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Yang Y, Pian Y, Li J, Xu L, Lu Z, Dai Y, Li Q. Integrative analysis of genome and transcriptome reveal the genetic basis of high temperature tolerance in pleurotus giganteus (Berk. Karun & Hyde). BMC Genomics 2023; 24:552. [PMID: 37723428 PMCID: PMC10506213 DOI: 10.1186/s12864-023-09669-8] [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: 03/29/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Pleurotus giganteus is a commonly cultivated mushroom with notable high temperature resistance, making it significant for the growth of the edible fungi industry in the tropics. Despite its practical importance,, the genetic mechanisms underlying its ability to withstand high temperature tolerance remain elusive. RESULTS In this study, we performed high-quality genome sequencing of a monokaryon isolated from a thermotolerant strain of P. giganteus. The genome size was found to be 40.11 Mb, comprising 17 contigs and 13,054 protein-coding genes. Notably, some genes related to abiotic stress were identified in genome, such as genes regulating heat shock protein, protein kinase activity and signal transduction. These findings provide valuable insights into the genetic basis of P. giganteus' high temperature resistance. Furthermore, the phylogenetic tree showed that P. giganteus was more closely related to P. citrinopileatus than other Pleurotus species. The divergence time between Pleurotus and Lentinus was estimated as 153.9 Mya, and they have a divergence time with Panus at 168.3 Mya, which proved the taxonomic status of P. giganteus at the genome level. Additionally, a comparative transcriptome analysis was conducted between mycelia treated with 40 °C heat shock for 18 h (HS) and an untreated control group (CK). Among the 2,614 differentially expressed genes (DEGs), 1,303 genes were up-regulated and 1,311 were down-regulated in the HS group. The enrichment analysis showed that several genes related to abiotic stress, including heat shock protein, DnaJ protein homologue, ubiquitin protease, transcription factors, DNA mismatch repair proteins, and zinc finger proteins, were significantly up-regulated in the HS group. These genes may play important roles in the high temperature adaptation of P. giganteus. Six DEGs were selected according to fourfold expression changes and were validated by qRT-PCR, laying a good foundation for further gene function analysis. CONCLUSION Our study successfully reported a high-quality genome of P. giganteus and identified genes associated with high-temperature tolerance through an integrative analysis of the genome and transcriptome. This study lays a crucial foundation for understanding the high-temperature tolerance mechanism of P. giganteus, providing valuable insights for genetic modification of P. giganteus strains and the development of high-temperature strains for the edible fungus industry, particularly in tropical regions.
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Affiliation(s)
- Yang Yang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
| | - Yongru Pian
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China
| | - Jingyi Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China
| | - Lin Xu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China
| | - Zhu Lu
- Jilin Academy of Vegetables and Flowers Sciences, Changchun, China
| | - Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.
| | - Qinfen Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China.
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China.
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Ortiz V, Chang HX, Sang H, Jacobs J, Malvick DK, Baird R, Mathew FM, Estévez de Jensen C, Wise KA, Mosquera GM, Chilvers MI. Population genomic analysis reveals geographic structure and climatic diversification for Macrophomina phaseolina isolated from soybean and dry bean across the United States, Puerto Rico, and Colombia. Front Genet 2023; 14:1103969. [PMID: 37351341 PMCID: PMC10282554 DOI: 10.3389/fgene.2023.1103969] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/20/2023] [Indexed: 06/24/2023] Open
Abstract
Macrophomina phaseolina causes charcoal rot, which can significantly reduce yield and seed quality of soybean and dry bean resulting from primarily environmental stressors. Although charcoal rot has been recognized as a warm climate-driven disease of increasing concern under global climate change, knowledge regarding population genetics and climatic variables contributing to the genetic diversity of M. phaseolina is limited. This study conducted genome sequencing for 95 M. phaseolina isolates from soybean and dry bean across the continental United States, Puerto Rico, and Colombia. Inference on the population structure using 76,981 single nucleotide polymorphisms (SNPs) revealed that the isolates exhibited a discrete genetic clustering at the continental level and a continuous genetic differentiation regionally. A majority of isolates from the United States (96%) grouped in a clade with a predominantly clonal genetic structure, while 88% of Puerto Rican and Colombian isolates from dry bean were assigned to a separate clade with higher genetic diversity. A redundancy analysis (RDA) was used to estimate the contributions of climate and spatial structure to genomic variation (11,421 unlinked SNPs). Climate significantly contributed to genomic variation at a continental level with temperature seasonality explaining the most variation while precipitation of warmest quarter explaining the most when spatial structure was accounted for. The loci significantly associated with multivariate climate were found closely to the genes related to fungal stress responses, including transmembrane transport, glycoside hydrolase activity and a heat-shock protein, which may mediate climatic adaptation for M. phaseolina. On the contrary, limited genome-wide differentiation among populations by hosts was observed. These findings highlight the importance of population genetics and identify candidate genes of M. phaseolina that can be used to elucidate the molecular mechanisms that underly climatic adaptation to the changing climate.
