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4. Chromosome-Scale Genome and Transcriptomic Analyses Reveal Differential Regulation of Terpenoid Secondary Metabolites in Hericium coralloides.

Author

Meng, Kexin, Lv, Junyi, Zhang, Tuo, Liu, Yuanyuan, Zhang, Peng, Zhang, Yue, Hu, Banghui, Huang, Qianhui, Xie, Baogui, and Fu, Junsheng

Subjects
METABOLITES, CHROMOSOMES, FRUITING bodies (Fungi), EDIBLE mushrooms, BIOSYNTHESIS
Abstract

Construction of the genome of Hericium coralloides, a species of edible mushroom, and identification of the genes involved in terpenoid biosynthesis can determine the biology and genetics of terpenoids. The present study describes the assembly of a high-quality chromosome-scale genome of H. coralloides using Pacbio HiFi sequencing and Hi-C technology. This genome consisted of 13 chromosomes, a total size of 43.6 Mb, contigs of N50 3.6 Mb, GC content at 54%, and BUSCOs integrity of 96.9%. Genes associated with terpenoid biosynthesis were predicted by KEGG enrichment analysis and homologous alignment. The Her011461 and Her008335 genes, encoding proteins in the terpenoid backbone synthesis pathway, were found to encode geranylgeranyl pyrophosphate and farnesyl diphosphate synthases, key enzymes in the biosynthesis of geranylgeranyl diphosphate, a precursor of several diterpenoids. Her011463 was found to be involved in regulating diterpene cyclase. The Her005433, Her006724, Her010605, and Her010608 genes were found to encode sesquiterpene synthesis. Most of these genes were more highly expressed in dikaryotic mycelia than in the primordium and fruiting bodies, indicating that terpenoids may be more abundant in dikaryotic mycelia. To our knowledge, this study is the first to assemble the H. coralloides genome at the chromosome scale and to identify the genes involved in terpenoid biosynthesis. [ABSTRACT FROM AUTHOR]

Published
2024
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13. Low temperature, mechanical wound, and exogenous salicylic acid (SA) can stimulate the SA signaling molecule as well as its downstream pathway and the formation of fruiting bodies in Flammulina filiformis

Author

Li, Ziyan, primary, Wen, Jin, additional, Jing, Zhuohan, additional, Li, Hui, additional, Huang, Jiahua, additional, Yuan, Chengjin, additional, Xian, Lijun, additional, Gao, Lingling, additional, Zhu, Jian, additional, Xie, Baogui, additional, and Tao, Yongxin, additional

Published
2023
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15. Flammutoxin, a Degradation Product of Transepithelial Electrical Resistance-Decreasing Protein, Induces Reactive Oxygen Species and Apoptosis in HepG2 Cells.

Author

Wu, Jianguo, Nong, Yu, Chen, Bingzhi, Jiang, Yuji, Chen, Yuanhao, Wei, Chuanzheng, Tao, Yongxin, and Xie, Baogui

Subjects
REACTIVE oxygen species, FRUITING bodies (Fungi), GASTROINTESTINAL cancer, APOPTOSIS, AMMONIUM sulfate
Abstract

Proteins from Flammulina filiformis were prepared by sodium chloride extraction and fractionated by ammonium sulfate precipitation with increasing saturation degrees to obtain the protein fractions Ffsp-30, Ffsp-50, Ffsp-70, Ffsp-90, and Ffp-90. Among these protein fractions, Ffsp-50 possessed the most significant cytotoxic effect against three human gastrointestinal cancer cell lines, viz. HT-29, SGC-7901, and HepG2. SDS-PAGE and MALDI-TOF/TOF MS/MS analyses revealed that flammutoxin (FTX) was present as a dominating protein in Ffsp-50, which was further evidenced by HPLC-MS/MS determination. Furthermore, native FTX was purified from Ffsp-50 with a molecular weight of 26.78 kDa, exhibiting notable cytotoxicity against gastrointestinal cancer cell lines. Both Ffsp-50 and FTX exposure could enhance intercellular reactive oxygen species (ROS) generation and induce significant apoptosis in HepG2 cells. FTX was identified to be relatively conserved in basidiomycetes according to phylogenetic analysis, and its expression was highly upregulated in the primordium as well as the pileus of the fruiting body from the elongation and maturation stages, as compared with that in mycelium. Taken together, FTX could remarkably inhibit cell growth and induce ROS and apoptosis in HepG2 cells, potentially participating in the growth and development of the fruiting body. These findings from our investigation provided insight into the antigastrointestinal cancer activity of FTX, which could serve as a biological source of health-promoting and biomedical applications. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Spermidine Synthase and Saccharopine Reductase Have Co-Expression Patterns Both in Basidiomycetes with Fusion Form and Ascomycetes with Separate Form

