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Yu H, Zhang L, Shang X, Peng B, Li Y, Xiao S, Tan Q, Fu Y. Chromosomal genome and population genetic analyses to reveal genetic architecture, breeding history and genes related to cadmium accumulation in Lentinula edodes. BMC Genomics 2022; 23:120. [PMID: 35144543 PMCID: PMC8832684 DOI: 10.1186/s12864-022-08325-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 01/19/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Lentinula edodes (Berk.) is the second most productive mushroom in the world. It contains compounds effective for antiviral, antitumor, antioxidant and immune regulation. Although genomes have previously been reported for this species, a high-quality chromosome-level reference for L. edodes is unavailable. This hinders detailed investigation of population genetics, breeding history of strains and genes related to environmental stress responses. RESULTS A high-quality chromosome-level genome was constructed. We separated a monokaryon from protoplasts of the commercial L. edodes strain L808 and assembled the genome of L. edodes using PacBio long-read and Illumina short-read sequencing, along with the high-throughput chromatin conformation capture (Hi-C) technique. We assembled a 45.87 Mb genome, and 99% of the sequences were anchored onto 10 chromosomes. The contig and scaffold N50 length were 2.17 and 4.94 Mb, respectively. Over 96% of the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) were identified, and 9853 protein-coding genes were predicted. We performed population genome resequencing using 34 wild strains and 65 commercial cultivars of L. edodes originating from China, Japan, the United States and Australia. Based on whole-genome variants, we showed substantial differences in the Chinese wild population, which divided into different branches according to the main areas of their geographical distribution. We also determined the breeding history of L. edodes at the molecular level, and demonstrated that the cultivated strains in China mainly originated from wild strains from China and Northeast Asia. Phenotypic analysis showed that 99 strains exhibited differences on the Cd accumulation. Three significant loci in the of L. edodes genome were identified using the genome-wide association study (GWAS) of Cd accumulation traits. Functional genes associated with Cd accumulation traits were related to DNA ligase and aminoacyl tRNA synthetase, indicating that DNA damage repair and in vivo protein translation may be responses to Cd stress. CONCLUSIONS A high-quality chromosome-level genome and population genetic data of L. edodes provide genetic resources for functional genomic, evolutionary and artificial breeding studies for L. edodes.
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Affiliation(s)
- Hailong Yu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China
| | - Lujun Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
| | - Xiaodong Shang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
| | - Bing Peng
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China
| | - Yu Li
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China
| | - Shijun Xiao
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China.
- Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing, 314000, China.
| | - Qi Tan
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China.
| | - Yongping Fu
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China.
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Ma X, Fan X, Wang G, Xu R, Yan L, Zhou Y, Gong Y, Xiao Y, Bian Y. Enhanced Expression of Thaumatin-like Protein Gene ( LeTLP1) Endows Resistance to Trichoderma atroviride in Lentinula edodes. Life (Basel) 2021; 11:863. [PMID: 34440607 PMCID: PMC8398078 DOI: 10.3390/life11080863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 01/17/2023] Open
Abstract
Lentinula edodes (shiitake mushrooms) is heavily affected by the infection of Trichoderma atroviride, causing yield loss and decreases quality in shiitake mushrooms. The selection and breeding of fungal-resistant L. edodes species are an important approach to protecting L. edodes from T. atroviride infection. Herein, a highly resistant L. edodes strain (Y3334) and a susceptible strain (Y55) were obtained by using a resistance evaluation test. Transcriptome analyses and qRT-PCR detection showed that the expression level of LeTLP1 (LE01Gene05009) was strongly induced in response to T. atroviride infection in the resistant Y3334. Then, LeTLP1-silenced and LeTLP1-overexpression transformants were obtained. Overexpression of LeTLP1 resulted in resistance to T. atroviride. Compared with the parent strain Y3334, LeTLP1-silenced transformants had reduced resistance relative to T. atroviride. Additionally, the LeTLP1 protein (Y3334) exhibited significant antifungal activity against T. atroviride. These findings suggest that overexpression of LeTLP1 is a major mechanism for the resistance of L. edodes to T. atroviride. The molecular basis provides a theoretical basis for the breeding of resistant L. edodes strains and can eventually contribute to the mushroom cultivation industry and human health.
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Affiliation(s)
- Xiaolong Ma
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Xiaolin Fan
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Gangzheng Wang
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Ruiping Xu
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Lianlian Yan
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Yan Zhou
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Yuhua Gong
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Yang Xiao
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
| | - Yinbing Bian
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.M.); (X.F.); (G.W.); (R.X.); (L.Y.); (Y.Z.); (Y.G.); (Y.X.)
- Key Laboratory of Agro-Microbial Resource and Development, Ministry of Agriculture, Wuhan 430070, China
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Jiang WZ, Yao FJ, Fang M, Lu LX, Zhang YM, Wang P, Meng JJ, Lu J, Ma XX, He Q, Shao KS, Khan AA, Wei YH. Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map. MYCOBIOLOGY 2021; 49:406-420. [PMID: 34512084 PMCID: PMC8409960 DOI: 10.1080/12298093.2021.1954321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined the GiC-126 genome with the published genome of G. incarnatum strain CCMJ2665 to construct a genetic linkage map (GiC-126 genome) that had 10 linkage groups (LGs), and the 15 assembly sequences of CCMJ2665 were integrated into 8 LGs. We identified 1912 simple sequence repeat (SSR) loci and detected 700 genes containing 768 SSRs in the genome; 65 and 100 of them were annotated with gene ontology (GO) terms and KEGG pathways, respectively. Carbohydrate-active enzymes (CAZymes) were identified in 20 fungal genomes and annotated; among them, 144 CAZymes were annotated in the GiC-126 genome. The A mating-type locus (MAT-A) of G. incarnatum was located on scaffold885 at 38.9 cM of LG1 and was flanked by two homeodomain (HD1) genes, mip and beta-fg. Fourteen segregation distortion markers were detected in the genetic linkage map, all of which were skewed toward the parent GiC-126. They formed three segregation distortion regions (SDR1-SDR3), and 22 predictive genes were found in scaffold1920 where three segregation distortion markers were located in SDR1. In this study, we corrected and updated the genomic information of G. incarnatum. Our results will provide a theoretical basis for fine gene mapping, functional gene cloning, and genetic breeding the follow-up of G. incarnatum.
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Affiliation(s)
- Wan-Zhu Jiang
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Fang-Jie Yao
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Ming Fang
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Li-Xin Lu
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - You-Min Zhang
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Peng Wang
- Economic Plants Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Jing-Jing Meng
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Jia Lu
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Xiao-Xu Ma
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Qi He
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Kai-Sheng Shao
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Asif Ali Khan
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Yun-Hui Wei
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, China
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Genetic diversity and population structure of Chinese Lentinula edodes revealed by InDel and SSR markers. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1183-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Abstract
This review article concisely describes methodology of biotechnological processes with the use of cultures of higher fungi, their application in bioremediation and to obtain biologically active preparations. Advantages and disadvantages of biotechnological methods used to cultivate mushrooms are analyzed. This paper contains overview of higher fungi species most commonly used in biotechnological processes, of cultivation methods applied to produce fungal biomass, of enzymes and bioactive metabolites and of the strategies for submerged cultivation of the mycelial cultures. The problems of optimization of strains and biotechnological processes are briefly discussed.
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