Genetic networks that govern sexual reproduction in the Pezizomycotina

Sexual development in filamentous fungi is a complex process that relies on the precise control of and interaction between a variety of genetic networks and pathways. The mating-type (MAT) genes are the master regulators of this process and typically act as transcription factors, which control the expression of genes involved at all stages of the sexual cycle. In many fungi, the sexual cycle typically begins when the mating pheromones of one mating type are recognized by a compatible partner, followed by physical interaction and fertilization. Subsequently, highly specialized sexual structures are formed, within which the sexual spores develop after rounds of meiosis and mitosis. These spores are then released and germinate, forming new individuals that initiate new cycles of growth. This review provides an overview of the known genetic networks and pathways that are involved in each major stage of the sexual cycle in filamentous ascomycete fungi.https://journals.asm.org/journal/mmbrhj2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Unidirectional mating-type switching confers self-fertility to Thielaviopsis cerberus, the only homothallic species in the genus

Sexual reproduction is ubiquitous in nature, and nowhere is this more so than in the fungi. Heterothallic behaviour is observed when there is a strict requirement of contact between two individuals of opposite mating type for sexual reproduction to occur. In contrast, a homothallic species can complete the entire sexual cycle in isolation, although several genetic mechanisms underpin this self-fertility. These can be inferred by characterising the structure and gene-content of the mating-type locus, which contains genes that are involved in the regulation of sexual reproduction. In this study, the genetic basis of homothallism in Thielaviopsis cerberus was investigated, the only known self-fertile species within this genus. Using genome sequencing and conventional molecular techniques, two versions of the mating-type locus were identified in this species. This is typical of species that have a unidirectional mating-type switching reproductive strategy. The first version was a self-fertile locus that contained four known mating-type genes, while the second was a self-sterile version with a single mating-type gene. The conversion from a self-fertile to a self-sterile locus is likely mediated by a homologous recombination event at two direct repeats present in the self-fertile locus, resulting in the deletion of three mating-type genes and one of the repeats. Both locus versions were present in isolates that were self-fertile, while self-sterility was caused by the presence of only a switched locus. This study provides a clear example of the architectural fluidity in the mating-type loci that is common among even closely related fungal species.The University of Pretoria, as well as the Department of Science and Innovation (DSI)/National Research Foundation (NRF) Centre of Excellence in Plant Health Biotechnology and the South African Research Chairs Initiative (SARChI) in Fungal Genomics.http://www.elsevier.com/locate/funbio2022-01-07hj2021BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Which MAT gene? Pezizomycotina (Ascomycota) mating-type gene nomenclature reconsidered

Filamentous fungi in the subdivision Pezizomycotina (Ascomycota) display an impressive diversity of mating strategies. These mating systems are all controlled by the mating-type (MAT) genes, some of which are conserved, even among distantly related genera. In order to facilitate effective communication between researchers, a system was established in 2000 to name these genes and this has subsequently been widely applied. However, due to the rapid growth in the number of described MAT genes in the Pezizomycotina, an evaluation of the manner in which the nomenclature system has been applied is warranted and revisions should be considered. We address this challenge by doing a systematic review of the nomenclature associated with the MAT1 locus and its associated genes described in the Pezizomycotina. Several problems in the application of the nomenclature system were identified and addressed. These included proposed revisions of the nomenclature system to provide a more accurate description of the mating-type genes. We anticipate that this review will reduce confusion and that it will be useful in future characterisation of mating-type genes.The University of Pretoria and the Department of Science and Technology (DST)/National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology and the SARCHI chair in Fungal Genomics.http://www.elsevier.com/locate/fbr2018-09-01hj2017Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Analysis of microsatellite markers in the genome of the plant pathogen Ceratocystis fimbriata