Author

Yang, Yayong, primary, Shi, Lei, additional, Xu, Xinyu, additional, Wen, Jin, additional, Xie, Tianyue, additional, Li, Hui, additional, Li, Xiaoyu, additional, Chen, Mengyu, additional, Dou, Xinyi, additional, Yuan, Chengjin, additional, Song, Hanbing, additional, Xie, Baogui, additional, and Tao, Yongxin, additional

Published
2023
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18. Preliminary study on the anti-CO2 stress and growth ability of hypsizygus marmoreus mutant strain HY68.

Author

Liu, Fang, Ma, Lin, Chen, Weifeng, Wang, Sifan, Wei, Chuanzheng, Huang, Chengpo, Jiang, Yimin, Wang, Song, Lin, Hongyan, Chen, Jian, Wang, Gang, Xie, Baogui, and Yuan, Zongsheng

Subjects
EDIBLE fungi, FRUITING bodies (Fungi), PROTEIN structure, FUNGAL growth, MALTOSE
Abstract

Background: A high concentration of CO2 will stagnate the development of the newly formed primordia of Hypsizygus marmoreus, hinder the development of the mushroom cap, thereby inhibiting the normal differentiation of the fruiting body. Moreover, in the previous experiment, our research group obtained the mutant strain HY68 of H. marmoreus, which can maintain normal fruiting under the condition of high concentration of CO2. Our study aimed to evaluate the CO2 tolerance ability of the mutant strain HY68, in comparison with the starting strain HY61 and the control strain HY62. We analyzed the mycelial growth of these strains under various conditions, including different temperatures, pH levels, carbon sources, and nitrogen sources, and measured the activity of the cellulose enzyme. Additionally, we identified and predicted β-glucosidase-related genes in HY68 and analyzed their gene and protein structures. Results: Our results indicate that HY68 showed superior CO2 tolerance compared to the other strains tested, with an optimal growth temperature of 25 °C and pH of 7, and maltose and beef paste as the ideal carbon and nitrogen sources, respectively. Enzyme activity assays revealed a positive correlation between β-glucosidase activity and CO2 tolerance, with Gene14147 identified as the most closely related gene to this activity. Inbred strains of HY68 showed trait segregation for CO2 tolerance. Conclusions: Both HY68 and its self-bred offspring could tolerate CO2 stress. The fruiting period of the strains resistant to CO2 stress was shorter than that of the strains not tolerant to CO2 stress. The activity of β-GC and the ability to tolerate CO2 were more closely related to the growth efficiency of fruiting bodies. This study lays the foundation for understanding how CO2 regulates the growth of edible fungi, which is conducive to the innovation of edible fungus breeding methods. The application of the new strain HY68 is beneficial to the research of energy-saving production in factory cultivation. [ABSTRACT FROM AUTHOR]

Published
2023
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33. Transcriptome Profiling Reveals Candidate Genes Related to Stipe Gradient Elongation of Flammulina filiformis.

Author

Yan, Junjie, Tong, Zongjun, Han, Xing, Gan, Ying, Liu, Yuanyuan, Chen, Jie, Duan, Xinlian, Lin, Junbin, Gan, Bingcheng, and Xie, Baogui

Subjects
FRUITING bodies (Fungi), GENES, TRANSCRIPTOMES, CELL anatomy, FATTY acids, GENE expression profiling
Abstract

Stipe gradient elongation is an important and remarkable feature in the development of most mushroom fruiting bodies. However, its molecular mechanism has rarely been described. Here, the decreasing trend of stipe elongation and increasing trend of cell length in a gradient from the top to the base of the stipe were determined in a model basidiomycete mushroom: Flammulina filiformis. According to RNA-seq results, 1409 differentially expressed genes (DEGs) were identified among elongation region (ER), transition region (TR), and stable region (SR) samples, including 26 transcription factors (TFs). Based on Short Time-series Expression Miner (STEM) clustering of DEGs, clusters 1 and 3, with obvious expression trends that were consistent with or in contrast to the elongation rate, were screened. The cluster 1 DEGs were mainly involved in the GO cellular component category and KEGG genetic information processing class; however, the cluster 3 DEGs were mainly involved in metabolic processes. Furthermore, qRT-PCR confirmed that key genes of the long-chain fatty acid synthesis pathway were involved in stipe gradient elongation and regulated by NADPH oxidase-derived ROS signaling molecules. These findings provide an essential basis for understanding the molecular mechanism of stipe gradient elongation. [ABSTRACT FROM AUTHOR]

