Genetic variability and population structure of the mushroom Pleurotus eryngii var. tuoliensis

Evolution and Genetic Differentiation of Pleurotus tuoliensis in Xinjiang, China, Based on Population Genomics

Pleurotus tuoliensis is a unique species discovered in Xinjiang, China, which is recognized for its significant edible, medicinal, and economic value. It has been successfully incorporated into industrial production. Controversy has emerged concerning the evolution and environmental adaptability of this species due to inadequate interspecific ecology and molecular data. This study examines the germplasm resources of P. tuoliensis in the Xinjiang region. A total of 225 wild and cultivated strains of P. tuoliensis were gathered from seven representative regions. Phylogenetic analysis revealed that seven populations were notably segregated into three distinct groups, primarily attributed to environmental factors as the underlying cause for this differentiation. Population historical size data indicate that P. tuoliensis underwent two expansion events, one between 2 and 0.9 Mya (Miocene) and the other between 15 and 4 Mya (Early Pleistocene). The ancient climate fluctuations in the Xinjiang region might have contributed to the comparatively modest population size during the Pliocene epoch. Moreover, through the integration of biogeography and ancestral state reconstruction, it was determined that group C of P. tuoliensis emerged initially and subsequently dispersed to groups D and B, in that order. Subsequently, group D underwent independent evolution, whereas group B continued to diversify into groups A and EFG. The primary factor influencing this mode of transmission route is related to the geographical conditions and prevailing wind direction of each group. Subsequent research endeavors focused on assessing the domestication adaptability of P. tuoliensis to different substrates. It was found that the metabolic processes adapted during the domestication process were mainly related to energy metabolism, DNA repair, and environmental adaptability. Processes adapted to the host adaptability include responses to the host (meiosis, cell cycle, etc.) and stress in the growth environment (cysteine and methionine metabolism, sulfur metabolism, etc.). This study analyzed the systematic evolution and genetic differentiation of P. tuoliensis in Xinjiang. The identified loci and genes provide a theoretical basis for the subsequent improvement of germplasm resources and conducting molecular breeding.

Comparative genomic analysis reveals contraction of gene families with putative roles in pathogenesis in the fungal boxwood pathogens Calonectria henricotiae and C. pseudonaviculata

Background

Boxwood blight disease caused by Calonectria henricotiae and C. pseudonaviculata is of ecological and economic significance in cultivated and native ecosystems worldwide. Prior research has focused on understanding the population genetic and genomic diversity of C. henricotiae and C. pseudonaviculata, but gene family evolution in the context of host adaptation, plant pathogenesis, and trophic lifestyle is poorly understood. This study applied bioinformatic and phylogenetic methods to examine gene family evolution in C. henricotiae, C. pseudonaviculata and 22 related fungi in the Nectriaceae that vary in pathogenic and saprobic (apathogenic) lifestyles.

Results

A total of 19,750 gene families were identified in the 24 genomes, of which 422 were rapidly evolving. Among the six Calonectria species, C. henricotiae and C. pseudonaviculata were the only species to experience high levels of rapid contraction of pathogenesis-related gene families (89% and 78%, respectively). In contrast, saprobic species Calonectria multiphialidica and C. naviculata, two of the closest known relatives of C. henricotiae and C. pseudonaviculata, showed rapid expansion of pathogenesis-related gene families.

Conclusions

Our results provide novel insight into gene family evolution within C. henricotiae and C. pseudonaviculata and suggest gene family contraction may have contributed to limited host-range expansion of these pathogens within the plant family Buxaceae.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02035-4.

