Search Results (64)

Pleurotus ostreatus is a widely cultivated edible fungus in China, renowned for its rich nutritional composition and diverse medicinal compounds. However, the quality of the currently published P. ostreatus genomes remained suboptimal, which limited in-depth research on its evolution, growth, and development. In this study, we conducted a chromosome-level genome assembly of the monokaryotic basidiospore strain PC80. The assembled genome spanned 40.6 Mb and consisted of 15 scaffolds. Ten of these scaffolds contained complete telomere-to-telomere structures. The scaffold N50 value was 3.6 Mb. Genome annotation revealed 634 carbohydrate-active enzyme (CAZyme) family genes. Through collinearity analysis, we further confirmed that the PC80 genome exhibited higher completeness and greater accuracy compared to the currently published genomes of P. ostreatus. At the matA locus of PC80, three hd1 genes and one hd2 gene were identified. At the matB locus, seven pheromone receptor genes and two pheromone precursor genes were detected. Further phylogenetic analysis indicated that three of these pheromone receptor genes are likely to have mating-specific functions. This complete genome assembly could provide a foundation for future genomic and genetic studies, facilitate the identification of key genes related to growth and developmental regulation, and promote technological innovations in P. ostreatus breeding and efficient utilization. Full article

The A mating-type locus in Schizophyllum commune, which encodes homeodomain (HD) transcription factors, is essential for regulating sexual compatibility and development. While the role of the Aα sublocus and its Y-Z HD protein complex is adequality understood, the function of HD proteins at the Aβ sublocus remains unclear. In this study, we analyzed the Aβ sublocus of eight monokaryotic S. commune strains derived from the parental dikaryotic strain 20R-7-Z01 and identified four HD genes, abr, abs, abv, and abq, located at the Aβ sublocus. These genes encode two HD1 proteins (S and Q) and two HD2 proteins (R and V). Protein structure prediction, interaction assays, and in vivo functional analyses revealed that R-S and V-Q interactions independently regulate sexual compatibility and fruiting body development. This research highlights the critical role of the Aβ sublocus in fungal reproduction and provides valuable insights for breeding edible and medicinal S. commune strains. Full article

Tamarix chinensis Lour. is a halophytic shrub native to coastal China, commonly used in afforestation and ecological restoration due to its high tolerance to salinity and drought. To understand how this species maintains genetic variation and adapts to extreme environments, we examined the genetic diversity, mating system, and spatial genetic structure of a natural T. chinensis population on the geographically isolated and environmentally harsh Wudi Seashell Island. Using both SSR and ISSR markers, we observed high levels of genetic diversity despite the small population size and spatial fragmentation. SSR markers revealed an average of 11.75 alleles per locus, with an expected heterozygosity (He) of 0.754 and an observed heterozygosity (Ho) of 0.702. ISSR markers showed a polymorphic locus rate of 97.87%, with a mean He of 0.402. Parentage analysis revealed relatively long seed and pollen dispersal distances, with most dispersal occurring within 150 m and seeds and pollens occasionally reaching 948 m and 447 m, respectively. The species exhibited a mixed mating system, with a multilocus outcrossing rate of 0.554, contributing to gene flow and reducing inbreeding. A fine-scale spatial genetic structure was detected within 75 m, consistent across both SSR and ISSR markers, suggesting limited local gene dispersal. These findings provide new insights into the adaptive strategies of T. chinensis in marginal habitats and offer valuable guidance for conservation and restoration efforts in vulnerable coastal ecosystems. Full article

Cyclocybe chaxingu is an edible wood-decaying fungus widely cultivated in China, valued for its nutritional and economic significance. Despite its importance, molecular and genetic breeding studies on C. chaxingu have been limited by the lack of comprehensive genomic information. In this study, we performed whole-genome sequencing of the type strain JAUCC1847 of C. chaxingu for the first time and conducted extensive genomic and transcriptomic analyses. We assembled a high-quality genome of the C. chaxingu strain C27, with a total length of 50.79 Mb and a GC content of 50.90%. Comparative genomic analysis revealed a close evolutionary relationship with species from the genera Agrocybe and Stropharia, suggesting a recent common ancestor. The high ANI values between C. chaxingu, Agrocybe chaxingu, and Agrocybe cylindracea indicate a close phylogenetic relationship, raising the possibility of synonymy among these strains. Genome annotation identified a rich array of 573 carbohydrate-active enzymes, highlighting the metabolic diversity of C. chaxingu, particularly in lignocellulose degradation. Comprehensive analysis of the A and B mating-type locus in C. chaxingu revealed the distribution and structural characteristics of mating-type genes, providing crucial genetic information for further studies on the reproductive biology of this species. Transcriptomic analysis revealed distinct gene expression patterns in mycelia, stipe, and cap, reflecting their functional specialization. GO and KEGG enrichment analyses demonstrated the stipe’s association with structural integrity and transport, while the cap is linked to metabolic activity, gene regulation, stress responses, and DNA repair. These insights clarify the taxonomic status of C. chaxingu, supporting its recognition within the genus Cyclocybe and providing a valuable resource for future research and breeding programs. Full article

