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Dong Y, Ma H, Sun L, He R, Ye X, Gan B, Zhang Q, Gong Z, Han X, Duan X, Yan J. Comparative Transcriptome Analysis of Candidate Genes Associated with Mycelia Growth from a He-Ne Laser with Pulsed Light Mutant of Phellinus igniarius (Agaricomycetes). Int J Med Mushrooms 2024; 26:71-85. [PMID: 38421697 DOI: 10.1615/intjmedmushrooms.2023051538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
A mutant Phellinus igniarius JQ9 with higher mycelial production was screened out by He-Ne laser with pulsed light irradiation, the mechanism underlying the higher mycelial production is still unknown. This study aims to obtain a comprehensive transcriptome assembly during the Ph. igniarius liquid fermentation and characterize the key genes associated with the mycelial growth and metabolism in Ph. igniarius JQ9. Our transcriptome data of Ph. iniarius JQ9 and the wild strain were obtained with the Illumina platform comparative transcriptome sequencing technology. The results showed that among all the 346 differentially expressed genes (DEGs), 245 were upregulated and 101 were downregulated. Candidate genes encoding endoglucanase, beta-glucosidase, cellulose 1,4-beta-cellobiosidase, glycoside hydrolase family 61 protein, were proposed to participate in the carbohydrate utilization from KEGG enrichment of the starch and sucrose metabolism pathways were upregulated in Ph. igniarius JQ9. In addition, three candidate genes encoding the laccase and another two candidate genes related with the cell growth were higher expressed in Ph. igniarius JQ9 than in the wild type of strain (CK). Analysis of these data revealed that increased these related carbohydrate metabolism candidate genes underlying one crucial way may cause the higher mycelia production.
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Affiliation(s)
- Yating Dong
- School of Food and Biological Engineering, Institute of Food Physical Processing, International Joint Research Center for Food Physical Processing, Jiangsu University, No. 301 Xuefu Road, Zhenjiang 212013, P.R. China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, National Agricultural Science & Technology Center (NASC), 9 Hupan West Road, Tianfu New Area, Chengdu, 610000, P.R. China
| | - Haile Ma
- School of Food and Biological Engineering, Institute of food physical processing, Jiangsu University
| | - Ling Sun
- School of Food and Biological Engineering, Jiangsu University, No. 301 Xuefu Road, Zhenjiang 212013, P.R. China
| | - Ronghai He
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang Jiangsu 212013, China
| | - Xiaofei Ye
- School of Food and Biological Engineering, Jiangsu University, No. 301 Xuefu Road, Zhenjiang 212013, P.R. China; Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville 37996, Tennessee, USA
| | - Bingcheng Gan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, National Agricultural Science & Technology Center (NASC), 9 Hupan West Road, Tianfu New Area, Chengdu, 610000 P.R. China
| | - Qin Zhang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, National Agricultural Science & Technology Center (NASC), Tianfu New Area, Chengdu, 610000, P.R. China
| | - ZongJun Gong
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, National Agricultural Science & Technology Center (NASC), Tianfu New Area, Chengdu, 610000, P.R. China
| | - Xing Han
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, National Agricultural Science & Technology Center (NASC), 9 Hupan West Road, Tianfu New Area, Chengdu, 610000, P.R. China
| | - Xinlian Duan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, National Agricultural Science & Technology Center (NASC), Tianfu New Area, Chengdu, 610000, P.R. China
| | - Junjie Yan
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, National Agricultural Science & Technology Center (NASC), 9 Hupan West Road, Tianfu New Area, Chengdu, 610000, P.R. China
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Meng H, Chen Z, Chen L, Tang W, He F, Yan X, Lin X, Se X, Xie M, Li Z, Lu L, Yu X. An outbreak of Amanita exitialis poisoning. Clin Toxicol (Phila) 2023; 61:270-275. [PMID: 36919497 DOI: 10.1080/15563650.2022.2159830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
BACKGROUND The mushroom Amanita exitialis is reported to cause acute liver injury. It is found in Southern China, and has been previously associated with a high incidence of mortality. METHODS We described a series of 10 patients with Amanita exitialis poisoning admitted to The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) in April 2022. Patient demographics, clinical features, laboratory results, therapeutic interventions, and outcome data were collected. RESULTS Among the 10 patients, 9 survived, while 1 died. Gastrointestinal symptoms were the first to appear (average latency period, 11 ± 4.2 h). Diarrhea was the most common clinical symptom (average duration, 4.4 days). Abdominal distention was an important sign, especially in severely-ill patients. Thrombocytopenia occurred on day 2 after mushroom ingestion and persisted for 3-4 days. Alanine aminotransferase and total bilirubin peaked on days 2-3. CONCLUSION Amanita exitialis poisoning is characterized by gastrointestinal symptoms and liver injury. In the patient who died, acute hepatic failure led to hepatic encephalopathy and cerebral edema. Abdominal distension accompanied by thrombocytopenia was common in critically ill patients in this outbreak.