Genetic Differentiation and Widespread Mitochondrial Heteroplasmy among Geographic Populations of the Gourmet Mushroom Thelephora ganbajun from Yunnan, China

The mitochondrial genomes are generally considered non-recombining and homoplasmic in nature. However, our previous study provided the first evidence of extensive and stable mitochondrial heteroplasmy in natural populations of the basidiomycete fungus Thelephora ganbajun from Yunnan province, China. The heteroplasmy was characterized by the presence of two types of introns residing at adjacent but different sites in the cytochrome oxidase subunits I (cox1) gene within an individual strain. However, the frequencies of these two introns among isolates from different geographical populations and the implications for the genetic structure in natural populations have not been investigated. In this study, we analyzed DNA sequence variation at the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA gene cluster among 489 specimens from 30 geographic locations from Yunnan and compared that variation with distribution patterns of the two signature introns in the cox1 gene that are indicative of heteroplasmy in this species. In our samples, evidence for gene flow, abundant genetic diversity, and genotypic uniqueness among geographic samples in Yunnan were revealed by ITS sequence variation. While there was insignificant positive correlation between geographic distance and genetic differentiation among the geographic samples based on ITS sequences, a moderate significant correlation was found between ITS sequence variation, geographical distance of sampling sites, and distribution patterns of the two heteroplasmic introns in the cox1 gene. Interestingly, there was a significantly negative correlation between the copy numbers of the two co-existing introns. We discussed the implications of our results for a better understanding of the spread of stable mitochondrial heteroplasmy, mito-nuclear interactions, and conservation of this important gourmet mushroom.

Antioxidation, anti-inflammation and anti-fibrosis effect of phosphorylated polysaccharides from Pleurotus djamor mycelia on adenine-induced chronic renal failure mice

The mycelia polysaccharides (MPS) from Pleurotus djamor were prepared and purified by anion exchange column chromatography, and the phosphate content of phosphorylated MPS (PMPS) was 15.22 ± 0.37%. FT-IR spectra, HPLC and ¹H and ¹³C-NMR results showed the PMPS contained α-pyranose structure and the peak area percentage composition of galacturonic acid and glucose were 13.01% and 85.82%, respectively. Animal experiment investigated the antioxidant, anti-inflammation, anti-fibrosis effects of PMPS on kidney in adenine-induced chronic renal failure (CRF) mice. All results including serum biochemical indices, histopathological observation, qRT-PCR, western blotting, immunohistochemical staining manifested the kidney injury could be remitted by PMPS interventions. This experiment suggested that PMPS could remit CRF and other kidney injury related diseases as one kind of dietary supplements and functional foods without toxic side effects.

Anti-Obesity Effect of DKB-117 through the Inhibition of Pancreatic Lipase and α-Amylase Activity

This study sought to evaluate the effects of Phaseolus multiflorus var. albus Bailey extract (PM extract) and Pleurotus eryngii var. ferulae extract (PF extract) on the inhibition of digestive enzymes and to confirm the anti-obesity effect of DKB-117 (a mixture of PM extract and PF extract) in digestive enzyme inhibition in a mouse model of obesity induced by a high-fat diet. In in vitro studies, PM extract and PF extract have increased dose-dependent inhibitory activity on α-amylase (Inhibitory concentration (IC₅₀ value: 6.13 mg/mL)) and pancreatic lipase (IC₅₀ value; 1.68 mg/mL), respectively. High-fat diet-induced obese mice were orally administered DKB-117 extracts at concentrations of 100, 200, and 300 mg/kg/day, while a positive control group was given orlistat (pancreatic lipase inhibitor) and Garcinia cambogia (inhibiting the enzymes needed to synthesize carbohydrates into fat) at concentrations of 40 and 200 mg/kg/day, respectively, for eight weeks. As a result, body weight, fat mass (total fat mass, abdominal fat, and subcutaneous fat) detected with microcomputed tomography, fat mass (abdominal fat and inguinal fat) after an autopsy, and liver triglyceride levels were decreased significantly in the DKB-117 (300 mg/kg/day) group compared to those in the HFD control group. Additionally, we obtained results indicating that the presence of carbohydrates was found more in the DKB-117-300 (300 mg/kg/day) group than in the HFD control group. These data clearly show that DKB-117 extracts are expected to have an anti-obesity effect through a complex mechanism that promotes carbohydrate release through the inhibition of carbohydrate-degrading enzymes while blocking lipid absorption through lipase inhibition.