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Affiliation(s)
- Viviana Ortiz
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - Janette Jacobs
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Dean K. Malvick
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Richard Baird
- BCH-EPP Department, Mississippi State University, Mississippi State, MS, United States
| | - Febina M. Mathew
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | | | - Kiersten A. Wise
- Department of Plant Pathology, College of Agriculture, Food and Environment, University of Kentucky, Princeton, KY, United States
| | - Gloria M. Mosquera
- Plant Pathology, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Palmira, Colombia
| | - Martin I. Chilvers
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, United States
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Huang Y, Liu J, Li J, Sun M, Duan Y. The heat shock protein 20 gene editing suppresses mycelial growth of Botryosphaeria dothidea and decreases its pathogenicity to postharvest apple fruits. Front Microbiol 2022; 13:930012. [PMID: 35966691 PMCID: PMC9363843 DOI: 10.3389/fmicb.2022.930012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Apple ring rot caused by Botryosphaeria dothidea is an essential and prevalent disease in the apple orchard in China. Our previous study demonstrated that dimethyl trisulfide (DT) from Chinese leek (Allium tuberosum) significantly suppressed the mycelial growth of B. dothidea and inhibited the incidence of apple ring rot postharvest. However, the mechanism underlying the inhibitory role of DT against B. dothidea is not fully understood. Comparing the control and the DT-treated B. dothidea mycelial transcriptomes revealed that heat shock protein 20 (Hsp20) strongly responded to DT treatment. This study identified four Hsp20 genes throughout the B. dothidea genome (BdHsp20_1-4). Each BdHsp20 gene had a conserved ACD with a variable N-terminal region and a short C-terminal extension. The segmental duplication event has contributed to the expansion of the BdHsp20 gene family. Compared to the wild-type strain, the CRISPR/Cas9 gene-edited BdHsp20 mutant (ΔBdHsp20) decreased the mycelial growth by 55.95% and reduced the disease symptom in postharvest apple fruit by 96.34%. However, the BdHsp20 complemented strain (ΔBdHsp20_C) significantly restored the growth and pathogenicity, which suggested that the BdHsp20 gene was closely involved in the growth and pathogenicity of B. dothidea. This study would accelerate the exploration of the molecular mechanism of the inhibitory effect of DT against B. dothidea and also provide new insights for the management of apple ring rot disease.
