Horizontal transfer of tRNA genes to mitochondrial plasmids facilitates gene loss from fungal mitochondrial DNA.

Fungal and plant mitochondria are known to exchange DNA with retroviral plasmids. Transfer of plasmid DNA to the organellar genome is best known and occurs through wholesale insertion of the plasmid. Less well known is the transfer of organellar DNA to plasmids, in particular tRNA genes. Presently, it is unknown whether fungal plasmids can adopt mitochondrial functions such as tRNA production through horizontal gene transfer. In this paper, we studied the exchange of DNA between fungal linear plasmids and fungal mtDNA, mainly focusing on the basidiomycete family Lyophyllaceae. We report at least six independent transfers of complete tRNA genes to fungal plasmids. Furthermore, we discovered two independent cases of loss of a tRNA gene from a fungal mitochondrial genome following transfer of such a gene to a linear mitochondrial plasmid. We propose that loss of a tRNA gene from mtDNA following its transfer to a plasmid creates a mutualistic dependency of the host mtDNA on the plasmid. We also find that tRNA genes transferred to plasmids encode codons that occur at the lowest frequency in the host mitochondrial genomes, possibly due to a higher number of unused transcripts. We discuss the potential consequences of mtDNA transfer to plasmids for both the host mtDNA and the plasmid.

Genetic population structure of the agaric Blastosporella zonata (Lyophyllaceae) reveals cryptic species and different roles for sexual and asexual spores in dispersal.

Blastosporella zonata is one of the few basidiomycete fungi that produce asexual spores (conidia) on the mushroom. The role of these conidia in the fungal lifecycle is not known. We tested whether conidia are being utilized in local dispersal by looking for signatures of clonality in 21 samples from three localities separated by about three kilometres in Murillo, Colombia. To identify clonally related individuals, we sequenced three polymorphic markers at two unlinked loci (nuclear rRNA: ITS and LSU, and TEFIα) for all collections plus three herbarium samples. We identified two sets of clonally related individuals growing closely together in one of the three localities, and only one pair shared between localities. In all three localities we observed multiple non-clonally related dikaryons showing that sexual reproduction is also important. Our results indicate that the conidia on the mushroom are primarily important for local dispersal. Unexpectedly, our results also indicate two reproductively isolated populations, possibly representing cryptic biological species. Citation: Van de Peppel LJJ, Baroni TJ, Franco-Molano AE, et al. 2022. Genetic population structure of the agaric Blastosporella zonata (Lyophyllacea) reveals cryptic species and different roles for sexual and asexual spores in dispersal. Persoonia 49: 195-200. https://doi.org/10.3767/persoonia.2022.49.06.

Three new species of Calocybe (Agaricales, Basidiomycota) from northeastern China are supported by morphological and molecular data.

Three new species, Calocybe aurantiaca, C. convexa, and C. decolorata, are described based on collections made in Shenyang City, Liaoning Province, China. The main characters of C. aurantiaca are its orange-yellow sporocarps and small and smooth basidiospores. Calocybe convexa is characterized by its orange-buff pileus, very small basidiospores, and tortuous stipe, whereas C. decolorata is mainly characterized by its gills that turn blue when bruised. The sequences of nuc rDNA ITS1-5.8S-ITS2 (ITS) and the 28S D1-D5 region of the Calocybe species were analyzed, and the results indicated that the three new species belonged to the genus Calocybe and differed from other species of Calocybe. The morphological similarities of the new species to other Calocybe species and the classification system within the genus Calocybe based on molecular data are also discussed. A key is provided for the Calocybe species as reported from China in order to facilitate future studies of the genus.

Gerhardtia tomentosa and Ossicaulis borealis (Agaricales, Lyophyllaceae)-Two new species from northeast China.

