytopathogen Corynespora cassiicola

Corynespora cassiicola, the causal agent of an extensive range of plant diseases worldwide, is a momentous fungus with diverse lifestyles and rich in intraspecies variations. In the present study, a total of 56 mitochondrial genomes of C. cassiicola were assembled (except two available online) and analyzed, of which 16 mitogenomes were newly sequenced here. All these circular mitochondrial DNA (mtDNA) molecules, ranging from 39,223 bp to 45,786 bp in length, comprised the same set of 13 core protein-coding genes (PCGs), two rRNAs and 27 tRNAs arranged in identical order. Across the above conserved genes, nad3 had the largest genetic distance between different isolates and was possibly subjected to positive selection pressure. Comparative mitogenomic analysis indicated that seven group I (IB, IC1, and IC2) introns with a length range of 1013-1876 bp were differentially inserted in three core PCGs (cox1, nad1, and nad5), resulting in the varied mitogenome sizes among C. cassiicola isolates. In combination with dynamic distribution of the introns, a well-supported mitogenome-wide phylogeny of the 56 C. cassiicola isolates revealed eight phylogenetic groups, which only had weak correlations with host range and toxin class. Different groups of isolates exhibited obvious differences in length and GC content of some genes, while a degree of variance in codon usage and tRNA structure was also observed. This research served as the first report on mitogenomic comparisons within C. cassiicola, and could provide new insights into its intraspecific microevolution and genetic diversity.

The complete mitochondrial genome of Ophiocordyceps gracilis and its comparison with related species

In this study, the complete mitochondrial genome of O. gracilis was sequenced and assembled before being compared with related species. As the second largest mitogenome reported in the family Ophiocordycipitaceae, the mitogenome of O. gracilis (voucher OG201301) is a circular DNA molecule of 134,288 bp that contains numerous introns and longer intergenomic regions. UCA was detected as anticodon in tRNA-Sec of O. gracilis, while comparative mitogenome analysis of nine Ophiocordycipitaceae fungi indicated that the order and contents of PCGs and rRNA genes were considerably conserved and could descend from a common ancestor in Ophiocordycipitaceae. In addition, the expansion of mitochondrial organization, introns, gene length, and order of O. gracilis were determined to be similar to those of O. sinensis, which indicated common mechanisms underlying adaptive evolution in O. gracilis and O. sinensis. Based on the mitochondrial gene dataset (15 PCGs and 2 RNA genes), a close genetic relationship between O. gracilis and O. sinensis was revealed through phylogenetic analysis. This study is the first to investigate the molecular evolution, phylogenetic pattern, and genetic structure characteristics of mitogenome in O. gracilis. Based on the obtained results, the mitogenome of O. gracilis can increase understanding of the genetic diversity and evolution of cordycipitoid fungi.

The first complete mitochondrial genome of mushroom Leucoagaricus naucinus (Agaricaceae, Agaricales) and insights into its phylogeny

Leucoagaricus naucinus (Fr.) Singer is a mycorrhizal fungus widely distributed in the northern Hemisphere. In the present study, the complete mitochondrial genome of Leucoagaricus naucinus was sequenced, assembled, and annotated. The L. naucinus mitochondrial genome was composed of circular DNA molecules, with the total size of 61,434 bp. The GC content of the L. naucinus mitochondrial genome was 26.07%. A total of 30 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 26 transfer RNA (tRNA) genes were detected in the L. naucinus mitochondrial genome. Phylogenetic analysis based on combined mitochondrial gene dataset indicated that the L. naucinus exhibited a close relationship with Agaricus bisporus.

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

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

The first complete mitochondrial genome of edible and medicinal fungus Chroogomphus rutilus (Gomphidiaceae, Boletales) and insights into its phylogeny

In the present study, we assembled and annotated the complete mitochondrial genome of Chroogomphus rutilus. The complete mitochondrial genome of C. rutilus was composed of circular DNA molecules, with a size of 37,508 bp. The GC content of the C. rutilus mitogenome was 22.82%. A total of 18 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, and 24 transfer RNA (tRNA) genes were detected in the C. rutilus mitogenome. Phylogenetic analysis based on combined mitochondrial gene dataset indicated that the C. rutilus exhibited a close relationship with species from the genus Rhizopogon. This study served as the first report on the complete mitochondrial genome from the family Gomphidiaceae, which will promote the understanding of phylogeny, evolution, and taxonomy of this important fungal species.