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Affiliation(s)
- Yonghong Huang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China
- National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China
- *Correspondence: Yonghong Huang
| | - Junping Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China
- National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China
| | - Jinghui Li
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China
- National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China
| | - Meng Sun
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China
- National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China
| | - Yanxin Duan
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- Laboratory of Quality and Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, Qingdao, China
- National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), Qingdao, China
- Qingdao Key Laboratory of Modern Agriculture Quality and Safety Engineering, Qingdao, China
- Yanxin Duan
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Wang L, Ding X, Huang Q, Hu B, Liang L, Wang Q. Gllac7 Is Induced by Agricultural and Forestry Residues and Exhibits Allelic Expression Bias in Ganoderma lucidum. Front Microbiol 2022; 13:890686. [PMID: 35847055 PMCID: PMC9279560 DOI: 10.3389/fmicb.2022.890686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Ganoderma lucidum has a wide carbon spectrum, while the expression profile of key genes relevant to carbon metabolism on different carbon sources has been seldom studied. Here, the transcriptomes of G. lucidum mycelia cultured on each of 19 carbon sources were conducted. In comparison with glucose, 16 to 1,006 genes were upregulated and 7 to 1,865 genes were downregulated. Significant gene expression dynamics and induced activity were observed in laccase genes when using agricultural and forestry residues (AFRs) as solo carbon sources. Furthermore, study of laccase gene family in two haploids of G. lucidum GL0102 was conducted. Totally, 15 and 16 laccase genes were identified in GL0102_53 and GL0102_8, respectively, among which 15 pairs were allelic genes. Gene structures were conserved between allelic laccase genes, while sequence variations (most were SNPs) existed. Nine laccase genes rarely expressed on all the tested carbon sources, while the other seven genes showed high expression level on AFRs, especially Gllac2 and Gllac7, which showed 5- to 1,149-fold and 4- to 94-fold upregulation in mycelia cultured for 5 days, respectively. The expression of H53lac7 was consistently higher than that of H8lac7_1 on all the carbon sources except XM, exhibiting a case of allelic expression bias. A total of 47 SNPs and 3 insertions/deletions were observed between promoters of H53lac7 and H8lac7_1, which lead to differences in predicted binding sites of zinc fingers. These results provide scientific data for understanding the gene expression profile and regulatory role on different carbon sources and may support further functional research of laccase.
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Affiliation(s)
- Lining Wang
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaoxia Ding
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qinghua Huang
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Biao Hu
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Lei Liang
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingfu Wang
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
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Wang L, Lu C, Fan M, Liao B. Coriolopsis trogii hydrophobin genes favor a clustering distribution and are widely involved in mycelial growth and primordia formation. Gene 2021; 802:145863. [PMID: 34358628 DOI: 10.1016/j.gene.2021.145863] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/30/2021] [Indexed: 12/01/2022]
Abstract
Hydrophobins are small, secreted proteins with important physiological functions in mycelial growth and fungal development. Here, 1 nucleus-specific and 35 allelic hydrophobin genes were identified in the genome of a white rot fungus, Coriolopsis trogii. Among these, 22 were eight-cysteine class I hydrophobin genes and the other 14 were uncommon six-cysteine hydrophobin genes. The six-cysteine hydrophobins were speculated to have originated from a common ancestor. The hydrophobin genes favored a clustering distribution and two recent duplication pairs were identified. The genes had conserved gene structures with three exons and two introns. Cthyd18, Cthyd19, and Cthyd32 were constitutively highly expressed in all developmental stages. Cthyd20, Cthyd21, Cthyd22, Cthyd28, Cthyd30, Cthyd31, and Cthyd33 were highly expressed in mycelia, and Cthyd12 and Cthyd35 in the reproductive stages. Sixteen hydrophobin genes were regulated differently in the transition from mycelia to primordia; Cthyd35 showed maximal upregulation of 1922-fold, and Cthyd23 showed maximal downregulation of 552-fold. Most (32) hydrophobin genes showed significant differential expression between mycelia cultured in different media (potato dextrose agar or broth). Weighted gene co-expression network analysis and promoter analysis revealed that C2H2 zinc finger proteins may regulate hydrophobin genes. These results may support further research into the function and evolution of hydrophobins.
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Affiliation(s)
- Lining Wang
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou 510316, People's Republic of China
| | - Chuanli Lu
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou 510316, People's Republic of China
| | - Min Fan
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou 510316, People's Republic of China
| | - Baosheng Liao
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China.
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