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Affiliation(s)
- Hui Meng
- Department of Critical Care Medicine, The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) (Longgang District People's Hospital of Shenzhen), Shenzhen, China
| | - ZhaoYin Chen
- Department of Critical Care Medicine, The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) (Longgang District People's Hospital of Shenzhen), Shenzhen, China
| | - LanChun Chen
- Department of Critical Care Medicine, The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) (Longgang District People's Hospital of Shenzhen), Shenzhen, China
| | - WeiXin Tang
- Department of Critical Care Medicine, The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) (Longgang District People's Hospital of Shenzhen), Shenzhen, China
| | - Fang He
- Department of Health Management, The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) (Longgang District People's Hospital of Shenzhen), Shenzhen, China
| | - XianRang Yan
- Department of Critical Care Medicine, The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) (Longgang District People's Hospital of Shenzhen), Shenzhen, China
| | - XiaoHong Lin
- Department of Critical Care Medicine, The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) (Longgang District People's Hospital of Shenzhen), Shenzhen, China
| | - XiaoLong Se
- Department of Critical Care Medicine, The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) (Longgang District People's Hospital of Shenzhen), Shenzhen, China
| | - MingFei Xie
- Department of Critical Care Medicine, The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) (Longgang District People's Hospital of Shenzhen), Shenzhen, China
| | - ZhanHan Li
- Department of Critical Care Medicine, The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) (Longgang District People's Hospital of Shenzhen), Shenzhen, China
| | - LiJuan Lu
- Department of Critical Care Medicine, The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) (Longgang District People's Hospital of Shenzhen), Shenzhen, China
| | - Xuetao Yu
- Department of Critical Care Medicine, The Second Affiliated Hospital of the Chinese University of Hong Kong (Shenzhen) (Longgang District People's Hospital of Shenzhen), Shenzhen, China
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Shu L, Wang M, Xu H, Qiu Z, Li T. De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia. Sci Rep 2022; 12:11075. [PMID: 35773379 PMCID: PMC9247108 DOI: 10.1038/s41598-022-15382-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/23/2022] [Indexed: 11/11/2022] Open
Abstract
The genes associated with fruiting body formation of Sparasis latifolia are valuable for improving mushroom breeding. To investigate this process, 4.8 × 108 RNA-Seq reads were acquired from three stages: hyphal knot (SM), primordium (SP), and primordium differentiation (SPD). The de novo assembly generated a total of 48,549 unigenes, of which 71.53% (34,728) unigenes could be annotated by at least one of the KEGG (Kyoto Encyclopedia of Genes and Genomes), GO (Gene Ontology), and KOG (Eukaryotic Orthologous Group) databases. KEGG and KOG analyses respectively mapped 32,765 unigenes to 202 pathways and 19,408 unigenes to 25 categories. KEGG pathway enrichment analysis of DEGs (differentially expressed genes) indicated primordium initiation was significantly related to 66 pathways, such as "Ribosome", "metabolism of xenobiotics by cytochrome P450", and "glutathione metabolism" (among others). The MAPK and mTOR signal transduction pathways underwent significant adjustments during the SM to SP transition. Further, our research revealed the PI3K-Akt signaling pathway related to cell proliferation could play crucial functions during the development of SP and SPD. These findings provide crucial candidate genes and pathways related to primordium differentiation and development in S. latifolia, and advances our knowledge about mushroom morphogenesis.