Schizophyllum commune, a Basidiomycota fungus with a tetrapolar mating system, serves as a key model for studying sexual reproduction. In this study, two distinct mating subtypes (I and II) were identified in strain 20R-7-ZF01, isolated from subseafloor sediment, which exhibited eight different mating interaction phenotypes. Intra-subtypes exhibited colony-symmetric tetrapolar interactions (G1), whereas inter-subtype crosses yielded colony-asymmetric phenotypes (G2) and a reduced number of fruiting bodies. Nuclear migration analysis revealed that both subtypes follow the same sexual reproductive process, suggesting functional similarities despite the different reproductive outcomes. Gene silencing of mating-type loci identified the genes bbp2-9 and bbp2-7 within the B locus as key factors in determining mating subtype identity. Additionally, a similar pattern of mating subtype differentiation was observed in five other S. commune strains from both subseafloor and terrestrial environments. These findings highlight the genetic diversity within S. commune, challenge the classical understanding of fungal mating systems, and provide new insights into the genetic evolutionary mechanisms governing fungi with tetrapolar mating systems. Full article

During sexual reproduction, the freshwater ciliate Tetrahymena thermophila sheds membrane-bound vesicles into the extracellular environment (cEMVs: ciliary extracellular micro-vesicles). We provide evidence that 100 nm vesicles shed from the cilia of starved cells promote mating between cells of complementary mating types. A proteomic analysis revealed that these EMVs are decorated with mating-type proteins expressed from the MAT locus, proteins that define a cell’s sex (one of seven). Once the mating junction is established between cells, smaller 60 nm vesicles (junction vesicles) appear within the extracellular gap that separates mating partners. Junction vesicles (jEMVs) may play a role in remodeling the mating junction through which gametic pronuclei are exchanged. Evidence is presented demonstrating that cells must be able to internalize extracellular signals via some form of endocytosis in order to trigger conjugation. Finally, an evolutionarily conserved fusogen (Hap2) implicated in pore formation also appears necessary for jEMV processing. This system offers an excellent opportunity for studies on ectosome shedding, intercellular signaling and shed vesicle uptake by macro-pinocytosis, as they relate to sexual reproduction in the ciliate Tetrahymena thermophila. Full article

Species of the genus Diaporthe have a mating-type system with the two mating types MAT1-1 and MAT1-2, like other ascomycetes. They can either be heterothallic, which means that any isolate only possesses one of the two mating types and needs a mating partner for sexual reproduction, or homothallic, which means that they possess both mating types and are self-fertile. For several Diaporthe species, no sexual reproduction has been observed so far. Using PCR with primers specific to the defining genes MAT1-1-1 and MAT1-2-1, we determined the mating types of 33 isolates of Diaporthe caulivora, D. eres, D. longicolla, and D. novem from central Europe. In addition, we partially sequenced the mating-type genes of 25 isolates. We found that different D. longicolla isolates either possess MAT1-1-1 or MAT1-2-1, making the species heterothallic, which is in contrast to previous studies and the general assumption that D. longicolla only reproduces asexually. D. eres and D. novem were also found to be heterothallic. Using genomic sequence information and re-sequencing of DNA and RNA, we identified the MAT1-1-1 gene in D. caulivora and present here the full sequence of the mating-type locus of this homothallic species. Finally, we used sequence information from MAT1-1-1 and MAT1-2-1, respectively, for improved phylogenetic resolution of our isolates. Full article