The first complete mitochondrial genome of Macalpinomyces bursus (Ustilaginales: Ustilaginaceae) and insights into its phylogeny

In the present study, the complete mitochondrial genome of Macalpinomyces bursus (Berk.) Vanky 2002 was sequenced and assembled. The complete mitochondrial genome of M. bursus was 49,024 bp in length, with the GC content of 30.4%. The M. bursus mitochondrial genome contained 27 protein-coding genes, 2 ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. Phylogenetic analysis based on combined mitochondrial gene dataset indicated that the M. bursus exhibited a close relationship with species from the genera Ustilago, Sporisorium, and Anthracocystis.

An Update on Trichoderma Mitogenomes: Complete De Novo Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma harzianum (Hypocreales, Sordariomycetes), an Ex-Neotype Strain CBS 226.95, and Tracing the Evolutionary Divergences of Mitogenomes in Trichoderma

Members of the genus Trichoderma (Hypocreales), widely used as biofungicides, biofertilizers, and as model fungi for the industrial production of CAZymes, have actively been studied for the applications of their biological functions. Recently, the study of the nuclear genomes of Trichoderma has expanded in the directions of adaptation and evolution to gain a better understanding of their ecological traits. However, Trichoderma's mitochondria have received much less attention despite mitochondria being the most necessary element for sustaining cell life. In this study, a mitogenome of the fungus Trichoderma harzianum CBS 226.95 was assembled de novo. A 27,632 bp circular DNA molecule was revealed with specific features, such as the intronless of all core PCGs, one homing endonuclease, and a putative overlapping tRNA, on a closer phylogenetic relationship with T. reesei among hypocrealean fungi. Interestingly, the mitogenome of T. harzianum CBS 226.95 was predicted to have evolved earlier than those of other Trichoderma species and also assumed with a selection pressure in the cox3. Considering the bioavailability, both for the ex-neotype strain of the T. harzianum species complex and the most globally representative commercial fungal biocontrol agent, our results on the T. harzianum CBS 226.95 mitogenome provide crucial information which will be helpful criteria in future studies on Trichoderma.

Mitogenomics, Phylogeny and Morphology Reveal Ophiocordyceps pingbianensis Sp. Nov., an Entomopathogenic Fungus from China

The new entomopathogenic fungus Ophiocordyceps pingbianensis, collected from Southeast China, was described by mitogenomic, morphological, and phylogenetic evidence. The systematic position of O. pingbianensis was determined by phylogenetic analyses based on six nuclear gene (ITS, tef1-α, nrSSU, nrLSU, rpb1 and rpb2) and 14 mitochondrial protein-coding gene (PCGs) (cox1, cox2, cox3, atp6, atp8, atp9, cob, nad1, nad2, nad3, nad4, nad5, nad6 and nad4L) data. Phylogenetic analyses reveal that O. pingbianensis was belonged to the Hirsutella nodulosa clade in the genus Ophiocordyceps of Ophiocordycipiaceae. This fungus exhibits distinctive characteristics which differed from other related Ophiocordyceps species with slender and geminate stromata, monophialidic conidiogenous cells with an inflated awl-shaped base, a twisty and warty phialide neck and a fusiform or oval conidia, as well as being found on a tiger beetle of Coleoptera buried in moss at the cave. The complete mitochondrial genome of O. pingbianensis was a circular DNA molecule 80,359 bp in length, containing 15 PCGs, 24 open reading frames genes (ORFs), 25 transfer RNA genes (tRNAs) and 27 introns. Ophiocordyceps pingbianensis, containing 27 introns, has the second largest mitogenome in Ophiocordycipiaceae and was next to O. sinensis. To our knowledge, this is the first report of the mitogenome from a new entomopathogenic fungus, and thus provides an important foundation for future studies on taxonomy, genetics and evolutionary biology of Ophiocordycipiaceae.

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.