Ceratocystis fimbriata sensu lato represents a complex of cryptic and commonly plant pathogenic species that are morphologically similar. Species in this complex have been described using morphological characteristics, intersterility tests and phylogenetics. Microsatellite markers have been useful to study the population structure and origin of some species in the complex. In this study we sequenced the genome of C. fimbriata. This provided an opportunity to mine the genome for microsatellites, to develop new microsatellite markers, and map previously developed markers onto the genome. Over 6000 microsatellites were identified in the genome and their abundance and distribution was determined. Ceratocystis fimbriata has a medium level of microsatellite density and slightly smaller genome when compared with other fungi for which similar microsatellite analyses have been performed. This is the first report of a microsatellite analysis conducted on a genome sequence of a fungal species in the order Microascales. Forty-seven microsatellite markers have been published for population genetic studies, of which 35 could be mapped onto the C. fimbriata genome sequence. We developed an additional ten microsatellite markers within putative genes to differentiate between species in the C. fimbriata s.l. complex. These markers were used to distinguish between 12 species in the complex.The National Research Foundation (NRF), the South African Biosystematics Initiative (SABI), members of the Tree Protection Co-Operative Programme (TPCP), and the Department of Science and Technology (DST)/ NRF Centre of Excellence in Tree Health Biotechnology (CTHB), South Africa.http://www.elsevier.com/locate/funbiohj201

Both mating types in the heterothallic fungus Ophiostoma quercus contain MAT1-1 and MAT1-2 genes

In heterothallic Ascomycota, two opposite but distinct mating types control all sexual processes. Using mating crosses, mating types were assigned to ten isolates of the heterothallic fungal species Ophiostoma quercus. Primers were subsequently designed to target the MAT1-1-1, MAT1-1-3 (of the mating type 1 idiomorph), and MAT1-2-1 (of the mating type 2 idiomorph) genes in these isolates. Results showed that all isolates contained the full gene sequence for the MAT1-2-1 gene. In addition, fragments of the MAT1-1-1 and MAT1-1-3 genes were sequenced from all isolates. These results were unexpected, as each isolate from a heterothallic species would typically contain only one of the two possible MAT idiomorphs.The University of Pretoria, the National Research Foundation (NRF) and the DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB) South Africa provided financial support that made this study possible.http://www.elsevier.com/locate/funbionf201

Unisexual reproduction in Huntiella moniliformis

Sexual reproduction in fungi is controlled by genes present at the mating type (MAT) locus, which typically harbors transcription factors that influence the expression of many sex-related genes. The MAT locus exists as two alternative idiomorphs in ascomycetous fungi and sexual reproduction is initiated when genes from both idiomorphs are expressed. Thus, the gene content of this locus determines whether a fungus is heterothallic (self-sterile) or homothallic (self-fertile). Recently, a unique sub-class of homothallism has been described in fungi, where individuals possessing a single MAT idiomorph can reproduce sexually in the absence of a partner. Using various mycological, molecular and bioinformatic techniques, we investigated the sexual strategies and characterized the MAT loci in two tree wound-infecting fungi, Huntiella moniliformis and Huntiella omanensis. H. omanensis was shown to exhibit a typically heterothallic sexual reproductive cycle, with isolates possessing either the MAT1-1 or MAT1-2 idiomorph. This was in contrast to the homothallism via unisexual reproduction that was shown in H. moniliformis, where only the MAT1-2-1 gene was present in sexually reproducing cultures. While the evolutionary benefit and mechanisms underpinning a unisexual mating strategy remain unknown, it could have evolved to minimize the costs, while retaining the benefits, of normal sexual reproduction.University of Pretoria, the Department of Science and Technology (DST)/National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology and the Genomics Research Institute (University of Pretoria Institutional Research Theme) and the National Research Foundation of South Africa. specific unique reference number (UID) 83924).http://www.elsevier.com/locate/yfgbi2016-07-31hb201

Homothallism : an umbrella term for describing diverse sexual behaviours

Sexual reproduction is notoriously complex in fungi with species able to produce sexual progeny by utilizing a variety of different mechanisms. This is even more so for species employing multiple sexual strategies, which is a surprisingly common occurrence. While heterothallism is relatively well understood in terms of its physiological and molecular underpinnings, homothallism remains greatly understudied. This can be attributed to it involving numerous genetically distinct mechanisms that all result in self-fertility; including primary homothallism, pseudohomothallism, mating type switching, and unisexual reproduction. This review highlights the need to classify these homothallic mechanisms based on their molecular determinants and illustrates what is currently known about the multifaceted behaviours associated with homothallism.The University of Pretoria, the Department of Science and Technology (DST)/National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology and the Genomics Research Institute (University of Pretoria Institutional Research Theme) as well grants from the National Research Foundation of South Africa (including Grant specific unique reference number (UID) 83924).http://www.imafungus.orgam201

Mutualism and asexual reproduction influence recognition genes in a fungal symbiont