Background/Objectives: The increasing pressure from pathogens and parasites on Apis mellifera populations is resulting in significant colony losses. It is desirable to identify resistance-associated single-nucleotide polymorphisms (SNPs) and their variability for the purpose of breeding resilient honeybee lines. This study examined the genetic diversity of 13 SNPs previously studied for associations with various resistance-providing traits, including six linked to Varroa-specific hygiene, five linked to suppressed mite reproduction, one linked to immune response, and one linked to chalkbrood resistance. Methods: Genotyping was performed using a novel SNaPshot genotyping panel designed for this study. The sample pool consisted of 308 honeybee samples in total, covering all 77 administrative districts of the Czech Republic. Results: All examined loci were polymorphic. The frequency of positive alleles in our population is medium to low, depending on the specific SNP. An analysis of genotype frequencies revealed that most loci exhibited the Hardy–Weinberg equilibrium. A comparison of the allele and genotype frequencies of the same locus between samples from hives and samples from flowers revealed no significant differences. The genetic diversity, as indicated by the heterozygosity values, ranged from 0.05 to 0.50. The fixation index (F) was, on average, close to zero, indicating minimal influence of inbreeding or non-random mating on the genetic structure of the analyzed samples. Conclusions: The obtained results provide further insights into the genetic variation of SNPs associated with the immune response and resistance to pathogens in honeybee populations in the Czech Republic. This research provides a valuable foundation for future studies of honeybee diversity and breeding. Full article

Pholiota nameko (T. Ito) S. Ito and S. Imai is an emerging wild mushroom species belonging to the genus Pholiota. Its unique brown–yellow appearance and significant biological activity have garnered increasing attention in recent years. However, there is a relative lack of research on the biological characteristics and genetics of P. nameko, which greatly limits the potential for an in-depth exploration of this mushroom in the research fields of molecular breeding and evolutionary biology. This study aimed to address that gap by employing Illumina and Nanopore sequencing technologies to perform whole-genome sequencing, de novo assembly, and annotation analysis of the P. nameko ZZ1 strain. Utilizing bioinformatics methods, we conducted a comprehensive analysis of the genomic characteristics of this strain and successfully identified candidate genes associated with its mating type, carbohydrate-active enzymes, virulence factors, pan-genome, and drug resistance functions. The genome of P. nameko ZZ1 is 24.58 Mb in size and comprises 33 contigs, with a contig N50 of 2.11 Mb. A hylogenetic analysis further elucidated the genetic relationship between P. nameko and other Pholiota, revealing a high degree of collinearity between P. nameko and ZZ1. In our enzyme analysis, we identified 246 enzymes in the ZZ1 genome, including 68 key carbohydrate-active enzymes (CAZymes), and predicted the presence of 11 laccases, highlighting the strain’s strong potential for cellulose degradation. We conducted a pan-genomic analysis of five closely related strains of Pholiota, yielding extensive genomic information. Among these, there were 2608 core genes, accounting for 21.35% of the total genes, and 135 dispensable genes, highlighting significant genetic diversity among Pholiota and further confirming the value of pan-genomic analysis in uncovering species diversity. Notably, while we successfully identified the A-mating-type locus, composed of the homeodomain protein genes HD1 and HD2 in ZZ1, we were unable to obtain the B-mating-type locus due to technical limitations, preventing us from acquiring the pheromone receptor of the B-mating-type. We plan to supplement these data in future studies and explore the potential impact of the B-mating-type locus on the current findings. In summary, the genome data of ZZ1 presented in this study are not only valuable resources for understanding the genetic basis of this species, but also serve as a crucial foundation for subsequent genome-assisted breeding, research into cultivation technology, and the exploration of its nutritional and potential medicinal value. Full article

The methylotrophic yeast Komagataella kurtzmanii belongs to the group of homothallic fungi that are able to spontaneously change their mating type by inversion of chromosomal DNA in the MAT locus region. As a result, natural and genetically engineered cultures of these yeasts typically contain a mixture of sexually dimorphic cells that are prone to self-diploidisation and spore formation accompanied by genetic rearrangements. These characteristics pose a significant challenge to the development of genetically stable producers for industrial use. In the present study, we constructed heterothallic strains of K. kurtzmanii, ensuring a constant mating type by unifying the genetic sequences in the active and silent MAT loci. To obtain such strains, we performed site-directed inactivation of one of the two yeast MAT loci, replacing its sequence with a selective HIS4 gene surrounded by I-SceI meganuclease recognition sites. We then used transient expression of the SCE1 gene, encoding a recombinant I-SceI meganuclease, to induce site-specific cleavage of HIS4, followed by damage repair by homologous recombination in mutant cells. As a result, heterothallic strains designated ‘Y-727-2(alpha)’ and ‘Y-727-9(a)’, which correspond to the α and a mating type, respectively, were obtained. The strains demonstrated a loss of the ability to self-diploidize. The results of PCR and whole genome analysis confirmed the identity of the contents of the MAT loci. Analysis of the genomes of the final strains, however, revealed a fusion of chromosome 3 and chromosome 4 in strain Y-727-2(alpha)-1. This finding was subsequently confirmed by pulsed-field gel electrophoresis of yeast chromosomes. However, the ability of the Y-727-2(alpha)-derived producers to efficiently secrete recombinant β-galactosidase was unaffected by this genomic rearrangement. Full article

Population genetics describes evolutionary processes, focusing on the variation within and between species and the forces shaping this diversity. Evolution reflects information accumulated in genomes, enhancing organisms’ adaptation to their environment. In this paper, I propose a model that begins with the distribution of mating based on mutual fitness and progresses to viable adult genotype distribution. At each stage, the changes result in different measures of information. The evolutionary dynamics at each stage of the model correspond to certain aspects of interest, such as the type of mating, the distribution of genotypes in regard to mating, and the distribution of genotypes and haplotypes in the next generation. Changes to these distributions are caused by variations in fitness and result in Jeffrey’s divergence values other than zero. As an example, a model of hybrid sterility is developed of a biallelic locus, comparing the information indices associated with each stage of the evolutionary process. In conclusion, the informational perspective seems to facilitate the connection between cause and effect and allows the development of statistical tests to perform hypothesis testing against zero-information null models (random mating, no selection, etc.). The informational perspective could contribute to clarify, deepen, and expand the mathematical foundations of evolutionary theory. Full article

Frogeye leaf spot on soybeans is traditionally considered as a southern disease in the United States but its impact in North Central USA has been rising in recent years. In this study, we investigated the population structure and mating type distribution in the C. sojina population from Indiana, USA. Based on 27 single nucleotide polymorphism markers, 49 multi-locus genotypes (MLGs) were identified in 234 isolates collected from 29 counties in Indiana in 2020. Bayesian analysis grouped the 49 MLGs into three clusters. This grouping was supported by principal coordinate analysis and, in large part, by the unweighted pair group method with arithmetic mean and minimal spanning tree. Only one mating-type idiomorph was found in each isolate and in each MLG. The MAT1-1 idiomorph was found in 22 MLGs and the MAT1-2 idiomorph was found in 27 MLGs. Based on clone-corrected data, the distribution of mating-type idiomorphs did not deviate significantly from 1:1 ratio in Indiana as a whole and in 22 out of 24 counties where two or more MLGs were found. Thirty MLGs contained QoI-resistant isolates and 22 MLGs contained QoI-sensitive isolates, with three MLGs containing both types of isolates. MLG1, the most common MLG with 90 isolates, contained mostly QoI-resistant isolates. Interestingly, MLG1 was also the dominant genotype in the Tennessee population collected in 2015, suggesting that MLG1 has been a dominant genotype in a wider region for many years. Based on the standard index of association ($\overline{r}$_d), the Indiana population as a whole was in significant linkage disequilibrium. However, in five out of 16 counties where three or more MLGs were found, the null hypothesis of linkage equilibrium was not rejected. Tests of linkage disequilibrium between locus pairs showed that 33.3% of locus pairs on the same contigs were in significant disequilibrium and 17.7% of locus pairs on different contigs were in significant disequilibrium. The possibility of a cryptic sexual stage was discussed. Full article

Sexual reproduction in ascomycetes is controlled by the mating-type (MAT) locus. (Pseudo)homothallic reproduction has been hypothesized on the basis of genetic data from Hirsutella sinensis (Genotype #1 of Ophiocordyceps sinensis). However, the differential occurrence and differential transcription of mating-type genes in the MAT1-1 and MAT1-2 idiomorphs were found in the genome and transcriptome assemblies of H. sinensis, and the introns of the MAT1-2-1 transcript were alternatively spliced with an unspliced intron I that contains stop codons. These findings reveal that O. sinensis reproduction is controlled at the genetic, transcriptional, and coupled transcriptional-translational levels. This study revealed that mutant mating proteins could potentially have various secondary structures. Differential occurrence and transcription of the a-/α-pheromone receptor genes were also found in H. sinensis. The data were inconsistent with self-fertilization under (pseudo)homothallism but suggest the self-sterility of H. sinensis and the requirement of mating partners to achieve O. sinensis sexual outcrossing under heterothallism or hybridization. Although consistent occurrence and transcription of the mating-type genes of both the MAT1-1 and MAT1-2 idiomorphs have been reported in natural and cultivated Cordyceps sinensis insect-fungi complexes, the mutant MAT1-1-1 and α-pheromone receptor transcripts in natural C. sinensis result in N-terminal or middle-truncated proteins with significantly altered overall hydrophobicity and secondary structures of the proteins, suggesting heterogeneous fungal source(s) of the proteins and hybridization reproduction because of the co-occurrence of multiple genomically independent genotypes of O. sinensis and >90 fungal species in natural C. sinensis. Full article