Water Extract of Pleurotus eryngii var. ferulae Prevents High-Fat Diet-Induced Obesity by Inhibiting Pancreatic Lipase

Pleurotus eryngii var. ferulae (PEF) is traditionally used in the prevention and treatment of lifestyle-related diseases. In this study, we investigated the ability of PEF extract to prevent obesity and metabolic diseases and explored the underlying mechanism. Mice were fed a high-fat diet (HFD) containing PEF extract for 12 weeks, and their body weight, adipose tissue and liver weights, and lipid profiles and blood glucose levels, were monitored. Fecal triglyceride (TG) levels were also measured and olive oil-loading tests were performed. Furthermore, the effect of PEF extract on pancreatic lipase (PL) activity was examined in vitro. Treatment with PEF extract for 12 weeks resulted in a significant decrease in the HFD-induced increases in body weight, white adipose tissue weight, liver weights, and lipid profiles, and improved glucose tolerance and insulin sensitivity. To assess the mechanism underlying the effect of PEF extract on obesity and diabetes, we investigated its role in inhibiting lipid absorption. Consumption of an HFD containing PEF extract significantly increased the TG level in feces compared with the controls, suggesting inhibition of TG absorption in the digestive tract. Furthermore, PEF extract suppressed the increase in serum TG levels resulting from oral administration of a lipid emulsion to mice, confirming inhibition of TG absorption. Moreover, PEF extract inhibited PL activity in vitro. Our combined results indicate that the anti-obesity and antidiabetic effect of PEF extract in mice fed an HFD may be caused by inhibition of lipid absorption as a result of reduced PL activity.

Genetic diversity of Lepista nuda (Agaricales, Basidiomycota) in Northeast China as indicated by SRAP and ISSR markers

Lepista nuda is a popular wild edible mushroom that grows in China. In this study, we used ISSR and SRAP molecular markers to analyze the genetic diversity of 72 samples of L. nuda from eight populations in Northeast China. In total, six ISSR primers and five pairs of SRAP primers that produced clear and polymorphic banding profiles were selected for assessing L. nuda genetic diversity. The results revealed a high level of genetic variation among the 72 samples (94.4% polymorphism) but a low degree of gene flow among the populations. Among L. nuda populations, genetic distance was not correlated significantly with geographic distance. The antioxidant activity of the samples from each population was also tested and the result showed that all the selected samples had more than 60% DPPH scavenging activities. Nonetheless, the antioxidant activity diversity is not coincident with both the genetic diversity and the geographic distribution. The results indicate that ISSR and SRAP molecular markers are useful for studying the genetic diversity of L. nuda. The results also suggest that L. nuda populations in Northeast China require protection.

Assessment of Genetic Diversity among Pleurotus spp. Isolates from Jordan

Pleurotus is considered an important genus that belongs to the family Pleurotaceae and includes the edible King Oyster mushroom (Pleurotus eryngii). In the present study, 19 Pleurotus isolates were collected from two locations in the north of Jordan (Tell ar-Rumman and Um-Qais). The morphological characteristics among collected isolates revealed that there was a morphological similarity among the collected isolates. Nucleotide sequence analysis of the internal transcribed spacer (ITS1⁻5.8S rDNA⁻ITS4 region) and 28S nuclear large subunit (nLSU) in the ribosomal DNA gene of the isolated stains showed that all of them share over 98% sequence similarity with P. eryngii. Genetic diversity among the collected strains was assessed using inter simple sequence repeat (ISSR) analysis using 18 different primer pairs. Using this approach, 141 out of 196 bands obtained were considered polymorphic and the highest percentage of polymorphism was observed using primer UBC827 (92.3%) with an overall Polymorphism Information Content (PIC) value of 70.56%. Cluster analysis showed that the Jordanian Pleurotus isolates fall into two main clades with a coefficient of similarity values ranging from 0.59 to 0.74 with a clear clustering based on collection sites. The results of the present study reveal that molecular techniques of ISSR and rDNA sequencing can greatly aid in classification and identification of Pleurotus spp. in Jordan.

Comparative Transcriptome Analysis Identified Candidate Genes Related to Bailinggu Mushroom Formation and Genetic Markers for Genetic Analyses and Breeding

Bailinggu (Pleurotus tuoliensis) is a major, commercially cultivated mushroom and widely used for nutritional, medicinal, and industrial applications. Yet, the mushroom’s genetic architecture and the molecular mechanisms underlying its formation are largely unknown. Here we performed comparative transcriptomic analysis during Bailinggu’s mycelia, primordia, and fruiting body stages to identify genes regulating fruiting body development and develop EST-SSR markers assessing the genetic value of breeding materials. The stage-specific and differentially expressed unigenes (DEGs) involved in morphogenesis, primary carbohydrate metabolism, cold stimulation and blue-light response were identified using GO and KEGG databases. These unigenes might help Bailinggu adapt to genetic and environmental factors that influence fructification. The most pronounced change in gene expression occurred during the vegetative-to-reproductive transition, suggesting that is most active and key for Bailinggu development. We then developed 26 polymorphic and informative EST-SSR markers to assess the genetic diversity in 82 strains of Bailinggu breeding materials. These EST-SSRs exhibited high transferability in closely related species P. eryngii var. ferulae and var. eryngii. Genetic population structure analysis indicated that China’s Bailinggu has low introgression with these two varieties and likely evolved independently. These findings provide new genes, SSR markers, and germplasm to enhance the breeding of commercially cultivated Bailinggu.

The famous cultivated mushroom Bailinggu is a separate species of the Pleurotus eryngii species complex

The mushroom of the genus Pleurotus in western China, called Bailinggu, is a precious edible fungus with high economic value. However, its taxonomical position is unclear. Some researchers regard it as a variety of P. eryngii, namely P. eryngii var. tuoliensis, whereas others consider it to be a subspecies of P. eryngii, viz. P. eryngii subsp. tuoliensis. A total of 51 samples representing seven genetic groups of the genus Pleurotus were subjected to a phylogenetic analysis of partial sequences of the translation elongation factor 1 alpha gene (ef1a), the RNA polymerase II largest subunit gene (rpb1), the RNA polymerase II second largest subunit gene (rpb2) and nuc rDNA internal transcribed spacers (ITS). Our data indicate that the mushroom Bailinggu is a lineage independent of P. eryngii and should be lifted as its own species, namely P. tuoliensis. In addition, its known distribution range consists of both western China and Iran.

De Novo Sequencing and Transcriptome Analysis of Pleurotus eryngii subsp. tuoliensis (Bailinggu) Mycelia in Response to Cold Stimulation

Cold stimulation of Bailinggu's mycelia is the main factor that triggers primordia initiation for successful production of fruiting bodies under commercial cultivation. Yet, the molecular-level mechanisms involved in mycelia response to cold stimulation are still unclear. Here, we performed comparative transcriptomic analysis using RNA-Seq technology to better understand the gene expression regulation during different temporal stages of cold stimulation in Bailinggu. A total of 21,558 Bailinggu mycelia unigenes were de novo assembled and annotated from four libraries (control at 25 °C, plus cold stimulation treatments at -3 °C for a duration of 1-2 days, 5-6 days, and 9-10 days). GO and KEGG pathway analysis indicated that functional groups of differentially expressed unigenes associated with cell wall and membrane stabilization, calcium signaling and mitogen-activated protein kinases (MAPK) pathways, and soluble sugars and protein biosynthesis and metabolism pathways play a vital role in Bailinggu's response to cold stimulation. Six hundred and seven potential EST-based SSRs loci were identified in these unigenes, and 100 EST-SSR primers were randomly selected for validation. The overall polymorphism rate was 92% by using 10 wild strains of Bailinggu. Therefore, these results can serve as a valuable resource for a better understanding of the molecular mechanisms associated with Bailinggu's response to cold stimulation.

Phylogenetic relationship of two popular edible Pleurotus in China, Bailinggu (P. eryngii var. tuoliensis) and Xingbaogu (P. eryngii), determined by ITS, RPB2 and EF1α sequences

The aims of this study are to assess the utility of the internal transcribed spacer (ITS) region, and partial translation elongation factor (EF1α) and RNA polymerase II (RPB2) genes, for differentiation of Bailinggu, P. eryngii, and P. nebrodensis; to reconstruct phylogenetic relationships between the three species; and to confirm the taxonomic status of Bailinggu based on ribosomal and protein-coding genes. Pairwise genetic distances between Bailinggu, P. eryngii, and related Pleurotus strains were calculated by using the p-distance model, and molecular phylogeny of these isolates was estimated based on ITS, RPB2, and EF1α using maximum parsimony and Bayesian methods. Differences in ITS, RPB2, and EF1α sequences show that Bailinggu, P. eryngii, and P. nebrodensis are distinct at the species level. Phylogenetic analyses reveal that P. eryngii is closer to P. nebrodensis than to Bailinggu. Sequence analyses of ribosomal and protein-coding genes confirm that P. eryngii var. tuoliensis is identical to Bailinggu. P. eryngii var. tuoliensis should be raised to species level or a new name should be introduced for Bailinggu after a thorough investigation into Pleurotus isolates from Ferula in Xinjiang Province. This study helps to resolve uncertainty regarding Bailinggu, P. eryngii and P. nebrodensis, improving the resource management of these strains. ITS, EF1α, and RPB2 sequences can be used to distinguish Bailinggu, P. eryngii and P. nebrodensis as three different species, and P. eryngii var. tuoliensis should be the scientific name for Bailinggu at present.

Evidence for Inbreeding and Genetic Differentiation among Geographic Populations of the Saprophytic Mushroom Trogia venenata from Southwestern China

During the past 40 years, more than 400 Sudden Unexplained Deaths (SUDs) have occurred in Yunnan, southwestern China. Epidemiological and toxicological analyses suggested that a newly discovered mushroom called Trogia venenata was the leading culprit for SUDs. At present, relatively little is known about the genetics and natural history of this mushroom. In this study, we analyzed the sequence variation at four DNA fragments among 232 fruiting bodies of T. venenata collected from seven locations. Our ITS sequence analyses confirmed that all the isolates belonged to the same species. The widespread presence of sequence heterozygosity within many strains at each of three protein-coding genes suggested that the fruiting bodies were diploid, dikaryotic or heterokaryotic. Within individual geographic populations, we found significant deviations of genotype frequencies from Hardy-Weinberg expectations, with the overall observed heterozygosity lower than that expected under random mating, consistent with prevalent inbreeding within local populations. The geographic populations were overall genetically differentiated. Interestingly, while a positive correlation was found between population genetic distance and geographic distance, there was little correlation between genetic distance and barium concentration difference for the geographic populations. Our results suggest frequent inbreeding, geographic structuring, and limited gene flow among geographic populations of T. venenata from southwestern China.

Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species

Twenty-four start codon targeted (SCoT) markers were used to assess genetic diversity and population structure of indigenous, introduced and domesticated ramie (Boehmeria nivea L. Gaudich.). A total of 155 genotypes from five populations were investigated for SCoT polymorphism, which produced 136 amplicons with 87.5% polymorphism. Polymorphism information content and resolving power of the SCoT markers were 0.69 and 3.22, respectively. The Indian ramie populations exhibited high SCoT polymorphism (> 50%), high genetic differentiation (G_ST = 0.27) and moderate gene flow (N_m = 1.34). Analysis of molecular variance identified significant differences for genetic polymorphism among the populations explaining 13.1% of the total variation. The domesticated population exhibited higher genetic polymorphism and heterozygosity compared to natural populations. Cluster analysis supported population genetic analysis and suggested close association between introduced and domesticated genotypes. The present study shows effectiveness of employing SCoT markers in a cross pollinated heterozygous species like Boehmeria, and would be useful for further studies in population genetics, conservation genetics and cultivar improvement.

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Genetic diversity and population structure of ramie (Boehmeria nivea) were assessed by SCoT markers.

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SCoT markers revealed high polymorphism and resolving ability in Boehmeria nivea.

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The wild ramie showed moderate heterozygosity and gene flow with high genetic variation, suggesting unidirectional gene flow.

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The domesticated population exhibited highest heterozygosity and close association with introduced population.