Published
2023
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38. Identifying a melanogenesis-related candidate gene by a high-quality genome assembly and population diversity analysis in Hypsizygus marmoreus

Author

Wang, Gang, primary, Chen, Lianfu, additional, Tang, Weiqi, additional, Wang, Yuanyuan, additional, Zhang, Qing, additional, Wang, Hongbo, additional, Zhou, Xuan, additional, Wu, Haofeng, additional, Guo, Lin, additional, Dou, Meijie, additional, Liu, Lei, additional, Wang, Baiyu, additional, Lin, Jingxian, additional, Xie, Baogui, additional, Wang, Zhengchao, additional, Liu, ZhongJian, additional, Ming, Ray, additional, and Zhang, Jisen, additional

Published
2021
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44. A second HD mating type sublocus of Flammulina velutipes is at least di-allelic and active : New primers for identification of HD - A and HD-b subloci

Author

Wang, Wei, Mukhtar, Irum, Chou, Tiansheng, Jiang, Siyuan, Liu, Xinrui, Van Peer, Arend F., Xie, Baogui, Wang, Wei, Mukhtar, Irum, Chou, Tiansheng, Jiang, Siyuan, Liu, Xinrui, Van Peer, Arend F., and Xie, Baogui

Abstract

Background: Sexual development in Flammulina velutipes is controlled by two different mating type loci (HD and PR). The HD locus contains homeodomain (Hd) genes on two separate HD subloci: HD-a and HD-b. While the functionality of the HD-b sublocus has been largely confirmed, the status and content of the HD-a sublocus has remained unclear. Methods: To examine the function of the HD-a sublocus, genome sequences of a series of F. velutipes strains were analyzed and tested through series of amplification by specific primer sets. Furthermore, activity of di-allelic HD-a locus was confirmed by crossing strains with different combinations of HD-a and HD-b subloci. Results: Sublocus HD-b contained a large variety of fixed Hd1/Hd2 gene pairs, while the HD-a sublocus either contained a conserved Hd2 gene or, a newly discovered Hd1 gene that was also conserved. Identification of whole HD loci, that is, the contents of HD-a and HD-b subloci in a strain, revealed that strains with similar HD-b subloci could still form normal dikaryons if the two genes at the HD-a sublocus differed. At least di-allelic HD-a sublocus, is thus indicated to be actively involved in mating type compatibility. Conclusions: HD-a sublocus is active and di-allelic. Using the new information on the HD subloci, primers sets were developed that specifically amplify HD-a or HD-b subloci in the majority of F. velutipes strains. In this way, unknown HD mating types of F. velutipes can now be quickly identified, and HD mating type compatibility conferred by HD-a or HD-b can be confirmed by PCR.

Published
2019

45. Three rapid methods for direct PCR of powdery mildew samples for later sequencing

Author

Mukhtar, Irum, Van Peer, Arend F., Vazquez-Marrufo, Gerardo, Ma Vazquez-Garciduenas, Soledad, and Xie, Baogui

Subjects
PBR Mushroom research, Its, DNA isolation, Powdery mildews, PBR Paddenstoelen
Abstract

Powdery mildews are an important obligate parasitic fungal group reported in nearly all regions of the world. DNA isolation for molecular identification of powdery mildew samples is now a standard practice and is becoming more affordable but remains a lengthy process. In this study, three direct DNA isolation methods have been developed for rDNA internal transcribed spacer (ITS) amplification of different powdery mildew species. This reduces time taken for traditional DNA extraction from hours to minutes and rapid PCR means large quantities of DNA are available for sequencing in an hour. Methods proposed in this paper were found rapid and efficient for sequencing. ITS sequences obtained, were neat, clear and comparable to sequences obtained by conventional DNA extraction methods. However, ITS remains insufficient for separation of certain closely related species. In conclusion, our methods are simple, cost-effective and produced enough genomic DNA for quick and high quality sequences. Methods should be trialed further for preparation of DNA libraries of further genomic regions for rapid and accurate powdery mildew identification.

Published
2018

50. Intra-specific comparison of mitochondrial genomes reveals host gene fragment exchange via intron mobility in Tremella fuciformis Brief Intron variation in mitochondrial genomes of Tremella fuciformis

Author

Deng, Youjin, primary, Zhang, Xunxiao, additional, Xie, Baogui, additional, Lin, Longji, additional, Hsiang, Tom, additional, Lin, Xiangzhi, additional, Lin, Yiying, additional, Zhang, Xingtan, additional, Ma, Yanhong, additional, Miao, Wenjing, additional, and Ming, Ray, additional

Published
2019
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