Nitrogen is an essential element for maize growth, but excessive application can lead to various environmental and ecological issues, including water pollution, air pollution, greenhouse gas emissions, and biodiversity loss. Hence, developing maize hybrids resilient to low-N conditions is vital for sustainable agriculture, particularly in nitrogen-deficient soils. Combining ability and genetic relationships among parental lines is crucial for breeding superior hybrids under diverse nitrogen levels. This study aimed to assess the genetic diversity of maize inbred lines using simple sequence repeat (SSR) markers and evaluate their combining ability to identify superior hybrids under low-N and recommended conditions. Local and exotic inbred lines were genotyped using SSR markers, revealing substantial genetic variation with high gene diversity (He = 0.60), moderate polymorphism information content (PIC = 0.54), and an average of 3.64 alleles per locus. Twenty-one F1 hybrids were generated through a diallel mating design using these diverse lines. These hybrids and a high yielding commercial check (SC-131) were field-tested under low-N and recommended N conditions. Significant variations (p < 0.01) were observed among nitrogen levels, hybrids, and their interaction for all recorded traits. Additive genetic variances predominated over non-additive genetic variances for grain yield and most traits. Inbred IL3 emerged as an effective combiner for developing early maturing genotypes with lower ear placement. Additionally, inbreds IL1, IL2, and IL3 showed promise as superior combiners for enhancing grain yield and related traits under both low-N and recommended conditions. Notably, hybrids IL1×IL4, IL2×IL5, IL2×IL6, and IL5×IL7 exhibited specific combining abilities for increasing grain yield and associated traits under low-N stress conditions. Furthermore, strong positive associations were identified between grain yield and specific traits like plant height, ear length, number of rows per ear, and number of kernels per row. Due to their straightforward measurability, these relationships underscore the potential of using these traits as proxies for indirect selection in early breeding generations, particularly under low-N stress. This research contributes to breeding nitrogen-efficient maize hybrids and advances our understanding of the genetic foundations for tolerance to nitrogen limitations. Full article

Keteleeria davidiana var. calcarea is an endangered plant endemic to China. It is mainly distributed in the karst areas of the Guangxi and Guizhou Provinces. It is characterized by small populations and intermittent distribution. This study aimed to explore the genetic diversity and mating system of wild populations of Keteleeria davidiana var. calcarea in fragmented habitats. To achieve this, we genotyped 46 maternal trees and 214 progenies from four fragmented populations of Keteleeria davidiana var. calcarea using nine pairs of microsatellite primers. The genetic diversity of Keteleeria davidiana var. calcarea (Ho = 0.68, He = 0.63) was lower than that of the species overall but higher than that of other Keteleeria plants. The incidence of unbiased expected heterozygosity (uHe) and allelic richness (Ar) was higher in the maternal generation than in the progeny. This suggests that the genetic diversity of the progeny was lower than that of the maternal generation. Keteleeria davidiana var. calcarea is divided into four populations, but there is significant genetic exchange between the populations according to STRUCTURE and gene flow analyses. The multilocus mating system analysis (MLTR) results indicate that the multilocus outcrossing rate (t_m) was 0.902, the single-locus outcrossing rate (t_s) was 0.606, the bimaternal inbreeding coefficient (t_m-t_s) was 0.295, and the coefficient of inbreeding depression(δ) was 0.904. These results suggest a certain degree of selfing and inbreeding in Keteleeria davidiana var. calcarea. To prevent problems associated with inbreeding and conserve the genetic diversity of Keteleeria davidiana var. calcarea, we recommend establishing seed gardens, using artificial pollination, and employing asexual propagation techniques for conservation intervention. Full article