Background: Gerhardtia and Ossicaulis are two genera within the family Lyophyllaceae, which show an apparently poor species diversity worldwide. During the field investigation on wild macrofungi, six interesting collections within Gerhardtia and Ossicaulis genera are discovered in the northeastern China. Methods: To identify whether these collections of Gerhardtia and Ossicaulis are novel species, we performed phylogenetic analyzes using the following DNA regions: the internal transcribed spacer (ITS) region and the large subunit nuclear ribosomal RNA (nrLSU) region. Moreover, a traditional morphological method also be conducted based on both the macro-morphological and micro-morphological features. Results: The results indicated that these collections tested formed two independent lineages in each genus with a high support. In addition, they can easily be separated from all other taxa of the two genera in morphology. Based on the combination of morphological and molecular data, Gerhardtia tomentosa and Ossicaulis borealis, are confirmed as two new species to science. Discussions: This study provided a theoretical basis is for the two lyophylloid genera and indicated that the biodiversity resources of northeastern China might be underestimated.

Morphology and Phylogeny of Lyophylloid Mushrooms in China with Description of Four New Species.

The lyophylloid agarics are a group of ecologically highly diversified macrofungi, some of which are very popular edible mushrooms. However, we know little about lyophylloid species diversity in China. In this study, we described four new species from China: Lyophyllum atrofuscum, L. subalpinarum, L. subdecastes, and Ossicaulis sichuanensis. We conducted molecular phylogenetic analyses of Lyophyllaceae based on the nuclear ribosomal RNA gene (nLSU) and the internal transcribed spacer regions (ITS). Phylogenetic analyses by the maximum likelihood method and Bayesian inference showed that the four new species are unique monophyletic species. A key to the species of Lyophyllum from China and a key to Ossicaulis worldwide were given.

Taxonomic revision of Termitomyces species found in Ryukyu Archipelago, Japan, based on phylogenetic analyses with three loci.

Fungi in the genus Termitomyces are external symbionts of fungus-growing termites. The three rhizogenic Termitomyces species T. eurrhizus, T. clypeatus, and T. intermedius, and one species similar to T. microcarpus that lacks pseudorrhiza, have been reported from Ryukyu Archipelago, Japan. In contrast, only two genetic groups (types A and B) of Termitomyces vegetative mycelia have been detected in nests of the fungus-growing termite Odontotermes formosanus. In this study, we investigated the relationships between the mycelial genetic groups and the basidiomata of Termitomyces samples from the Ryukyu Archipelago. We found that all the basidioma specimens and the type B mycelia formed one clade that we identified as T. intermedius. Another clade consisted of the type A mycelia, which showed similarity to T. microcarpus, was identified as T. fragilis. Our results indicate that the Japanese T. eurrhizus and T. clypeatus specimens should re-named as T. intermedius.

Ancestral predisposition toward a domesticated lifestyle in the termite-cultivated fungus Termitomyces.

The ancestor of termites relied on gut symbionts for degradation of plant material, an association that persists in all termite families.1,2 However, the single-lineage Macrotermitinae has additionally acquired a fungal symbiont that complements digestion of food outside the termite gut.3 Phylogenetic analysis has shown that fungi grown by these termites form a clade-the genus Termitomyces-but the events leading toward domestication remain unclear.4 To address this, we reconstructed the lifestyle of the common ancestor of Termitomyces using a combination of ecological data with a phylogenomic analysis of 21 related non-domesticated species and 25 species of Termitomyces. We show that the closely related genera Blastosporella and Arthromyces also contain insect-associated species. Furthermore, the genus Arthromyces produces asexual spores on the mycelium, which may facilitate insect dispersal when growing on aggregated subterranean fecal pellets of a plant-feeding insect. The sister-group relationship between Arthromyces and Termitomyces implies that insect association and asexual sporulation, present in both genera, preceded the domestication of Termitomyces and did not follow domestication as has been proposed previously. Specialization of the common ancestor of these two genera on an insect-fecal substrate is further supported by similar carbohydrate-degrading profiles between Arthromyces and Termitomyces. We describe a set of traits that may have predisposed the ancestor of Termitomyces toward domestication, with each trait found scattered in related taxa outside of the termite-domesticated clade. This pattern indicates that the origin of the termite-fungus symbiosis may not have required large-scale changes of the fungal partner.

Enrichment of G4DNA and a Large Inverted Repeat Coincide in the Mitochondrial Genomes of Termitomyces.

Mitochondria retain their own genome, a hallmark of their bacterial ancestry. Mitochondrial genomes (mtDNA) are highly diverse in size, shape, and structure, despite their conserved function across most eukaryotes. Exploring extreme cases of mtDNA architecture can yield important information on fundamental aspects of genome biology. We discovered that the mitochondrial genomes of a basidiomycete fungus (Termitomyces spp.) contain an inverted repeat (IR), a duplicated region half the size of the complete genome. In addition, we found an abundance of sequences capable of forming G-quadruplexes (G4DNA); structures that can disrupt the double helical formation of DNA. G4DNA is implicated in replication fork stalling, double-stranded breaks, altered gene expression, recombination, and other effects. To determine whether this occurrence of IR and G4DNA was correlated within the genus Termitomyces, we reconstructed the mitochondrial genomes of 11 additional species including representatives of several closely related genera. We show that the mtDNA of all sampled species of Termitomyces and its sister group, represented by the species Tephrocybe rancida and Blastosporella zonata, are characterized by a large IR and enrichment of G4DNA. To determine whether high mitochondrial G4DNA content is common in fungi, we conducted the first broad survey of G4DNA content in fungal mtDNA, revealing it to be a highly variable trait. The results of this study provide important direction for future research on the function and evolution of G4DNA and organellar IRs.

The complete mitochondrial genome of the Basidiomycete edible fungus Hypsizygus marmoreus.

The complete mitochondrial genome of the edible fungus Hypsizygus marmoreus was published in this paper. It was determined using Pacbio and Illumina sequencing. The complete mitochondrial DNA (mtDNA) is 106,417 bp in length with a GC content of 31.74%, which was the fourth large mitogenome in Agaricales. The circular mitogenome encoded 67 protein-coding genes and one ribosomal RNAs (rns). Among these genes, 13 conserved protein-coding genes were determined in the genome, including 6 subunits of NAD dehydrogenase (nad1-4, 4L and 6), three cytochrome oxidases (cox1-3), one apocytochrome b (cob) and three ATP synthases (atp6, apt 8 and apt 9). The phylogenic analysis confirmed that H. marmoreus (Lyophyllaceae) clustered together with Tricholoma matsutake (Tricholomataceae).

Calocybella, a new genus for Rugosomyces pudicus (Agaricales, Lyophyllaceae) and emendation of the genus Gerhardtia.

Calocybella is a new genus established to accommodate Rugosomyces pudicus. Phylogenetic analyses based on a LSU-ITS sequence dataset place Calocybella sister to Gerhardtia from which it differs morphologically in the presence of clamp-connections and reddening context. The genus Gerhardtia is emended to also include taxa with smooth spores. According to our morphological analysis of voucher material, Calocybe juncicola s. auct. is shown to be Calocybella pudica.

Cadinane sesquiterpenes from the mushroom Lyophyllum transforme.

Two rare cadinane-type sesquiterpenes, lyophyllone A (1) and lyophyllanetriol A (2), were isolated from the mushroom Lyophyllum transforme. The structures were elucidated on the basis of exhaustive NMR techniques, together with MS, UV-Vis and molecular modelling. The absolute configuration of lyophyllone A was determined by ab initio theoretical CD calculation performed by Density Functional Theory (DFT) using the B3PW91/6-31G(d,p) basis set. The experimental CD were found to be in good agreement with the corresponding population-weighted theoretical CD spectra, allowing for the determination of the absolute stereochemistry of the compound.