Mutualism between microbes and insects is common and alignment of the reproductive interests of microbial symbionts with this lifestyle typically involves clonal reproduction and vertical transmission by insect partners. Here the Amylostereum funguseSirex woodwasp mutualism was used to consider whether their prolonged association and predominance of asexuality have affected the mating system of the fungal partner. Nucleotide information for the pheromone receptor gene rab1, as well as the translation elongation factor 1a gene and ribosomal RNA internal transcribed spacer region were utilized. The identification of rab1 alleles in Amylostereum chailletii and Amylostereum areolatum populations revealed that this gene is more polymorphic than the other two regions, although the diversity of all three regions was lower than what has been observed in free-living Agaricomycetes. Our data suggest that suppressed recombination might be implicated in the diversification of rab1, while no evidence of balancing selection was detected. We also detected positive selection at only two codons, suggesting that purifying selection is important for the evolution of rab1. The symbiotic relationship with their insect partners has therefore influenced the diversity of this gene and influenced the manner in which selection drives and maintains this diversity in A. areolatum and A. chailletii.The National Research Foundation (NRF), members of the Tree Pathology Cooperative Programme (TPCP) and the THRIP initiative of the Department of Trade and Industry (DTI), South Africa.http://www.elsevier.com/locate/funbiohb201

Unexpected placement of the MAT1-1-2 gene in the MAT1-2 idiomorph of Thielaviopsis

Sexual reproduction in the Ascomycota is controlled by genes encoded at the mating-type or MAT1 locus. The two allelic versions of this locus in heterothallic species, referred to as idiomorphs, are defined by the MAT1-1-1 (for the MAT1-1 idiomorph) and MAT1-2-1 (for the MAT1-2 idiomorph) genes. Both idiomorphs can contain additional genes, although the contents of each is typically specific to and conserved within particular Pezizomycotina lineages. Using full genome sequences, complemented with conventional PCR and Sanger sequencing, we compared the mating-type idiomorphs in heterothallic species of Thielaviopsis (Ceratocystidaceae). The analyses showed that the MAT1-1 idiomorph of T. punctulata, T. paradoxa, T. euricoi, T. ethacetica and T. musarum harboured only the expected MAT1-1-1 gene. In contrast, the MAT1-2 idiomorph of T. punctulata, T. paradoxa and T. euricoi encoded the MAT1-2-1, MAT1-2-7 and MAT1-1-2 genes. Of these, MAT1-2-1 and MAT1-2-7 are genes previously reported in this idiomorph, while MAT1-1-2 is known only in the MAT1-1 idiomorph. Phylogenetic analysis showed that the Thielaviopsis MAT1-1-2 groups with the known homologues of this gene in other Microascales, thus confirming its annotation. Previous work suggests that MAT1-1-2 is involved in fruiting body development, a role that would be unaffected by its idiomorphic position. This notion is supported by our findings for the MAT1 locus structure in Thielaviopsis species. This also serves as the first example of a MAT1-1-specific gene restricted to only the MAT1-2 idiomorph.The Claude Leon Foundation in the form of Postdoctoral Fellowship to PMW, the University of Pretoria and the Department of Science and Technology (DST)- National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology and the SARCHI chair in Fungal Genomics.http://www.elsevier.com/locate/yfgbi2019-04-01hj2018BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Doing it alone : unisexual reproduction in filamentous ascomycete fungi

Unisexuality in fungi is the result of sexual reproduction in a single isolate that harbors genes associated with only a single mating type. To date, unisexual reproduction has been described in only three genera of filamentous fungi. Consequently, our understanding of this unusual pathway is limited. In this critical review, we compare genetic, genomic and transcriptomic data from a variety of unisexual species to similar data from their primary homothallic and heterothallic relatives. These analyses show that unisexual reproduction is likely derived from heterothallism via the mutation of genes involved in the initiation of sexual reproduction. We show that significant changes in mating-type genes, pheromone precursor genes and pheromone receptor genes are common in unisexual species, but that similar changes are not evident in their primary homothallic or heterothallic relatives. These findings are particularly notable because the unisexual species are accommodated in unrelated genera, illustrating that a similar transition to unisexuality has likely occurred independently in their lineages.The University of Pretoria, the Department of Science and Innovation (DSI)/National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology and the Genomics Research Institute (University of Pretoria Institutional Research Theme).http://www.elsevier.com/locate/fbr2022-01-13hj2021BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog