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Fang Y, Wu D, Gao N, Lv M, Zhou M, Ma C, Sun Y, Cui B. Whole-genome sequencing and comparative genomic analyses of the medicinal fungus Sanguinoderma infundibulare in Ganodermataceae. G3 (BETHESDA, MD.) 2024; 14:jkae005. [PMID: 38366555 PMCID: PMC10989896 DOI: 10.1093/g3journal/jkae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024]
Abstract
Sanguinoderma infundibulare is a newly discovered species of Ganodermataceae known to have high medicinal and ecological values. In this study, the whole-genome sequencing and comparative genomic analyses were conducted to further understand Ganodermataceae's genomic structural and functional characteristics. Using the Illumina NovaSeq and PacBio Sequel platforms, 88 scaffolds were assembled to obtain a 48.99-Mb high-quality genome of S. infundibulare. A total of 14,146 protein-coding genes were annotated in the whole genome, with 98.6% of complete benchmarking universal single-copy orthologs (BUSCO) scores. Comparative genomic analyses were conducted among S. infundibulare, Sanguinoderma rugosum, Ganoderma lucidum, and Ganoderma sinense to determine their intergeneric differences. The 4 species were found to share 4,011 orthogroups, and 24 specific gene families were detected in the genus Sanguinoderma. The gene families associated with carbohydrate esterase in S. infundibulare were significantly abundant, which was reported to be involved in hemicellulose degradation. One specific gene family in Sanguinoderma was annotated with siroheme synthase, which may be related to the typical characteristics of fresh pore surface changing to blood red when bruised. This study enriched the available genome data for the genus Sanguinoderma, elucidated the differences between Ganoderma and Sanguinoderma, and provided insights into the characteristics of the genome structure and function of S. infundibulare.
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Affiliation(s)
- Yuxuan Fang
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Dongmei Wu
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China
| | - Neng Gao
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832061, China
| | - Mengxue Lv
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Miao Zhou
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Chuangui Ma
- Beijing Jingcheng Biotechnology Co., Ltd, Beijing 100083, China
| | - Yifei Sun
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Baokai Cui
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
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Wang M, Meng G, Yang Y, Wang X, Xie R, Dong C. Telomere-to-Telomere Genome Assembly of Tibetan Medicinal Mushroom Ganoderma leucocontextum and the First Copia Centromeric Retrotransposon in Macro-Fungi Genome. J Fungi (Basel) 2023; 10:15. [PMID: 38248925 PMCID: PMC10817607 DOI: 10.3390/jof10010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/23/2024] Open
Abstract
A complete telomere-to-telomere (T2T) genome has been a longstanding goal in the field of genomic research. By integrating high-coverage and precise long-read sequencing data using multiple assembly strategies, we present here the first T2T gap-free genome assembly of Ganoderma leucocontextum strain GL72, a Tibetan medicinal mushroom. The T2T genome, with a size of 46.69 Mb, consists 13 complete nuclear chromosomes and typical telomeric repeats (CCCTAA)n were detected at both ends of 13 chromosomes. The high mapping rate, uniform genome coverage, a complete BUSCOs of 99.7%, and base accuracy exceeding 99.999% indicate that this assembly represents the highest level of completeness and quality. Regions characterized by distinct structural attributes, including highest Hi-C interaction intensity, high repeat content, decreased gene density, low GC content, and minimal or no transcription levels across all chromosomes may represent potential centromeres. Sequence analysis revealed the first Copia centromeric retrotransposon in macro-fungi genome. Phylogenomic analysis identified that G. leucocontextum and G. tsugae diverged from the other Ganoderma species approximately 9.8-17.9 MYA. The prediction of secondary metabolic clusters confirmed the capability of this fungus to produce a substantial quantity of metabolites. This T2T gap-free genome will contribute to the genomic 'dark matter' elucidation and server as a great reference for genetics, genomics, and evolutionary studies of G. leucocontextum.
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Affiliation(s)
- Miao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (M.W.); (G.M.); (Y.Y.); (X.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoliang Meng
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (M.W.); (G.M.); (Y.Y.); (X.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (M.W.); (G.M.); (Y.Y.); (X.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofang Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (M.W.); (G.M.); (Y.Y.); (X.W.)
| | - Rong Xie
- Institute of Vegetable Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China;
| | - Caihong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (M.W.); (G.M.); (Y.Y.); (X.W.)
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Sonets IV, Dovidchenko NV, Ulianov SV, Yarina MS, Koshechkin SI, Razin SV, Krasnopolskaya LM, Tyakht AV. Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing. J Fungi (Basel) 2023; 9:1020. [PMID: 37888276 PMCID: PMC10608111 DOI: 10.3390/jof9101020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/28/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023] Open
Abstract
Ganoderma lucidum exhibits the ability to synthesize a diverse range of biologically active molecules with significant pharmaceutical potential, including xylomannan and fucogalactan, which have demonstrated antitumor activity. However, there exists considerable intra-species variability in the capacity to produce these metabolites at high concentrations, likely reflecting the high genomic diversity observed from a limited number of strains sequenced to date. We employed high-throughput shotgun sequencing to obtain the complete genome sequence of G. lucidum strain 5.1, which is distinguished by its remarkable xylomannan synthesis capabilities. Through the utilization of semi-automatic reordering based on conformation capture (Hi-C) data, we substantially enhanced the assembly process, resulting in the generation of 12 chromosome-level scaffolds with a cumulative length of 39 Mbp. By employing both de novo and homology-based approaches, we performed comprehensive annotation of the genome, thereby identifying a diverse repertoire of genes likely involved in polysaccharide biosynthesis. The genome sequence generated in this study serves as a valuable resource for elucidating the molecular mechanisms underlying the medicinal potential of Ganoderma species, discovering novel pharmaceutically valuable compounds, and elucidating the ecological mechanisms of the species. Furthermore, the chromosome contact map obtained for the first time for this species extends our understanding of 3D fungal genomics and provides insights into the functional and structural organization within the fungal kingdom.
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Affiliation(s)
- Ignat V. Sonets
- Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia; (I.V.S.); (S.V.U.); (S.V.R.); (A.V.T.)
| | - Nikita V. Dovidchenko
- Knomics LLC, 34 Bld. 1 Narodnogo Opolcheniya Street, 123423 Moscow, Russia; (N.V.D.); (S.I.K.)
- Institute of Protein Research, 4 Institutskaya Street, 142290 Pushchino, Russia
| | - Sergey V. Ulianov
- Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia; (I.V.S.); (S.V.U.); (S.V.R.); (A.V.T.)
- Faculty of Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
| | - Maria S. Yarina
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, 119021 Moscow, Russia;
| | - Stanislav I. Koshechkin
- Knomics LLC, 34 Bld. 1 Narodnogo Opolcheniya Street, 123423 Moscow, Russia; (N.V.D.); (S.I.K.)
| | - Sergey V. Razin
- Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia; (I.V.S.); (S.V.U.); (S.V.R.); (A.V.T.)
- Faculty of Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia
| | | | - Alexander V. Tyakht
- Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia; (I.V.S.); (S.V.U.); (S.V.R.); (A.V.T.)
- Knomics LLC, 34 Bld. 1 Narodnogo Opolcheniya Street, 123423 Moscow, Russia; (N.V.D.); (S.I.K.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia
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Hao J, Wang X, Shi Y, Li L, Chu J, Li J, Lin W, Yu T, Hou D. Integrated omic profiling of the medicinal mushroom Inonotus obliquus under submerged conditions. BMC Genomics 2023; 24:554. [PMID: 37726686 PMCID: PMC10507853 DOI: 10.1186/s12864-023-09656-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/06/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND The Inonotus obliquus mushroom, a wondrous fungus boasting edible and medicinal qualities, has been widely used as a folk medicine and shown to have many potential pharmacological secondary metabolites. The purpose of this study was to supply a global landscape of genome-based integrated omic analysis of the fungus under lab-growth conditions. RESULTS This study presented a genome with high accuracy and completeness using the Pacbio Sequel II third-generation sequencing method. The de novo assembled fungal genome was 36.13 Mb, and contained 8352 predicted protein-coding genes, of which 365 carbohydrate-active enzyme (CAZyme)-coding genes and 19 biosynthetic gene clusters (BCGs) for secondary metabolites were identified. Comparative transcriptomic and proteomic analysis revealed a global view of differential metabolic change between seed and fermentation culture, and demonstrated positive correlations between transcription and expression levels of 157 differentially expressed genes involved in the metabolism of amino acids, fatty acids, secondary metabolites, antioxidant and immune responses. Facilitated by the widely targeted metabolomic approach, a total of 307 secondary substances were identified and quantified, with a significant increase in the production of antioxidant polyphenols. CONCLUSION This study provided the comprehensive analysis of the fungus Inonotus obliquus, and supplied fundamental information for further screening of promising target metabolites and exploring the link between the genome and metabolites.
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Affiliation(s)
- Jinghua Hao
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China
| | - Xiaoli Wang
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China
| | - Yanhua Shi
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China
| | - Lingjun Li
- School of Modern Agriculture and Environment, Weifang Institute of Technology, Weifang, 261053, China
| | - Jinxin Chu
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China
| | - Junjie Li
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China
| | - Weiping Lin
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China.
| | - Tao Yu
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China.
| | - Dianhai Hou
- School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, China.
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Ma X, Lu L, Yao F, Fang M, Wang P, Meng J, Shao K, Sun X, Zhang Y. High-quality genome assembly and multi-omics analysis of pigment synthesis pathway in Auricularia cornea. Front Microbiol 2023; 14:1211795. [PMID: 37396365 PMCID: PMC10308021 DOI: 10.3389/fmicb.2023.1211795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023] Open
Abstract
Owing to its great market potential for food and health care, white Auricularia cornea, a rare edible fungus, has received increased attention in recent years. This study presents a high-quality genome assembly of A. cornea and multi-omics analysis of its pigment synthesis pathway. Continuous Long Reads libraries, combined with Hi-C-assisted assembly were used to assemble of white A. cornea. Based on this data, we analyzed the transcriptome and metabolome of purple and white strains during the mycelium, primordium, and fruiting body stages. Finally, we obtained the genome of A.cornea assembled from 13 clusters. Comparative and evolutionary analysis suggests that A.cornea is more closely related to Auricularia subglabra than to Auricularia heimuer. The divergence of white/purple A.cornea occurred approximately 40,000 years ago, and there were numerous inversions and translocations between homologous regions of the two genomes. Purple strain synthesized pigment via the shikimate pathway. The pigment in the fruiting body of A. cornea was γ-glutaminyl-3,4-dihydroxy-benzoate. During pigment synthesis, α-D-glucose-1P, citrate, 2-Oxoglutarate, and glutamate were four important intermediate metabolites, whereas polyphenol oxidase and other 20 enzyme genes were the key enzymes. This study sheds light on the genetic blueprint and evolutionary history of the white A.cornea genome, revealing the mechanism of pigment synthesis in A.cornea. It has important theoretical and practical implications for understanding the evolution of basidiomycetes, molecular breeding of white A.cornea, and deciphering the genetic regulations of edible fungi. Additionally, it provides valuable insights for the study of phenotypic traits in other edible fungi.
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Affiliation(s)
- Xiaoxu Ma
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
- Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Edible Fungi Breeding, Guiyang, China
| | - Lixin Lu
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Fangjie Yao
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
- Country Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Ming Fang
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Peng Wang
- Economic Plants Research Insitute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jingjing Meng
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Kaisheng Shao
- Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Edible Fungi Breeding, Guiyang, China
| | - Xu Sun
- Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Edible Fungi Breeding, Guiyang, China
| | - Youmin Zhang
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
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Increasing the production of the bioactive compounds in medicinal mushrooms: an omics perspective. Microb Cell Fact 2023; 22:11. [PMID: 36647087 PMCID: PMC9841694 DOI: 10.1186/s12934-022-02013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Macroscopic fungi, mainly higher basidiomycetes and some ascomycetes, are considered medicinal mushrooms and have long been used in different areas due to their pharmaceutically/nutritionally valuable bioactive compounds. However, the low production of these bioactive metabolites considerably limits the utilization of medicinal mushrooms both in commerce and clinical trials. As a result, many attempts, ranging from conventional methods to novel approaches, have been made to improve their production. The novel strategies include conducting omics investigations, constructing genome-scale metabolic models, and metabolic engineering. So far, genomics and the combined use of different omics studies are the most utilized omics analyses in medicinal mushroom research (both with 31% contribution), while metabolomics (with 4% contribution) is the least. This article is the first attempt for reviewing omics investigations in medicinal mushrooms with the ultimate aim of bioactive compound overproduction. In this regard, the role of these studies and systems biology in elucidating biosynthetic pathways of bioactive compounds and their contribution to metabolic engineering will be highlighted. Also, limitations of omics investigations and strategies for overcoming them will be provided in order to facilitate the overproduction of valuable bioactive metabolites in these valuable organisms.
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Wu P, Xiao W, Luo Y, Xiong Z, Chen X, He J, Sha A, Gui M, Li Q. Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes. Front Microbiol 2023; 14:1170790. [PMID: 37213503 PMCID: PMC10192751 DOI: 10.3389/fmicb.2023.1170790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/12/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Codon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon usage in the mitochondrial genome of Ganoderma species remain unknown. Methods In this study, we investigated the codon bias of 12 mitochondrial core protein-coding genes (PCGs) in 9 Ganoderma species, including 13 Ganoderma strains. Results The codons of all Ganoderma strains showed a preference for ending in A/T. Additionally, correlations between codon base composition and the codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) were identified, demonstrating the impact of base composition on codon bias. Various base bias indicators were found to vary between or within Ganoderma strains, including GC3s, the CAI, the CBI, and the FOP. The results also revealed that the mitochondrial core PCGs of Ganoderma have an average effective number of codons (ENC) lower than 35, indicating strong bias toward certain codons. Evidence from neutrality plot and PR2-bias plot analysis indicates that natural selection is a major factor affecting codon bias in Ganoderma. Additionally, 11 to 22 optimal codons (ΔRSCU>0.08 and RSCU>1) were identified in 13 Ganoderma strains, with GCA, AUC, and UUC being the most widely used optimal codons in Ganoderma. By analyzing the combined mitochondrial sequences and relative synonymous codon usage (RSCU) values, the genetic relationships between or within Ganoderma strains were determined, indicating variations between them. Nevertheless, RSCU-based analysis illustrated the intra- and interspecies relationships of certain Ganoderma species. Discussion This study deepens our insight into the synonymous codon usage characteristics, genetics, and evolution of this important fungal group.
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Affiliation(s)
- Peng Wu
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wenqi Xiao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Yingyong Luo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Zhuang Xiong
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Xiaodie Chen
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Jing He
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Ajia Sha
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Mingying Gui
- Yunnan Plateau Characteristic Agricultural Industry Research Institute, Yunnan Agricultural University, Kunming, Yunnan, China
- *Correspondence: Mingying Gui,
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering and Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu, Sichuan, China
- Qiang Li,
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Sun YF, Fang YX, Cui BK. Taxonomy and phylogeny of Sanguinoderma rugosum complex with descriptions of a new species and a new combination. Front Microbiol 2022; 13:1087212. [PMID: 36620035 PMCID: PMC9811172 DOI: 10.3389/fmicb.2022.1087212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022] Open
Abstract
Sanguinoderma is distributed in tropical and subtropical areas as a member of Amauroderma s. lat., and the economic values of Sanguinoderma led to high attention in the taxonomic studies. Previously, 16 species have been developed into Sanguinoderma. In this study, the taxonomic system of Sanguinoderma was reconducted based on morphological and multi-gene phylogenetic analyses, especially making a distinction for Sanguinoderma rugosum complex. Morphological analysis was based on the notes of macro- and micro morphological observations. Multi-gene phylogenetic analyses were used maximum likelihood (ML) and Bayesian inference (BI) analyses inferred from combined dataset of ITS, nLSU, rpb2, tef1, mtSSU, and nSSU. Combined with morphological characters and phylogenetic evidence, the results demonstrated that S. rugosum complex consists of five taxa, in which Sanguinoderma leucomarginatum was described as a new species, and it is characterized by the orbicular pilei with white to buff margin when fresh and clavate apical cells of pileipellis with septa. In addition, Amauroderma preussii was transferred to Sanguinoderma as a new combination due to its blood-red color-changed pore surface; it is characterized by the funnel-shaped, greyish brown, and glabrous pilei with strongly incurved margin. Detailed descriptions and photographs of the two species were provided. With the extension of this study, 18 species were accepted in Sanguinoderma, and 12 species among them were distributed in China. A key to accepted species of Sanguinoderma was also provided.
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Wang Q, Qi P, Zhao C, Zhang Y, Wang L, Yu H. Tandem expression of Ganoderma sinense sesquiterpene synthase and IDI promotes the production of gleenol in E. coli. Appl Microbiol Biotechnol 2022; 106:7779-7791. [DOI: 10.1007/s00253-022-12248-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/10/2022] [Accepted: 10/15/2022] [Indexed: 11/10/2022]
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Jiang N, Li Z, Dai Y, Liu Z, Han X, Li Y, Li Y, Xiong H, Xu J, Zhang G, Xiao S, Yuan X, Fu Y. Massive genome investigations reveal insights of prevalent introgression for environmental adaptation and triterpene biosynthesis in Ganoderma. Mol Ecol Resour 2022. [PMID: 36214617 DOI: 10.1111/1755-0998.13718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/26/2022] [Accepted: 10/06/2022] [Indexed: 11/29/2022]
Abstract
Genome introgression is one of the driving forces that can increase species and genetic diversity and facilitate the adaptive evolution of organisms and biodiversity conservation. However, the genomic introgression and its contribution to biodiversity of macrofungi are still unclear. The genus Ganoderma is a typical macrofungal group that plays crucial roles in forest ecosystem as saprophytic organisms and plant pathogens, and is also involved in human health as medicinal mushrooms. Most public Ganoderma genomes are fragmented, and reference genomes and whole-genome information of diverse germplasm resources for many Ganoderma species are lacking, thus hindering functional and evolutionary genomic investigations among Ganoderma species. In this study, we provide high-quality genomes of 10 Ganoderma species and whole-genome variants data of 224 individuals from various ecoregions, enabling us to infer the phylogeny of Ganoderma species and their historical population dynamics. Based on whole-genome variants, widespread and genome-wide introgression among Ganoderma species is revealed. Genes with significant introgression signals were related to stress response, digestive absorption, and secondary metabolite synthesis, factors that may contribute to environmental adaptation and important biocomponent metabolism. CYP512U6, an essential functional gene in the CYP450 family related to Ganoderma triterpene synthesis, was detected with significant introgression and selection signals combined with Ganoderma metabolomic analysis, indicating that both ancient gene exchange and recent domestication have contributed to the categories and content of secondary metabolites of Ganoderma. The reference genomes, whole-genome variants, and metabolite profiles could serve as abundant and valuable genetic resources for evolution, ecology, and conservation investigations of Ganoderma species and other macrofungi.
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Affiliation(s)
- Nan Jiang
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
- College of Plant Protection, Jilin Agricultural University, Jilin, Changchun, China
| | - Zhenhao Li
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Yueting Dai
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Zhenhua Liu
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Xuerong Han
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Yu Li
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Yong Li
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Hui Xiong
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Jing Xu
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Guoliang Zhang
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Shijun Xiao
- Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing, Zhejiang, China
| | - Xiaohui Yuan
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Yongping Fu
- College of Plant Protection, Jilin Agricultural University, Jilin, Changchun, China
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Li Q, Zhang T, Li L, Bao Z, Tu W, Xiang P, Wu Q, Li P, Cao M, Huang W. Comparative Mitogenomic Analysis Reveals Intraspecific, Interspecific Variations and Genetic Diversity of Medical Fungus Ganoderma. J Fungi (Basel) 2022; 8:jof8080781. [PMID: 35893149 PMCID: PMC9394262 DOI: 10.3390/jof8080781] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Ganoderma species are widely distributed in the world with high diversity. Some species are considered to be pathogenic fungi while others are used as traditional medicine in Asia. In this study, we sequenced and assembled four Ganoderma complete mitogenomes, including G. subamboinense s118, G. lucidum s37, G. lingzhi s62, and G. lingzhi s74. The sizes of the four mitogenomes ranged from 50,603 to 73,416 bp. All Ganoderma specimens had a full set of core protein-coding genes (PCGs), and the rps3 gene of Ganoderma species was detected to be under positive or relaxed selection. We found that the non-conserved PCGs, which encode RNA polymerases, DNA polymerases, homing endonucleases, and unknown functional proteins, are dynamic within and between Ganoderma species. Introns were thought to be the main contributing factor in Ganoderma mitogenome size variation (p < 0.01). Frequent intron loss/gain events were detected within and between Ganoderma species. The mitogenome of G. lucidum s26 gained intron P637 in the cox3 gene compared with the other two G. lucidum mitogenomes. In addition, some rare introns in Ganoderma were detected in distinct Basidiomycetes, indicating potential gene transfer events. Comparative mitogenomic analysis revealed that gene arrangements also varied within and between Ganoderma mitogenomes. Using maximum likelihood and Bayesian inference methods with a combined mitochondrial gene dataset, phylogenetic analyses generated identical, well-supported tree topologies for 71 Agaricomycetes species. This study reveals intraspecific and interspecific variations of the Ganoderma mitogenomes, which promotes the understanding of the origin, evolution, and genetic diversity of Ganoderma species.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Ting Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Lijiao Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Zhijie Bao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Wenying Tu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Peng Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Qian Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Q.L.); (T.Z.); (L.L.); (Z.B.); (W.T.); (P.X.); (Q.W.)
| | - Ping Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd., Chengdu 610061, China;
| | - Mei Cao
- Core Laboratory, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
- Correspondence: (M.C.); (W.H.); Tel.: +86-028-84592187 (W.H.)
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd., Chengdu 610061, China;
- Correspondence: (M.C.); (W.H.); Tel.: +86-028-84592187 (W.H.)
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12
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Mao Z, Yang P, Liu H, Mao Y, Lei Y, Hou D, Ma H, Liao X, Jiang W. Whole-Genome Sequencing and Analysis of the White-Rot Fungus Ceriporia lacerata Reveals Its Phylogenetic Status and the Genetic Basis of Lignocellulose Degradation and Terpenoid Synthesis. Front Microbiol 2022; 13:880946. [PMID: 35685935 PMCID: PMC9171200 DOI: 10.3389/fmicb.2022.880946] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/22/2022] [Indexed: 12/02/2022] Open
Abstract
Ceriporia lacerata is an endophytic white-rot fungus that has lignocellulolytic and terpenoid-biosynthetic abilities. However, little is known about the genomic architecture of this fungus, even at the genus level. In this study, we present the first de novo genome assembly of C. lacerata (CGMCC No. 10485), based on PacBio long-read and Illumina short-read sequencing. The size of the C. lacerata genome is approximately 36 Mb (N50, 3.4 Mb). It encodes a total of 13,243 genes, with further functional analysis revealing that these genes are primarily involved in primary metabolism and host interactions in this strain's saprophytic lifestyle. Phylogenetic analysis based on ITS demonstrated a primary evolutionary position for C. lacerata, while the phylogenetic analysis based on orthogroup inference and average nucleotide identity revealed high-resolution phylogenetic details in which Ceriporia, Phlebia, Phlebiopsis, and Phanerochaete belong to the same evolutionary clade within the order Polyporales. Annotation of carbohydrate-active enzymes across the genome yielded a total of 806 genes encoding enzymes that decompose lignocellulose, particularly ligninolytic enzymes, lytic polysaccharides monooxygenases, and enzymes involved in the biodegradation of aromatic components. These findings illustrate the strain's adaptation to woody habitats, which requires the degradation of lignin and various polycyclic aromatic hydrocarbons. The terpenoid-production potential of C. lacerata was evaluated by comparing the genes of terpenoid biosynthetic pathways across nine Polyporales species. The shared genes highlight the major part of terpenoid synthesis pathways, especially the mevalonic acid pathway, as well as the main pathways of sesquiterpenoid, monoterpenoid, diterpenoid, and triterpenoid synthesis, while the strain-specific genes illustrate the distinct genetic factors determining the synthesis of structurally diverse terpenoids. This is the first genomic analysis of a species from this genus that we are aware of, and it will help advance functional genome research and resource development of this important fungus for applications in renewable energy, pharmaceuticals, and agriculture.
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Affiliation(s)
- Zhitao Mao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ping Yang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Huanhuan Liu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
| | - Yufeng Mao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yu Lei
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dongwei Hou
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongwu Ma
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xiaoping Liao
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Wenxia Jiang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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13
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Sun YF, Lebreton A, Xing JH, Fang YX, Si J, Morin E, Miyauchi S, Drula E, Ahrendt S, Cobaugh K, Lipzen A, Koriabine M, Riley R, Kohler A, Barry K, Henrissat B, Grigoriev IV, Martin FM, Cui BK. Phylogenomics and Comparative Genomics Highlight Specific Genetic Features in Ganoderma Species. J Fungi (Basel) 2022; 8:jof8030311. [PMID: 35330313 PMCID: PMC8955403 DOI: 10.3390/jof8030311] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/11/2022] Open
Abstract
The Ganoderma species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven Ganoderma genomes, including three new genomes, G. australe, G. leucocontextum, and G. lingzhi. The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that Ganoderma species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the Ganoderma species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, G. australe has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. G. australe also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of G. australe secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the Ganoderma species.
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Affiliation(s)
- Yi-Fei Sun
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
| | - Annie Lebreton
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Jia-Hui Xing
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
| | - Yu-Xuan Fang
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
| | - Jing Si
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
| | - Shingo Miyauchi
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829 Cologne, Germany
| | - Elodie Drula
- INRAE, Aix Marseille University, UMR1163 Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France;
| | - Steven Ahrendt
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Kelly Cobaugh
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Maxim Koriabine
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Robert Riley
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
- Department of Biological Sciences, King Abdulaziz University, Jeddah 999088, Saudi Arabia
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.A.); (K.C.); (A.L.); (M.K.); (R.R.); (K.B.); (I.V.G.)
- Department of Microbial and Plant Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Francis M. Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes (IAM), Centre INRAE Grand Est-Nancy, 54280 Champenoux, France; (A.L.); (E.M.); (S.M.); (A.K.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Correspondence: (F.M.M.); (B.-K.C.); Tel.: +33-383394080 (F.M.M.); +86-1062336309 (B.-K.C.)
| | - Bao-Kai Cui
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (Y.-F.S.); (J.-H.X.); (Y.-X.F.); (J.S.)
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Correspondence: (F.M.M.); (B.-K.C.); Tel.: +33-383394080 (F.M.M.); +86-1062336309 (B.-K.C.)
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14
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Cao R, Wu X, Wang Q, Qi P, Zhang Y, Wang L, Sun C. Characterization of γ-Cadinene Enzymes in Ganoderma lucidum and Ganoderma sinensis from Basidiomycetes Provides Insight into the Identification of Terpenoid Synthases. ACS OMEGA 2022; 7:7229-7239. [PMID: 35252713 PMCID: PMC8892675 DOI: 10.1021/acsomega.1c06792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Enzymes boost protein engineering, directed evolution, and the biochemical industry and are also the cornerstone of metabolic engineering. Basidiomycetes are known to produce a large variety of terpenoids with unique structures. However, basidiomycetous terpene synthases remain largely untapped. Therefore, we provide a modeling method to obtain specific terpene synthases. Aided by bioinformatics analysis, three γ-cadinene enzymes from Ganoderma lucidum and Ganoderma sinensis were accurately predicted and identified experimentally. Based on the highly conserved amino motifs of the characterized γ-cadinene enzymes, the enzyme was reassembled as model 1. Using this model as a template, 67 homologous sequences of the γ-cadinene enzyme were screened from the National Center for Biotechnology Information (NCBI). According to the 67 sequences, the same gene structure, and similar conserved motifs to model 1, the γ-cadinene enzyme model was further improved by the same construction method and renamed as model 2. The results of bioinformatics analysis show that the conservative regions of models 1 and 2 are highly similar. In addition, five of these sequences were verified, 100% of which were γ-cadinene enzymes. The accuracy of the prediction ability of the γ-cadinene enzyme model was proven. In the same way, we also reanalyzed the identified Δ6-protoilludene enzymes in fungi and (-)-α-bisabolol enzymes in plants, all of which have their own unique conserved motifs. Our research method is expected to be used to study other terpenoid synthases with a similar or the same function in basidiomycetes, ascomycetes, bacteria, and plants and to provide rich enzyme resources.
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Affiliation(s)
- Rui Cao
- School
of Chinese Materia Medica, Tianjin University
of Traditional Chinese Medicine, Tianjin 301617, P. R. China
| | - Xinlong Wu
- College
of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, P. R. China
| | - Qi Wang
- School
of Chinese Materia Medica, Tianjin University
of Traditional Chinese Medicine, Tianjin 301617, P. R. China
| | - Pengyan Qi
- School
of Chinese Materia Medica, Tianjin University
of Traditional Chinese Medicine, Tianjin 301617, P. R. China
| | - Yuna Zhang
- School
of Chinese Materia Medica, Tianjin University
of Traditional Chinese Medicine, Tianjin 301617, P. R. China
| | - Lizhi Wang
- School
of Chinese Materia Medica, Tianjin University
of Traditional Chinese Medicine, Tianjin 301617, P. R. China
| | - Chao Sun
- Institute
of Medicinal Plant Development, Chinese
Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, P. R. China
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15
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Nasrullah, Hussain A, Ahmed S, Rasool M, Shah AJ. DNA methylation across the tree of life, from micro to macro-organism. Bioengineered 2022; 13:1666-1685. [PMID: 34986742 PMCID: PMC8805842 DOI: 10.1080/21655979.2021.2014387] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is a process in which methyl (CH3) groups are added to the DNA molecule. The DNA segment does not change in the sequence, but DNA methylation could alter the action of DNA. Different enzymes like DNA methyltransferases (DNMTs) take part in methylation of cytosine/adenine nucleosides in DNA. In prokaryotes, DNA methylation is performed to prevent the attack of phage and also plays a role in the chromosome replication and repair. In fungi, DNA methylation is studied to see the transcriptional changes, as in insects, the DNA methylation is not that well-known, it plays a different role like other organisms. In mammals, the DNA methylation is related to different types of cancers and plays the most important role in the placental development and abnormal DNA methylation connected with diseases like cancer, autoimmune diseases, and rheumatoid arthritis.
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Affiliation(s)
- Nasrullah
- Center for Advanced Studies in Vaccinology & Biotechnology (Casvab), University of Baluchistan, Quetta- Pakistan. E-mails:
| | - Abrar Hussain
- Department of Biotechnology, Faculty of Life Sciences, Buitems, Quetta-Pakistan. E-mails:
| | - Sagheer Ahmed
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan. E-mails:
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. E-mails:
| | - Abdul Jabbar Shah
- Department of Pharmaceutical Sciences, Comsats University, Abbottabad. E-mails:
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16
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Yang J, Gu D, Wu S, Zhou X, Chen J, Liao Y, Zeng L, Yang Z. Feasible strategies for studying the involvement of DNA methylation and histone acetylation in the stress-induced formation of quality-related metabolites in tea (Camellia sinensis). HORTICULTURE RESEARCH 2021; 8:253. [PMID: 34848699 PMCID: PMC8632975 DOI: 10.1038/s41438-021-00679-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 08/17/2021] [Indexed: 05/26/2023]
Abstract
Tea plants are subjected to multiple stresses during growth, development, and postharvest processing, which affects levels of secondary metabolites in leaves and influences tea functional properties and quality. Most studies on secondary metabolism in tea have focused on gene, protein, and metabolite levels, whereas upstream regulatory mechanisms remain unclear. In this review, we exemplify DNA methylation and histone acetylation, summarize the important regulatory effects that epigenetic modifications have on plant secondary metabolism, and discuss feasible research strategies to elucidate the underlying specific epigenetic mechanisms of secondary metabolism regulation in tea. This information will help researchers investigate the epigenetic regulation of secondary metabolism in tea, providing key epigenetic data that can be used for future tea genetic breeding.
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Affiliation(s)
- Jie Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Dachuan Gu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Shuhua Wu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Xiaochen Zhou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Jiaming Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Yinyin Liao
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Lanting Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Ziyin Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, No. 723 Xingke Road, Tianhe District, Guangzhou, 510650, China.
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17
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Jiang N, Hu S, Peng B, Li Z, Yuan X, Xiao S, Fu Y. Genome of Ganoderma Species Provides Insights Into the Evolution, Conifers Substrate Utilization, and Terpene Synthesis for Ganoderma tsugae. Front Microbiol 2021; 12:724451. [PMID: 34603250 PMCID: PMC8481371 DOI: 10.3389/fmicb.2021.724451] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/16/2021] [Indexed: 12/30/2022] Open
Abstract
Ganoderma tsugae is an endemic medicinal mushroom in Northeast China, providing important source of pharmaceutical product. Comparing with other Ganoderma species, wild G. tsugae can utilize coniferous wood. However, functional genes related to medicinal component synthesis and the genetic mechanism of conifer substrate utilization is still obscure. Here, we assembled a high-quality G. tsugae genome with 18 contigs and 98.5% BUSCO genes and performed the comparative genomics with other Ganoderma species. G. tsugae diverged from their common ancestor of G. lingzhi and G. sinense about 21 million years ago. Genes in G. tsugae-specific and G. tsugae-expanded gene families, such as salh, phea, cyp53a1, and cyp102a, and positively selected genes, such as glpk and amie, were functionally enriched in plant-pathogen interaction, benzoate degradation, and fanconi anemia pathway. Those functional genes might contribute to conifer substrate utilization of G. tsugae. Meanwhile, gene families in the terpene synthesis were identified and genome-wide SNP variants were detected in population. Finally, the study provided valuable genomic resources and offered useful hints for the functional gene mapping and investigation of key gene contributing to conifer cultivation substrate utilization and medicinal component biosynthesis.
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Affiliation(s)
- Nan Jiang
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Shuang Hu
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Bing Peng
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Zhenhao Li
- Shouxiangu Botanical Drug Institute Co., Ltd., Jinhua, China
| | - Xiaohui Yuan
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China.,Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing, China
| | - Shijun Xiao
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Yongping Fu
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
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Fessner ND, Nelson DR, Glieder A. Evolution and enrichment of CYP5035 in Polyporales: functionality of an understudied P450 family. Appl Microbiol Biotechnol 2021; 105:6779-6792. [PMID: 34459954 PMCID: PMC8426240 DOI: 10.1007/s00253-021-11444-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/29/2021] [Accepted: 07/03/2021] [Indexed: 11/29/2022]
Abstract
Abstract Bioprospecting for innovative basidiomycete cytochrome P450 enzymes (P450s) is highly desirable due to the fungi’s enormous enzymatic repertoire and outstanding ability to degrade lignin and detoxify various xenobiotics. While fungal metagenomics is progressing rapidly, the biocatalytic potential of the majority of these annotated P450 sequences usually remains concealed, although functional profiling identified several P450 families with versatile substrate scopes towards various natural products. Functional knowledge about the CYP5035 family, for example, is largely insufficient. In this study, the families of the putative P450 sequences of the four white-rot fungi Polyporus arcularius, Polyporus brumalis, Polyporus squamosus and Lentinus tigrinus were assigned, and the CYPomes revealed an unusual enrichment of CYP5035, CYP5136 and CYP5150. By computational analysis of the phylogeny of the former two P450 families, the evolution of their enrichment could be traced back to the Ganoderma macrofungus, indicating their evolutionary benefit. In order to address the knowledge gap on CYP5035 functionality, a representative subgroup of this P450 family of P. arcularius was expressed and screened against a test set of substrates. Thereby, the multifunctional enzyme CYP5035S7 converting several plant natural product classes was discovered. Aligning CYP5035S7 to 102,000 putative P450 sequences of 36 fungal species from Joint Genome Institute-provided genomes located hundreds of further CYP5035 family members, which subfamilies were classified if possible. Exemplified by these specific enzyme analyses, this study gives valuable hints for future bioprospecting of such xenobiotic-detoxifying P450s and for the identification of their biocatalytic potential. Graphical abstract ![]()
Key points • The P450 families CYP5035 and CYP5136 are unusually enriched in P. arcularius. • Functional screening shows CYP5035 assisting in the fungal detoxification mechanism. • Some Polyporales encompass an unusually large repertoire of detoxification P450s. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11444-2.
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Affiliation(s)
- Nico D Fessner
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010, Graz, Austria
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010, Graz, Austria.
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Shokrollahi N, Ho CL, Zainudin NAIM, Wahab MABA, Wong MY. Identification of non-ribosomal peptide synthetase in Ganoderma boninense Pat. that was expressed during the interaction with oil palm. Sci Rep 2021; 11:16330. [PMID: 34381084 PMCID: PMC8358039 DOI: 10.1038/s41598-021-95549-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Basal stem rot (BSR) of oil palm is a disastrous disease caused by a white-rot fungus Ganoderma boninense Pat. Non-ribosomal peptides (NRPs) synthesized by non-ribosomal peptide synthetases (NRPSs) are a group of secondary metabolites that act as fungal virulent factors during pathogenesis in the host. In this study, we aimed to isolate NRPS gene of G. boninense strain UPMGB001 and investigate the role of this gene during G. boninense-oil palm interaction. The isolated NRPS DNA fragment of 8322 bp was used to predict the putative peptide sequence of different domains and showed similarity with G. sinense (85%) at conserved motifs of three main NRPS domains. Phylogenetic analysis of NRPS peptide sequences demonstrated that NRPS of G. boninense belongs to the type VI siderophore family. The roots of 6-month-old oil palm seedlings were artificially inoculated for studying NRPS gene expression and disease severity in the greenhouse. The correlation between high disease severity (50%) and high expression (67-fold) of G. boninense NRPS gene at 4 months after inoculation and above indicated that this gene played a significant role in the advancement of BSR disease. Overall, these findings increase our knowledge on the gene structure of NRPS in G. boninense and its involvement in BSR pathogenesis as an effector gene.
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Affiliation(s)
- Neda Shokrollahi
- grid.11142.370000 0001 2231 800XDepartment of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Chai-Ling Ho
- grid.11142.370000 0001 2231 800XDepartment of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Nur Ain Izzati Mohd Zainudin
- grid.11142.370000 0001 2231 800XDepartment of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Mohd As’wad Bin Abul Wahab
- grid.11142.370000 0001 2231 800XDepartment of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Mui-Yun Wong
- grid.11142.370000 0001 2231 800XDepartment of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia ,grid.11142.370000 0001 2231 800XInstitute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
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20
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Wang G, Chen L, Tang W, Wang Y, Zhang Q, Wang H, Zhou X, Wu H, Guo L, Dou M, Liu L, Wang B, Lin J, Xie B, Wang Z, Liu Z, Ming R, Zhang J. Identifying a melanogenesis-related candidate gene by a high-quality genome assembly and population diversity analysis in Hypsizygus marmoreus. J Genet Genomics 2021; 48:75-87. [PMID: 33744162 DOI: 10.1016/j.jgg.2021.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
Hypsizygus marmoreus is one of the most important edible fungi in Basidiomycete division and includes white and gray strains. However, very limited knowledge is known about the genomic structures and the genetic basis for the white/gray diversity of this mushroom. Here, we report the near-complete high-quality H. marmoreus genome at the chromosomal level. Comparative genomics analysis indicates that chromosome structures were relatively conserved, and variations in collinearity and chromosome number were mainly attributed by chromosome split/fusion events in Aragicales, whereas the fungi genome experienced many genomic chromosome fracture, fusion, and genomic replication events after the split of Aragicales from Basidiomycetes. Resequencing of 57 strains allows us to classify the population into four major groups and associate genetic variations with morphological features, indicating that white strains were not originated independently. We further generated genetic populations and identified a cytochrome P450 as the candidate causal gene for the melanogenesis in H. marmoreus based on bulked segregant analysis (BSA) and comparative transcriptome analysis. The high-quality H. marmoreus genome and diversity data compiled in this study provide new knowledge and resources for the molecular breeding of H. marmoreus as well as the evolution of Basidiomycete.
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Affiliation(s)
- Gang Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; School of Geographical Science, Nantong University, Nantong 226001, China
| | - Lianfu Chen
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weiqi Tang
- Institute of Oceanography, Marine Biotechnology Center, Minjiang University, Fuzhou 350108, China
| | - Yuanyuan Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongbo Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuan Zhou
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haofeng Wu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lin Guo
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meijie Dou
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Liu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baiyu Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingxian Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baogui Xie
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhengchao Wang
- Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Fujian Normal University, Fuzhou 350007, China
| | - ZhongJian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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21
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Lin W, Shi Y, Jia G, Sun H, Sun T, Hou D. Genome sequencing and annotation and phylogenomic analysis of the medicinal mushroom Amauroderma rugosum, a traditional medicinal species in the family Ganodermataceae. Mycologia 2021; 113:268-277. [PMID: 33555992 DOI: 10.1080/00275514.2020.1851135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Amauroderma rugosum is one of the traditional Chinese medicinal mushrooms and is used to reduce inflammation, treat diuretic and upset stomach, and prevent cancer. Here, we present a genomic resource of Amauroderma rugosum (ACCC 51706) for further understanding its biology and exploration of the synthesis pathway of bioactive compounds. Genomic DNA was extracted and then subjected to Illumina HiSeq X Ten and PacBio Sequel I sequencing. The final genome is 40.66 Mb in size, with an N50 scaffold size of 36.6 Mb, and encodes 10 181 putative predicted genes. Among them, 6931 genes were functionally annotated. Phylogenomic analysis suggested that A. rugosum and Ganoderma sinense were not clustered together into a group and the latter was grouped with the Polyporaceae. Further, we also identified 377 carbohydrate-active enzymes (CAZymes) and 15 secondary metabolite biosynthetic gene clusters. This is the first genome-scale assembly and annotation for an Amauroderma species. The identification of novel secondary metabolite biosynthetic gene clusters would promote pharmacological research and development of novel bioactive compounds in the future.
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Affiliation(s)
- Weiping Lin
- School of Bioscience and Technology, Weifang Medical University, Weifang 261053, China.,Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Medical University, Weifang 261053, China
| | - Yanhua Shi
- School of Bioscience and Technology, Weifang Medical University, Weifang 261053, China.,Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Medical University, Weifang 261053, China
| | - Guangtao Jia
- School of Bioscience and Technology, Weifang Medical University, Weifang 261053, China.,Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Medical University, Weifang 261053, China
| | - Hengyi Sun
- Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Medical University, Weifang 261053, China
| | - Tongyi Sun
- School of Bioscience and Technology, Weifang Medical University, Weifang 261053, China.,Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Medical University, Weifang 261053, China
| | - Dianhai Hou
- School of Bioscience and Technology, Weifang Medical University, Weifang 261053, China.,Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Medical University, Weifang 261053, China
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22
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Nai YS, Huang YC, Yen MR, Chen PY. Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation Patterns. Front Microbiol 2021; 11:616922. [PMID: 33552027 PMCID: PMC7862722 DOI: 10.3389/fmicb.2020.616922] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/28/2020] [Indexed: 11/24/2022] Open
Abstract
DNA methyltransferases (DNMTs) are a group of proteins that catalyze DNA methylation by transferring a methyl group to DNA. The genetic variation in DNMTs results in differential DNA methylation patterns associated with various biological processes. In fungal species, DNMTs and their DNA methylation profiles were found to be very diverse and have gained many research interests. We reviewed fungal DNMTs in terms of their biological functions, protein domain structures, and their associated epigenetic regulations compared to those known in plant and animal systems. In addition, we summarized recent reports on potential RNA-directed DNA methylation (RdDM) related to DNMT5 in fungi. We surveyed up to 40 fungal species with published genome-wide DNA methylation profiles (methylomes) and presented the associations between the specific patterns of fungal DNA methylation and their DNMTs based on a phylogenetic tree of protein domain structures. For example, the main DNMTs in Basidiomycota, DNMT1 with RFD domain + DNMT5, contributing to CG methylation preference, were distinct from RID + Dim-2 in Ascomycota, resulting in a non-CG methylation preference. Lastly, we revealed that the dynamic methylation involved in fungal life stage changes was particularly low in mycelium and DNA methylation was preferentially located in transposable elements (TEs). This review comprehensively discussed fungal DNMTs and methylomes and their connection with fungal development and taxonomy to present the diverse usages of DNA methylation in fungal genomes.
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Affiliation(s)
- Yu-Shin Nai
- Department of Entomology, National Chung Hsing University, Taichung, Taiwan.,Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chun Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei, Taiwan.,Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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23
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Bonner C, Sproule A, Rowland O, Overy D, Subramaniam R. DNA Methylation Is Responsive to the Environment and Regulates the Expression of Biosynthetic Gene Clusters, Metabolite Production, and Virulence in Fusarium graminearum. FRONTIERS IN FUNGAL BIOLOGY 2021; 1:614633. [PMID: 37743878 PMCID: PMC10512235 DOI: 10.3389/ffunb.2020.614633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/07/2020] [Indexed: 09/26/2023]
Abstract
Histone modifications play a significant role in the regulation of biosynthetic gene clusters (BGCs) in the phytopathogen Fusarium graminearum, by contrast, epigenetic regulation by DNA methyltransferases (DNMTs) is less documented. In this study, we characterized two DNMTs (FgDIM-2 and FgRID) in F. graminearum, with homologies to "Deficient in methylation" (DIM-2) and "Repeat-induced point (RIP) deficient" (RID) from Neurospora. The loss of DNMTs resulted in not only a decrease in average methylation density in the nutrient-poor, compared to nutrient-rich conditions, but also differences in the genes expressed between the WT and the DNMT mutant strains, implicating the external environment as an important trigger in altering DNA methylation patterns. Consequently, we observed significant changes in the regulation of multiple BGCs and alterations in the pathogenicity of the fungus.
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Affiliation(s)
- Christopher Bonner
- Department of Biology, Carleton University, Ottawa, ON, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Amanda Sproule
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Owen Rowland
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - David Overy
- Department of Biology, Carleton University, Ottawa, ON, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Rajagopal Subramaniam
- Department of Biology, Carleton University, Ottawa, ON, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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24
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Zhao S, Gao Q, Rong C, Wang S, Zhao Z, Liu Y, Xu J. Immunomodulatory Effects of Edible and Medicinal Mushrooms and Their Bioactive Immunoregulatory Products. J Fungi (Basel) 2020; 6:E269. [PMID: 33171663 PMCID: PMC7712035 DOI: 10.3390/jof6040269] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/19/2022] Open
Abstract
Mushrooms have been valued as food and health supplements by humans for centuries. They are rich in dietary fiber, essential amino acids, minerals, and many bioactive compounds, especially those related to human immune system functions. Mushrooms contain diverse immunoregulatory compounds such as terpenes and terpenoids, lectins, fungal immunomodulatory proteins (FIPs) and polysaccharides. The distributions of these compounds differ among mushroom species and their potent immune modulation activities vary depending on their core structures and fraction composition chemical modifications. Here we review the current status of clinical studies on immunomodulatory activities of mushrooms and mushroom products. The potential mechanisms for their activities both in vitro and in vivo were summarized. We describe the approaches that have been used in the development and application of bioactive compounds extracted from mushrooms. These developments have led to the commercialization of a large number of mushroom products. Finally, we discuss the problems in pharmacological applications of mushrooms and mushroom products and highlight a few areas that should be improved before immunomodulatory compounds from mushrooms can be widely used as therapeutic agents.
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Affiliation(s)
- Shuang Zhao
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (S.Z.); (Q.G.); (C.R.); (S.W.); (Z.Z.); (Y.L.)
| | - Qi Gao
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (S.Z.); (Q.G.); (C.R.); (S.W.); (Z.Z.); (Y.L.)
| | - Chengbo Rong
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (S.Z.); (Q.G.); (C.R.); (S.W.); (Z.Z.); (Y.L.)
| | - Shouxian Wang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (S.Z.); (Q.G.); (C.R.); (S.W.); (Z.Z.); (Y.L.)
| | - Zhekun Zhao
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (S.Z.); (Q.G.); (C.R.); (S.W.); (Z.Z.); (Y.L.)
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056038, China
| | - Yu Liu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (S.Z.); (Q.G.); (C.R.); (S.W.); (Z.Z.); (Y.L.)
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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25
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Zhou C, Zhang H, Fang H, Sun Y, Zhou H, Yang G, Lu F. Transcriptome based functional identification and application of regulator AbrB on alkaline protease synthesis in Bacillus licheniformis 2709. Int J Biol Macromol 2020; 166:1491-1498. [PMID: 33166558 DOI: 10.1016/j.ijbiomac.2020.11.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 11/30/2022]
Abstract
Bacillus licheniformis 2709 is the major alkaline protease producer, which has great potential value of industrial application, but how the high-producer can be regulated rationally is still not completely understood. It's meaningful to understand the metabolic processes during alkaline protease production in industrial fermentation medium. Here, we collected the transcription database at various enzyme-producing stages (preliminary stage, stable phase and decline phase) to specifically research the synthesized and regulatory mechanism of alkaline protease in B. licheniformis. The RNA-sequencing analysis showed differential expression of numerous genes related to several processes, among which genes correlated with regulators were concerned, especially the major differential gene abrB on enzyme (AprE) synthesis was investigated. It was further verified that AbrB is a repressor of AprE by plasmid-mediated over-expression due to the severely descending enzyme activity (11,300 U/mL to 2695 U/mL), but interestingly it is indispensable for alkaline protease production because the enzyme activity of the null abrB mutant was just about 2279 U/mL. Thus, we investigated the aprE transcription by eliminating the theoretical binding site (TGGAA) of AbrB protein predicated by computational strategy, which significantly improved the enzyme activity by 1.21-fold and gene transcription level by 1.77-fold in the mid-log phase at a cultivation time of 18 h. Taken together, it is of great significance to improve the production strategy, control the metabolic process and oriented engineering by rational molecular modification of regulatory network based on the high throughput sequencing and computational prediction.
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Affiliation(s)
- Cuixia Zhou
- School of Biology and Brewing Engineering, Taishan University, Taian 271018, PR China; Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Huitu Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Honglei Fang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Yanqing Sun
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Huiying Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China
| | - Guangcheng Yang
- School of Biology and Brewing Engineering, Taishan University, Taian 271018, PR China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, College of Biotechnology, Tianjin University of Science &Technology, Tianjin 300450, PR China.
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Zheng S, Zhu N, Shi C, Zheng H. Genomic data mining approaches for the discovery of anticancer peptides from Ganoderma sinense. PHYTOCHEMISTRY 2020; 179:112466. [PMID: 32823212 DOI: 10.1016/j.phytochem.2020.112466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Drug discovery from traditional Chinese medicine (TCM) typically involves the extraction of active ingredients from natural products with high biological activity and function from the vast repertoire of traditional Chinese medicine. This strategy cannot fully exploit the vast resources of TCM. Known as the longevity mushroom, Ganoderma spp. has been used as medicine for thousands of years. Recent studies have demonstrated its anticancer activity. While most research on Ganoderma spp. has focused on their polysaccharides or small molecules as potential anticancer components, possible anticancer peptides (ACPs) or proteins have been neglected. In this study, genomic data mining approaches were used to discover potential ACPs from Ganoderma sinense. A search against known ACPs identified 477 proteins in the G. sinense proteome that possess putative ACP sequences and that thus may serve as parent proteins. After in silico digestion by trypsin, 34 G. sinense proteins were predicted to release putative ACPs (by the mACPpred program). A subsequent sequence similarity comparison against known ACPs identified 15 trypsin-digested fragments as possible ACPs, of which 3 sequences were identical to known ACPs. The results indicated that ACPs may be involved in the anticancer activity of G. sinense and that genomic mining approaches can be effective strategies for discovering active components in TCM resources. The accumulation of genomic and proteomic data will undoubtedly accelerate drug discovery from TCM resources.
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Affiliation(s)
- Sheng Zheng
- Department of Traditional Chinese Medicine, Longyan First Affiliated Hospital of Fujian Medical University, Longyan, 364000, PR China
| | - Ning Zhu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Cheng Shi
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, PR China.
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Tian YZ, Wang ZF, Liu YD, Zhang GZ, Li G. The whole-genome sequencing and analysis of a Ganoderma lucidum strain provide insights into the genetic basis of its high triterpene content. Genomics 2020; 113:840-849. [PMID: 33091546 DOI: 10.1016/j.ygeno.2020.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/27/2020] [Accepted: 10/16/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Yong-Zhen Tian
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zheng-Feng Wang
- Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China.
| | - Yi-De Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Gui-Zhen Zhang
- SunYoKon Biotechnology Co., LTD, Tsingdao, 266400, PR China
| | - Gang Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China.