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Affiliation(s)
- Lili Shu
- School of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Miaoyue Wang
- School of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hui Xu
- School of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhiheng Qiu
- School of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Tianlai Li
- School of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
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Mei X, Wang Y, Li Z, Larousse M, Pere A, da Rocha M, Zhan F, He Y, Pu L, Panabières F, Zu Y. Root-associated microbiota drive phytoremediation strategies to lead of Sonchus Asper (L.) Hill as revealed by intercropping-induced modifications of the rhizosphere microbiome. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:23026-23040. [PMID: 34799796 PMCID: PMC8979924 DOI: 10.1007/s11356-021-17353-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 10/30/2021] [Indexed: 05/06/2023]
Abstract
Intercropping or assistant endophytes promote phytoremediation capacities of hyperaccumulators and enhance their tolerance to heavy metal (HM) stress. Findings from a previous study showed that intercropping the hyperaccumulator Sonchus asper (L.) Hill grown in HM-contaminated soils with maize improved the remediating properties and indicated an excluder-to-hyperaccumulator switched mode of action towards lead. In the current study, RNA-Seq analysis was conducted on Sonchus roots grown under intercropping or monoculture systems to explore the molecular events underlying this shift in lead sequestering strategy. The findings showed that intercropping only slightly affects S. asper transcriptome but significantly affects expression of root-associated microbial genomes. Further, intercropping triggers significant reshaping of endophytic communities associated with a 'root-to-shoot' transition of lead sequestration and improved phytoremediation capacities of S. asper. These findings indicate that accumulator activities of a weed are partially attributed to the root-associated microbiota, and a complex network of plant-microbe-plant interactions shapes the phytoremediation potential of S. asper. Analysis showed that intercropping may significantly change the structure of root-associated communities resulting in novel remediation properties, thus providing a basis for improving phytoremediation practices to restore contaminated soils.
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Affiliation(s)
- Xinyue Mei
- College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Ying Wang
- College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, China
| | - Zuran Li
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China
| | - Marie Larousse
- Université Côte d'Azur, INRAE, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Arthur Pere
- Université Côte d'Azur, INRAE, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Martine da Rocha
- Université Côte d'Azur, INRAE, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Fangdong Zhan
- College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, China
| | - Yongmei He
- College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, China
| | - Linlong Pu
- College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, China
| | - Franck Panabières
- Université Côte d'Azur, INRAE, CNRS, ISA, 06903, Sophia Antipolis, France.
| | - Yanqun Zu
- College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, China.
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Kessler SC, Chooi YH. Out for a RiPP: challenges and advances in genome mining of ribosomal peptides from fungi. Nat Prod Rep 2022; 39:222-230. [PMID: 34581394 DOI: 10.1039/d1np00048a] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Covering up to June 2021Ribosomally synthesized and post-translationally modified peptides (RiPPs) from fungi are an underexplored class of natural products, despite their propensity for diverse bioactivities and unique structural features. Surveys of fungal genomes for biosynthetic gene clusters encoding RiPPs have been limited in their scope due to our incomplete understanding of fungal RiPP biosynthesis. Through recent discoveries, along with earlier research, a clearer picture has been emerging of the biosynthetic principles that underpin fungal RiPP pathways. In this Highlight, we trace the approaches that have been used for discovering currently known fungal RiPPs and show that all of them can be assigned to one of three distinct families based on hallmarks of their biosynthesis, which are in turn imprinted on their corresponding gene clusters. We hope that our systematic exposition of fungal RiPP structural and gene cluster features will facilitate more comprehensive approaches to genome mining efforts in the future.
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Affiliation(s)
- Simon C Kessler
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
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6
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Zhong J, Xu J, Zhang P. Diversity, Dispersal and Mode of Reproduction of Amanita exitialis in Southern China. Genes (Basel) 2021; 12:1907. [PMID: 34946858 PMCID: PMC8701279 DOI: 10.3390/genes12121907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022] Open
Abstract
Amanita exitialis is a poisonous mushroom and has caused many deaths in southern China. In this study, we collected 118 fruiting bodies of A. exitialis from seven different sites in Guangdong Province in southern China and investigated their genetic relationships using 14 polymorphic molecular markers. These 14 markers grouped the 118 fruiting bodies into 20 multilocus genotypes. Among these 20 genotypes, eight were each found only once while the remaining 12 were each represented by two to 54 fruiting bodies. Interestingly, among the 12 shared genotypes, four were shared between/among local populations that were separated by as far as over 80 km, a result consistent with secondary homothallic reproduction and long-distance spore dispersal. Despite the observed gene flow, significant genetic differentiations were found among the local populations, primarily due to the over-representation of certain genotypes within individual local populations. STRUCTURE analyses revealed that the 118 fruiting bodies belonged to three genetic clusters, consistent with divergence within this species in this geographic region. Interestingly, we found an excess of heterozygous individuals at both the local and the total sample level, suggesting potential inbreeding depression and heterozygous advantage in these populations of A. exitialis. We discuss the implications of our results for understanding the life cycle, dispersal, and evolution of this poisonous mushroom.