Evolutionary Insights Into Two Widespread Ectomycorrhizal Fungi (Pisolithus) From Comparative Analysis of Mitochondrial Genomes

The genus Pisolithus is a group of global ectomycorrhizal fungi. The characterizations of Pisolithus mitochondrial genomes have still been unknown. In the present study, the complete mitogenomes of two Pisolithus species, Pisolithus microcarpus, and Pisolithus tinctorius, were assembled and compared with other Boletales mitogenomes. Both Pisolithus mitogenomes comprised circular DNA molecules with sizes of 43,990 and 44,054 bp, respectively. Comparative mitogenomic analysis showed that the rps3 gene differentiated greatly between Boletales species, and this gene may be subjected to strong pressure of positive selection between some Boletales species. Several plasmid-derived genes and genes with unknown functions were detected in the two Pisolithus mitogenomes, which needs further analysis. The two Pisolithus species show a high degree of collinearity, which may represent the gene arrangement of the ancestors of ectomycorrhizal Boletales species. Frequent intron loss/gain events were detected in Boletales and basidiomycetes, and intron P717 was only detected in P. tinctorius out of the eight Boletales mitogenomes tested. We reconstructed phylogeny of 79 basidiomycetes based on combined mitochondrial gene dataset, and obtained well-supported phylogenetic topologies. This study served as the first report on the mitogenomes of the family Pisolithaceae, which will promote the understanding of the evolution of Pisolithus species.

An Unexpectedly Complex Mitoribosome in Andalucia godoyi, a Protist with the Most Bacteria-like Mitochondrial Genome

The mitoribosome, as known from studies in model organisms, deviates considerably from its ancestor, the bacterial ribosome. Deviations include substantial reduction of the mitochondrial ribosomal RNA (mt-rRNA) structure and acquisition of numerous mitochondrion-specific (M) mitoribosomal proteins (mtRPs). A broadly accepted view assumes that M-mtRPs compensate for structural destabilization of mt-rRNA resulting from its evolutionary remodeling. Since most experimental information on mitoribosome makeup comes from eukaryotes having derived mitochondrial genomes and mt-rRNAs, we tested this assumption by investigating the mitochondrial translation machinery of jakobids, a lineage of unicellular protists with the most bacteria-like mitochondrial genomes. We report here proteomics analyses of the Andalucia godoyi small mitoribosomal subunit and in silico transcriptomic and comparative genome analyses of four additional jakobids. Jakobids have mt-rRNA structures that minimally differ from their bacterial counterparts. Yet, with at least 31 small subunit and 44 large subunit mtRPs, the mitoriboproteome of Andalucia is essentially as complex as that in animals or fungi. Furthermore, the relatively high conservation of jakobid sequences has helped to clarify the identity of several mtRPs, previously considered to be lineage-specific, as divergent homologs of conserved M-mtRPs, notably mS22 and mL61. The coexistence of bacteria-like mt-rRNAs and a complex mitoriboproteome refutes the view that M-mtRPs were ancestrally recruited to stabilize deviations of mt-rRNA structural elements. We postulate instead that the numerous M-mtRPs acquired in the last eukaryotic common ancestor allowed mt-rRNAs to pursue a broad range of evolutionary trajectories across lineages: from dramatic reduction to acquisition of novel elements to structural conservatism.

Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny

In this study, the mitogenome of Hannaella oryzae was sequenced by next-generation sequencing (NGS) and successfully assembled. The H. oryzae mitogenome comprised circular DNA molecules with a total size of 26,444 bp. We found that the mitogenome of H. oryzae partially deleted the tRNA gene transferring cysteine. Comparative mitogenomic analyses showed that intronic regions were the main factors contributing to the size variations of mitogenomes in Tremellales. Introns of the cox1 gene in Tremellales species were found to have undergone intron loss/gain events, and introns of the H. oryzae cox1 gene may have different origins. Gene arrangement analysis revealed that H. oryzae contained a unique gene order different from other Tremellales species. Phylogenetic analysis based on a combined mitochondrial gene set resulted in identical and well-supported topologies, wherein H. oryzae was closely related to Tremella fuciformis. This study represents the first report of mitogenome for the Hannaella genus, which will allow further study of the population genetics, taxonomy, and evolutionary biology of this important phylloplane yeast and other related species.