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Genome-Wide Characterization and Comparative Analysis of MYB Transcription Factors in Ganoderma Species. G3-GENES GENOMES GENETICS 2020; 10:2653-2660. [PMID: 32471942 PMCID: PMC7407476 DOI: 10.1534/g3.120.401372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Numerous studies in plants have shown the vital roles of MYB transcription factors in signal transduction, developmental regulation, biotic/abiotic stress responses and secondary metabolism regulation. However, less is known about the functions of MYBs in Ganoderma. In this study, five medicinal macrofungi of genus Ganoderma were subjected to a genome-wide comparative analysis of MYB genes. A total of 75 MYB genes were identified and classified into four types: 1R-MYBs (52), 2R-MYBs (19), 3R-MYBs (2) and 4R-MYBs (2). Gene structure analysis revealed varying exon numbers (3-14) and intron lengths (7-1058 bp), and noncanonical GC-AG introns were detected in G. lucidum and G. sinense. In a phylogenetic analysis, 69 out of 75 MYB genes were clustered into 15 subgroups, and both single-copy orthologous genes and duplicated genes were identified. The promoters of the MYB genes harbored multiple cis-elements, and specific genes were co-expressed with the G. lucidum MYB genes, indicating the potential roles of these MYB genes in stress response, development and metabolism. This comprehensive and systematic study of MYB family members provides a reference and solid foundation for further functional analysis of MYB genes in Ganoderma species.
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Shao J, Wang L, Liu Y, Qi Q, Wang B, Lu S, Liu C. Identification of milRNAs and their target genes in Ganoderma lucidum by high-throughput sequencing and degradome analysis. Fungal Genet Biol 2020; 136:103313. [DOI: 10.1016/j.fgb.2019.103313] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/09/2019] [Accepted: 11/15/2019] [Indexed: 12/15/2022]
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The Pattern and Function of DNA Methylation in Fungal Plant Pathogens. Microorganisms 2020; 8:microorganisms8020227. [PMID: 32046339 PMCID: PMC7074731 DOI: 10.3390/microorganisms8020227] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 01/05/2023] Open
Abstract
To successfully infect plants and trigger disease, fungal plant pathogens use various strategies that are dependent on characteristics of their biology and genomes. Although pathogenic fungi are different from animals and plants in the genomic heritability, sequence feature, and epigenetic modification, an increasing number of phytopathogenic fungi have been demonstrated to share DNA methyltransferases (MTases) responsible for DNA methylation with animals and plants. Fungal plant pathogens predominantly possess four types of DNA MTase homologs, including DIM-2, DNMT1, DNMT5, and RID. Numerous studies have indicated that DNA methylation in phytopathogenic fungi mainly distributes in transposable elements (TEs), gene promoter regions, and the repetitive DNA sequences. As an important and heritable epigenetic modification, DNA methylation is associated with silencing of gene expression and transposon, and it is responsible for a wide range of biological phenomena in fungi. This review highlights the relevant reports and insights into the important roles of DNA methylation in the modulation of development, pathogenicity, and secondary metabolism of fungal plant pathogens. Recent evidences prove that there are massive links between DNA and histone methylation in fungi, and they commonly regulate fungal development and mycotoxin biosynthesis.
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Evaluation of DNA Methylation Changes by CRED-RA Analysis Following Prednisone Treatment of Endophyte, Fusarium oxysporum. Indian J Microbiol 2020; 60:254-258. [PMID: 32255859 DOI: 10.1007/s12088-020-00857-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/16/2020] [Indexed: 01/07/2023] Open
Abstract
Endophytes that represent a sub-set of plant resident microbes are a reservoir of bioactive metabolites. Many of the secondary metabolite biosynthetic gene clusters of endophytes are silent under axenic culture conditions. Epigenetic reprogramming of such cryptic pathways is possible by use of small molecule modulators like prednisone. Methylation changes induced by prednisone, a hypomethylating epigenetic modulator were studied in endophytic Fusarium oxysporum. CRED-RA analysis following exposure to non-cytotoxic dose (300 µM) revealed prednisone as effective in inducing non-methylation and semi-methylation pattern while inhibiting full-methylation of the genome. Effectiveness of prednisone as a DNA methyl transferase inhibitor can be explored in future to study alterations in secondary metabolite gene expression profile in endophytic F. oxysporum.
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Draft Genome Sequence of a Phytopathogenic Ganoderma sp. Strain That Causes Basal Stem Rot Disease on Oil Palm in Sabah, Malaysia. Microbiol Resour Announc 2020; 9:9/1/e01240-19. [PMID: 31896636 PMCID: PMC6940288 DOI: 10.1128/mra.01240-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Basal stem rot (BSR) disease on Elaeis guineens is known to be caused by members of the pathogenic fungal genus Ganoderma, especially the species Ganoderma boninense. This species affects oil palm plantation in Sabah, Malaysia. The genome sequence (52.28 Mbp) will add to the representation of this genus, especially in regard to BSR disease. Basal stem rot (BSR) disease on Elaeis guineens is known to be caused by members of the pathogenic fungal genus Ganoderma, especially the species Ganoderma boninense. This species affects oil palm plantation in Sabah, Malaysia. The genome sequence (52.28 Mbp) will add to the representation of this genus, especially in regard to BSR disease.
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Sbaraini N, Bellini R, Penteriche AB, Guedes RLM, Garcia AWA, Gerber AL, Vainstein MH, de Vasconcelos ATR, Schrank A, Staats CC. Genome-wide DNA methylation analysis of Metarhizium anisopliae during tick mimicked infection condition. BMC Genomics 2019; 20:836. [PMID: 31711419 PMCID: PMC6849299 DOI: 10.1186/s12864-019-6220-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/24/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The Metarhizium genus harbors important entomopathogenic fungi. These species have been widely explored as biological control agents, and strategies to improve the fungal virulence are under investigation. Thus, the interaction between Metarhizium species and susceptible hosts have been explored employing different methods in order to characterize putative virulence determinants. However, the impact of epigenetic modulation on the infection cycle of Metarhizium is still an open topic. Among the different epigenetic modifications, DNA methylation of cytosine bases is an important mechanism to control gene expression in several organisms. To better understand if DNA methylation can govern Metarhizium-host interactions, the genome-wide DNA methylation profile of Metarhizium anisopliae was explored in two conditions: tick mimicked infection and a saprophytic-like control. RESULTS Using a genome wide DNA methylation profile based on bisulfite sequencing (BS-Seq), approximately 0.60% of the total cytosines were methylated in saprophytic-like condition, which was lower than the DNA methylation level (0.89%) in tick mimicked infection condition. A total of 670 mRNA genes were found to be putatively methylated, with 390 mRNA genes uniquely methylated in the tick mimicked infection condition. GO terms linked to response to stimuli, cell wall morphogenesis, cytoskeleton morphogenesis and secondary metabolism biosynthesis were over-represented in the tick mimicked infection condition, suggesting that energy metabolism is directed towards the regulation of genes associated with infection. However, recognized virulence determinants known to be expressed at distinct infection steps, such as the destruxin backbone gene and the collagen-like protein gene Mcl1, were found methylated, suggesting that a dynamic pattern of methylation could be found during the infectious process. These results were further endorsed employing RT-qPCR from cultures treated or not with the DNA methyltransferase inhibitor 5-Azacytidine. CONCLUSIONS The set of genes here analyzed focused on secondary metabolites associated genes, known to be involved in several processes, including virulence. The BS-Seq pipeline and RT-qPCR analysis employing 5-Azacytidine led to identification of methylated virulence genes in M. anisopliae. The results provided evidences that DNA methylation in M. anisopliae comprises another layer of gene expression regulation, suggesting a main role of DNA methylation regulating putative virulence determinants during M. anisopliae infection cycle.
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Affiliation(s)
- Nicolau Sbaraini
- Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil.,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil
| | - Reinaldo Bellini
- Laboratório Nacional de Computação Científica, LNCC, Petrópolis, RJ, Brazil.,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil
| | | | - Rafael Lucas Muniz Guedes
- Laboratório Nacional de Computação Científica, LNCC, Petrópolis, RJ, Brazil.,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil
| | | | | | - Marilene Henning Vainstein
- Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil.,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil
| | - Ana Tereza Ribeiro de Vasconcelos
- Laboratório Nacional de Computação Científica, LNCC, Petrópolis, RJ, Brazil.,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil
| | - Augusto Schrank
- Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil.,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil
| | - Charley Christian Staats
- Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil. .,Rede Avançada em Biologia Computacional, RABICÓ, Petrópolis, RJ, Brazil.
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Dai Y, Li X, Song B, Sun L, Yang C, Zhang X, Wang Y, Zhang Z, Fu Y, Li Y. Genomic Analyses Provide Insights Into the Evolutionary History and Genetic Diversity of Auricularia Species. Front Microbiol 2019; 10:2255. [PMID: 31632371 PMCID: PMC6786273 DOI: 10.3389/fmicb.2019.02255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/17/2019] [Indexed: 12/27/2022] Open
Abstract
Species in the genus Auricularia play important roles for people’s food and nutrition especially Auricularia cornea and A. heimuer. To understand their evolutionary history, genome structure, and population-level genetic variation, we performed a high-quality genome sequencing of Auricularia cornea and the corresponding comparative genomic analysis. The genome size of A. cornea was similar to Auricularia subglabra, but 1.5 times larger than that of A. heimuer. Several factors were responsible for genome size variation including gene numbers, repetitive elements, and gene lengths. Phylogenomic analysis revealed that the estimated divergence time between A. heimuer and other Auricularia is ∼79.1 million years ago (Mya), while the divergence between A. cornea and A. subglabra occurred in ∼54.8 Mya. Population genomic analysis also provided insight into the demographic history of A. cornea and A. heimuer, indicating that their populations fluctuated over time with global climate change during Marine Isotope Stage 5-2. Moreover, despite the highly similar external morphologies of A. cornea and A. heimuer, their genomic properties were remarkably different. The A. cornea genome only shared 14% homologous syntenic blocks with A. heimuer and possessed more genes encoding carbohydrate-active enzymes and secondary metabolite biosynthesis proteins. The cross-taxa transferability rates of simple sequence repeat (SSR) and insertion or deletion (InDel) markers within the genus Auricularia were also lower than that previously observed for species within the same genus. Taken together, these results indicate a high level of genetic differentiation between these two Auricularia species. Consequently, our study provides new insights into the genomic evolution and genetic differentiation of Auricularia species that will facilitate future genetic breeding.
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Affiliation(s)
- Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Xiao Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Bing Song
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Lei Sun
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Chentao Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xin Zhang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yanfeng Wang
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun, China
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35
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Liu KS, Zhang C, Dong HL, Li KK, Han QB, Wan Y, Chen R, Yang F, Li HL, Ko CH, Han XQ. GSP-2, a polysaccharide extracted from Ganoderma sinense, is a novel toll-like receptor 4 agonist. PLoS One 2019; 14:e0221636. [PMID: 31442262 PMCID: PMC6707555 DOI: 10.1371/journal.pone.0221636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/12/2019] [Indexed: 01/07/2023] Open
Abstract
Ganoderma sinense is a Chinese unique medicinal fungus that has been used in folk medicine for thousands of years. Polysaccharides are considered to be biologically active ingredients due to their immune-modulating functions. Previously we found that GSP-2, a new polysaccharide isolated from Ganoderma sinense, exerts an immunomodulatory effect in human peripheral blood mononuclear cells but the underlying mechanism is unclear. The present study aimed to investigate how GSP-2 triggers immunologic responses and the implicated signaling pathways. GSP-2 effects were investigated both in a macrophagic cell line, RAW264.7, and in primary macrophages. Moreover, the molecular basis of GSP-2 recognition by immune cells, and the consequent activation of signaling cascades, were explored by employing recombinant human HEK293-TLR-Blue clones, individually overexpressing various Toll-like receptors. GSP-2 dose-dependently induced the overexpression of Toll-like receptor 4 (TLR4) but did not affect the expression of other TLRs. Moreover, GSP-2 induced TNFα secretion in primary macrophages from wild-type, but not TLR4-knockout mice. In addition, GSP-2 upregulated TLR4 protein expression and activated the MAPK pathway in RAW246.7 macrophages. Finally, GSP-2 induced the production of the cytokines TNFα, IL1β, and IL6. Our data demonstrated that GSP-2 was specifically recognized by TLR4, promoting cytokine secretion and immune modulation in macrophages.
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Affiliation(s)
- Kai-Sheng Liu
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Cheng Zhang
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Hong-Liang Dong
- Institute of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Kai-Kai Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Quan-Bin Han
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Yong Wan
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Rui Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Fang Yang
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Hai-Li Li
- The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Chun-Hay Ko
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
- * E-mail: (XQH); (CHK)
| | - Xiao-Qiang Han
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- * E-mail: (XQH); (CHK)
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Herbgenomics: A stepping stone for research into herbal medicine. SCIENCE CHINA-LIFE SCIENCES 2019; 62:913-920. [DOI: 10.1007/s11427-018-9472-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022]
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37
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Yang M, Lu L, Li S, Zhang J, Li Z, Wu S, Guo Q, Liu H, Wang C. Transcriptomic Insights into Benzenamine Effects on the Development, Aflatoxin Biosynthesis, and Virulence of Aspergillus flavus. Toxins (Basel) 2019; 11:E70. [PMID: 30691218 PMCID: PMC6410012 DOI: 10.3390/toxins11020070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 01/02/2023] Open
Abstract
Aspergillus flavus is a soilborne pathogenic fungus that poses a serious public health threat due to it contamination of food with carcinogenic aflatoxins. Our previous studies have demonstrated that benzenamine displayed strong inhibitory effects on the mycelial growth of A. flavus. In this study, we systematically investigated the inhibitory effects of benzenamine on the development, aflatoxin biosynthesis, and virulence in A. flavus, as well as the underlying mechanism. The results indicated that benzenamine exhibited great capacity to combat A. flavus at a concentration of 100 µL/L, leading to significantly decreased aflatoxin accumulation and colonization capacity in maize. The transcriptional profile revealed that 3589 genes show altered mRNA levels in the A. flavus after treatment with benzenamine, including 1890 down-regulated and 1699 up-regulated genes. Most of the differentially expressed genes participated in the biosynthesis and metabolism of amino acid, purine metabolism, and protein processing in endoplasmic reticulum. Additionally, the results brought us to a suggestion that benzenamine affects the development, aflatoxin biosynthesis, and pathogenicity of A. flavus via down-regulating related genes by depressing the expression of the global regulatory factor leaA. Overall, this study indicates that benzenamine have tremendous potential to act as a fumigant against pathogenic A. flavus. Furthermore, this work offers valuable information regarding the underlying antifungal mechanism of benzenamine against A. flavus at the level of transcription, and these potential targets may be conducive in developing new strategies for preventing aflatoxin contamination.
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Affiliation(s)
- Mingguan Yang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Laifeng Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Shuhua Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Jing Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Zhenjing Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Shufen Wu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Qingbin Guo
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Huanhuan Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Changlu Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
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Zeng Z, Wu J, Kovalchuk A, Raffaello T, Wen Z, Liu M, Asiegbu FO. Genome-wide DNA methylation and transcriptomic profiles in the lifestyle strategies and asexual development of the forest fungal pathogen Heterobasidion parviporum. Epigenetics 2019; 14:16-40. [PMID: 30633603 PMCID: PMC6380393 DOI: 10.1080/15592294.2018.1564426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/03/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022] Open
Abstract
Heterobasidion parviporum is the most devastating fungal pathogen of conifer forests in Northern Europe. The fungus has dual life strategies, necrotrophy on living trees and saprotrophy on dead woods. DNA cytosine methylation is an important epigenetic modification in eukaryotic organisms. Our presumption is that the lifestyle transition and asexual development in H. parviporum could be driven by epigenetic effects. Involvements of DNA methylation in the regulation of aforementioned processes have never been studied thus far. RNA-seq identified lists of highly induced genes enriched in carbohydrate-active enzymes during necrotrophic interaction with host trees and saprotrophic sawdust growth. It also highlighted signaling- and transcription factor-related genes potentially associated with the transition of saprotrophic to necrotrophic lifestyle and groups of primary cellular activities throughout asexual development. Whole-genome bisulfite sequencing revealed that DNA methylation displayed pronounced preference in CpG dinucleotide context across the genome and mostly targeted transposable element (TE)-rich regions. TE methylation level demonstrated a strong negative correlation with TE expression, reinforcing the protective function of DNA methylation in fungal genome stability. Small groups of genes putatively subject to methylation transcriptional regulation in response to saprotrophic and necrotrophic growth in comparison with free-living mycelia were also explored. Our study reported on the first methylome map of a forest pathogen. Analysis of transcriptome and methylome variations associated with asexual development and different lifestyle strategies provided further understanding of basic biological processes in H. parviporum. More importantly, our work raised additional potential roles of DNA methylation in fungi apart from controlling the proliferation of TEs.
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Affiliation(s)
- Zhen Zeng
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Jiayao Wu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Andriy Kovalchuk
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Tommaso Raffaello
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Zilan Wen
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Mengxia Liu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Fred O. Asiegbu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
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39
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Trends in herbgenomics. SCIENCE CHINA-LIFE SCIENCES 2018; 62:288-308. [PMID: 30128965 DOI: 10.1007/s11427-018-9352-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/03/2018] [Indexed: 02/06/2023]
Abstract
From Shen Nong's Herbal Classic (Shennong Bencao Jing) to the Compendium of Materia Medica (Bencao Gangmu) and the first scientific Nobel Prize for the mainland of China, each milestone in the historical process of the development of traditional Chinese medicine (TCM) involves screening, testing and integrating. After thousands of years of inheritance and development, herbgenomics (bencaogenomics) has bridged the gap between TCM and international advanced omics studies, promoting the application of frontier technologies in TCM. It is a discipline that uncovers the genetic information and regulatory networks of herbs to clarify their molecular mechanism in the prevention and treatment of human diseases. The main theoretical system includes genomics, functional genomics, proteomics, transcriptomics, metabolomics, epigenomics, metagenomics, synthetic biology, pharmacogenomics of TCM, and bioinformatics, among other fields. Herbgenomics is mainly applicable to the study of medicinal model plants, genomic-assisted breeding, herbal synthetic biology, protection and utilization of gene resources, TCM quality evaluation and control, and TCM drug development. Such studies will accelerate the application of cutting-edge technologies, revitalize herbal research, and strongly promote the development and modernization of TCM.
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40
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Massonnet M, Morales-Cruz A, Minio A, Figueroa-Balderas R, Lawrence DP, Travadon R, Rolshausen PE, Baumgartner K, Cantu D. Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum. Front Microbiol 2018; 9:1784. [PMID: 30150972 PMCID: PMC6099105 DOI: 10.3389/fmicb.2018.01784] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/16/2018] [Indexed: 12/30/2022] Open
Abstract
The Ascomycete fungus Phaeoacremonium minimum is one of the primary causal agents of Esca, a widespread and damaging grapevine trunk disease. Variation in virulence among Pm. minimum isolates has been reported, but the underlying genetic basis of the phenotypic variability remains unknown. The goal of this study was to characterize intraspecific genetic diversity and explore its potential impact on virulence functions associated with secondary metabolism, cellular transport, and cell wall decomposition. We generated a chromosome-scale genome assembly, using single molecule real-time sequencing, and resequenced the genomes and transcriptomes of multiple isolates to identify sequence and structural polymorphisms. Numerous insertion and deletion events were found for a total of about 1 Mbp in each isolate. Structural variation in this extremely gene dense genome frequently caused presence/absence polymorphisms of multiple adjacent genes, mostly belonging to biosynthetic clusters associated with secondary metabolism. Because of the observed intraspecific diversity in gene content due to structural variation we concluded that a transcriptome reference developed from a single isolate is insufficient to represent the virulence factor repertoire of the species. We therefore compiled a pan-transcriptome reference of Pm. minimum comprising a non-redundant set of 15,245 protein-coding sequences. Using naturally infected field samples expressing Esca symptoms, we demonstrated that mapping of meta-transcriptomics data on a multi-species reference that included the Pm. minimum pan-transcriptome allows the profiling of an expanded set of virulence factors, including variable genes associated with secondary metabolism and cellular transport.
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Affiliation(s)
- Mélanie Massonnet
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Daniel P. Lawrence
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Philippe E. Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture, Davis, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
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Co-extraction of genomic DNA & total RNA from recalcitrant woody tissues for next-generation sequencing studies. Future Sci OA 2018; 4:FSO309. [PMID: 30057786 PMCID: PMC6060392 DOI: 10.4155/fsoa-2018-0026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/28/2018] [Indexed: 12/03/2022] Open
Abstract
The successful implementation of next-generation sequencing techniques in plant and woody tissues depends on the quality of initial starting material. This study demonstrated the use of a modified protocol that enabled the simultaneous extraction of both genomic DNA and total RNA from recalcitrant woody material. The genetic material obtained by this protocol is of high quality and can be directly used in downstream analysis (e.g., next-generation sequencing). This protocol is particularly useful not only when the initial plant material is limited but also when genomic DNA features (e.g., methylation) have to be compared with the total RNA (e.g., gene expression). For such studies, the extraction from the same materials is highly preferred to minimize sample variation. The advancement of next-generation sequencing techniques has greatly facilitated almost all branches of biological and life-science studies. To guarantee reliable results and conclusions, high-quality starting genetic material (genomic DNA and total RNA) is essential. Our modified protocol, which is based on existing methods, enabled the efficient simultaneous extraction of genomic DNA and total RNA from the same recalcitrant woody sample. Thereby, it greatly minimizes the amount of initial plant materials needed for a specific study.
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Hao DC, Xiao PG. Deep in shadows: Epigenetic and epigenomic regulations of medicinal plants. CHINESE HERBAL MEDICINES 2018. [DOI: 10.1016/j.chmed.2018.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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43
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Zhang JJ, Su H, Zhang L, Liao BS, Xiao SM, Dong LL, Hu ZG, Wang P, Li XW, Huang ZH, Gao ZM, Zhang LJ, Shen L, Cheng RY, Xu J, Chen SL. Comprehensive Characterization for Ginsenosides Biosynthesis in Ginseng Root by Integration Analysis of Chemical and Transcriptome. Molecules 2017; 22:molecules22060889. [PMID: 28561788 PMCID: PMC6152789 DOI: 10.3390/molecules22060889] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 05/09/2017] [Accepted: 05/23/2017] [Indexed: 11/16/2022] Open
Abstract
Herbgenomics provides a global platform to explore the genetics and biology of herbs on the genome level. Panax ginseng C.A. Meyer is an important medicinal plant with numerous pharmaceutical effects. Previous reports mainly discussed the transcriptome of ginseng at the organ level. However, based on mass spectrometry imaging analyses, the ginsenosides varied among different tissues. In this work, ginseng root was separated into three tissues-periderm, cortex and stele-each for five duplicates. The chemical analysis and transcriptome analysis were conducted simultaneously. Gene-encoding enzymes involved in ginsenosides biosynthesis and modification were studied based on gene and molecule data. Eight widely-used ginsenosides were distributed unevenly in ginseng roots. A total of 182,881 unigenes were assembled with an N50 contig size of 1374 bp. About 21,000 of these unigenes were positively correlated with the content of ginsenosides. Additionally, we identified 192 transcripts encoding enzymes involved in two triterpenoid biosynthesis pathways and 290 transcripts encoding UDP-glycosyltransferases (UGTs). Of these UGTs, 195 UGTs (67.2%) were more highly expressed in the periderm, and that seven UGTs and one UGT were specifically expressed in the periderm and stele, respectively. This genetic resource will help to improve the interpretation on complex mechanisms of ginsenosides biosynthesis, accumulation, and transportation.
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Affiliation(s)
- Jing-Jing Zhang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China.
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
| | - He Su
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou 510006, China.
| | - Lei Zhang
- Data Center, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
| | - Bao-Sheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
| | - Shui-Ming Xiao
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
| | - Lin-Lin Dong
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
| | - Zhi-Gang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Ping Wang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Xi-Wen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
| | - Zhi-Hai Huang
- Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou 510006, China.
| | - Zhi-Ming Gao
- The Engineering Technology Research Center for Chinese Medicine, Henan Agricultural University, Zhengzhou 450002, China.
| | - Lian-Juan Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
| | - Liang Shen
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
| | - Rui-Yang Cheng
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
| | - Shi-Lin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medicinal Sciences, Beijing 100700, China.
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Chen H, Deng C, Nie H, Fan G, He Y. Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread ( Coptis chinensis Franch.) from different biotopes. PeerJ 2017; 5:e3303. [PMID: 28533961 PMCID: PMC5438583 DOI: 10.7717/peerj.3303] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/12/2017] [Indexed: 12/14/2022] Open
Abstract
Coptis chinensis Franch., the Chinese goldthread (‘Weilian’ in Chinese), one of the most important medicinal plants from the family Ranunculaceae, and its rhizome has been widely used in Traditional Chinese Medicine for centuries. Here, we analyzed the chemical components and the transcriptome of the Chinese goldthread from three biotopes, including Zhenping, Zunyi and Shizhu. We built comprehensive, high-quality de novo transcriptome assemblies of the Chinese goldthread from short-read RNA-Sequencing data, obtaining 155,710 transcripts and 56,071 unigenes. More than 98.39% and 95.97% of core eukaryotic genes were found in the transcripts and unigenes respectively, indicating that this unigene set capture the majority of the coding genes. A total of 520,462, 493,718, and 507,247 heterozygous SNPs were identified in the three accessions from Zhenping, Zunyi, and Shizhu respectively, indicating high polymorphism in coding regions of the Chinese goldthread (∼1%). Chemical analyses of the rhizome identified six major components, including berberine, palmatine, coptisine, epiberberine, columbamine, and jatrorrhizine. Berberine has the highest concentrations, followed by coptisine, palmatine, and epiberberine sequentially for all the three accessions. The drug quality of the accession from Shizhu may be the highest among these accessions. Differential analyses of the transcriptome identified four pivotal candidate enzymes, including aspartate aminotransferaseprotein, polyphenol oxidase, primary-amine oxidase, and tyrosine decarboxylase, were significantly differentially expressed and may be responsible for the difference of alkaloids contents in the accessions from different biotopes.
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Affiliation(s)
- Hanting Chen
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Cao Deng
- DNA Stories Bioinformatics Center, Chengdu, Sichuan, China
| | - Hu Nie
- DNA Stories Bioinformatics Center, Chengdu, Sichuan, China
| | - Gang Fan
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yang He
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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Clutterbuck AJ. Genomic CG dinucleotide deficiencies associated with transposable element hypermutation in Basidiomycetes, some lower fungi, a moss and a clubmoss. Fungal Genet Biol 2017; 104:16-28. [PMID: 28438577 DOI: 10.1016/j.fgb.2017.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/10/2017] [Accepted: 04/17/2017] [Indexed: 12/15/2022]
Abstract
Many Basidiomycete genomes include substantial fractions that are deficient in CG dinucleotides, in extreme cases amounting to 70% of the genome. CG deficiency is variable and correlates with genome size and, more closely, with transposable element (TE) content. Many species have limited CG deficiency; it is therefore likely that there are other mechanisms that can control TE proliferation. Examination of TEs confirms that C-to-T transition mutations in CG dinucleotides may comprise a conspicuous proportion of differences between paired elements, however transition/transversion ratios are never as high as those due to RIP in some Ascomycetes, suggesting that repeat-associated CG mutation is not totally pervasive. This has allowed gene family expansion in Basidiomycetes, although CG transition differences are often prominent in paired gene family members, and are evidently responsible for destruction of some copies. A few lower fungal genomes exhibit similar evidence of repeat-associated CG mutation, as do the genomes of the two lower plants Physcomitrella patens and Selaginella moellendorffii, in both of which mutation parallels published methylation of CHG as well as CG nucleotides. In Basidiomycete DNA methylation has been reported to be largely confined to CG dinucleotides in repetitive DNA, but while methylation and mutation are evidently associated, it is not clear which is cause and which effect.
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Affiliation(s)
- A John Clutterbuck
- Wolfson Link Building, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.
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Making Use of Genomic Information to Explore the Biotechnological Potential of Medicinal Mushrooms. MEDICINAL AND AROMATIC PLANTS OF THE WORLD 2017. [DOI: 10.1007/978-981-10-5978-0_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Abstract
Many Fungi have a well-developed secondary metabolism. The diversity of fungal species and the diversification of biosynthetic gene clusters underscores a nearly limitless potential for metabolic variation and an untapped resource for drug discovery and synthetic biology. Much of the ecological success of the filamentous fungi in colonizing the planet is owed to their ability to deploy their secondary metabolites in concert with their penetrative and absorptive mode of life. Fungal secondary metabolites exhibit biological activities that have been developed into life-saving medicines and agrochemicals. Toxic metabolites, known as mycotoxins, contaminate human and livestock food and indoor environments. Secondary metabolites are determinants of fungal diseases of humans, animals, and plants. Secondary metabolites exhibit a staggering variation in chemical structures and biological activities, yet their biosynthetic pathways share a number of key characteristics. The genes encoding cooperative steps of a biosynthetic pathway tend to be located contiguously on the chromosome in coregulated gene clusters. Advances in genome sequencing, computational tools, and analytical chemistry are enabling the rapid connection of gene clusters with their metabolic products. At least three fungal drug precursors, penicillin K and V, mycophenolic acid, and pleuromutilin, have been produced by synthetic reconstruction and expression of respective gene clusters in heterologous hosts. This review summarizes general aspects of fungal secondary metabolism and recent developments in our understanding of how and why fungi make secondary metabolites, how these molecules are produced, and how their biosynthetic genes are distributed across the Fungi. The breadth of fungal secondary metabolite diversity is highlighted by recent information on the biosynthesis of important fungus-derived metabolites that have contributed to human health and agriculture and that have negatively impacted crops, food distribution, and human environments.
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Affiliation(s)
- Gerald F Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77054
| | - James B Gloer
- Department of Chemistry, University of Iowa, Iowa City, IA 52245
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He Y, Xiao H, Deng C, Xiong L, Nie H, Peng C. Survey of the genome of Pogostemon cablin provides insights into its evolutionary history and sesquiterpenoid biosynthesis. Sci Rep 2016; 6:26405. [PMID: 27198881 PMCID: PMC4873823 DOI: 10.1038/srep26405] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 05/03/2016] [Indexed: 01/06/2023] Open
Abstract
Pogostemon cablin (Blanco) Benth. (Patchouli) is an important traditional Chinese medicinal plant that has both essential oil value and a broad range of therapeutic effects. Here we report the first de novo assembled 1.15-Gb draft genome sequence for P. cablin from next-generation sequencing technology. Our assembly, with a misassembly rate of <4 bp per 100 kb, is ~73% of the predicted genome size (1.57 Gb). Analysis of whole-genome sequences identified 3,147,333 heterozygous single-nucleotide polymorphisms and 490,407 insertions and deletions, giving an estimated heterozygosity rate of 0.274%. A comprehensive annotation pipeline indicated that repetitive sequences make up 58.55% of the assemblies, and that there are estimated 45,020 genes. Comparative genomics analysis showed that the Phrymaceae and Lamiaceae family split ~62.80 Mya, and the divergence between patchouli and sesame occurred ~52.42 Mya, implying a potentially shared recent whole-genome duplication event. Analysis of gene homologs involved in sesquiterpenoid biosynthesis showed that patchouli contains key genes involved in more sesquiterpenoid types and has more copies of genes for each sesquiterpenoid type than several other related plant species. The patchouli genome will facilitate future research on secondary metabolic pathways and their regulation as well as potential selective breeding of patchouli.
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Affiliation(s)
- Yang He
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Hongtao Xiao
- School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China.,Department of Pharmacy, Hospital of the University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu 610072, China
| | - Cao Deng
- DNA Stories Bioinformatics Center, Chengdu 610065, China
| | - Liang Xiong
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Hu Nie
- DNA Stories Bioinformatics Center, Chengdu 610065, China
| | - Cheng Peng
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
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Xiao H, Zhong JJ. Production of Useful Terpenoids by Higher-Fungus Cell Factory and Synthetic Biology Approaches. Trends Biotechnol 2016; 34:242-255. [DOI: 10.1016/j.tibtech.2015.12.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/01/2015] [Accepted: 12/15/2015] [Indexed: 01/11/2023]
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50
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Cell Factories of Higher Fungi for Useful Metabolite Production. BIOREACTOR ENGINEERING RESEARCH AND INDUSTRIAL APPLICATIONS I 2015; 155:199-235. [DOI: 10.1007/10_2015_335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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