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Affiliation(s)
- Juan Zhong
- College of Life Science, Hunan Normal University, Changsha 410081, China;
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada;
| | - Ping Zhang
- College of Life Science, Hunan Normal University, Changsha 410081, China;
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7
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Lüli Y, Zhou S, Li X, Chen Z, Yang Z, Luo H. Differential Expression of Amanitin Biosynthetic Genes and Novel Cyclic Peptides in Amanita molliuscula. J Fungi (Basel) 2021; 7:384. [PMID: 34069263 PMCID: PMC8156247 DOI: 10.3390/jof7050384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 02/05/2023] Open
Abstract
Amanita molliuscula is a basal species of lethal Amanita and intrigues the field because it does not produce discernable α-amanitin when inspected by High Performance Liquid Chromatography (HPLC), which sets it apart from all known amanitin-producing (lethal) Amanita species. In order to study the underlining genetic basis of the phenotype, we sequenced this species through PacBio and Illumina RNA-Seq platforms. In total, 17 genes of the "MSDIN" family (named after the first five amino acid residues of the precursor peptides) were found in the genome and 11 of them were expressed at the transcription level. The expression pattern was not even but in a differential fashion: two of the MSDINs were highly expressed (FPKM value > 100), while the majority were expressed at low levels (FPKM value < 1). Prolyl oligopeptidease B (POPB) is the key enzyme in the amanitin biosynthetic pathway, and high expression of this enzyme was also discovered (FPKM value > 100). The two MSDINs with highest transcription further translated into two novel cyclic peptides, the structure of which is distinctive from all known cyclic peptides. The result illustrates the correlation between the expression and the final peptide products. In contrast to previous HPLC result, the genome of A. molliuscula harbors α-amanitin genes (three copies), but the product was in trace amount indicated by MS. Overall, transcription of MSDINs encoding major toxins (α-amanitin, β-amanitin, phallacidin and phalloidin) were low, showing that these toxins were not actively synthesized at the stage. Collectively, our results indicate that the amanitin biosynthetic pathway is highly active at the mature fruiting body stage in A. molliuscula, and due to the differential expression of MSDIN genes, the pathway produces only a few cyclic peptides at the time.
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Affiliation(s)
- Yunjiao Lüli
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Y.L.); (S.Z.); (Z.Y.)
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengwen Zhou
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Y.L.); (S.Z.); (Z.Y.)
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Xuan Li
- Department of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650091, China;
| | - Zuohong Chen
- College of Life Science, Hunan Normal University, Changsha 410081, China;
| | - Zhuliang Yang
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Y.L.); (S.Z.); (Z.Y.)
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong Luo
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Y.L.); (S.Z.); (Z.Y.)
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Zhou S, Li X, Lüli Y, Li X, Chen ZH, Yuan P, Yang ZL, Li G, Luo H. Novel Cyclic Peptides from Lethal Amanita Mushrooms through a Genome-Guided Approach. J Fungi (Basel) 2021; 7:204. [PMID: 33799506 PMCID: PMC7998459 DOI: 10.3390/jof7030204] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
Most species in the genus Amanita are ectomycorrhizal fungi comprising both edible and poisonous mushrooms. Some species produce potent cyclic peptide toxins, such as α-amanitin, which places them among the deadliest organisms known to mankind. These toxins and related cyclic peptides are encoded by genes of the "MSDIN" family (named after the first five amino acid residues of the precursor peptides), and it is largely unknown to what extent these genes are expressed in the basidiocarps. In the present study, Amanita rimosa and Amanita exitialis were sequenced through the PacBio and Illumina techniques. Together with our two previously sequenced genomes, Amanita subjunquillea and Amanita pallidorosea, in total, 46 previously unknown MSDIN genes were discovered. The expression of over 80% of the MSDIN genes was demonstrated in A. subjunquillea. Through a combination of genomics and mass spectrometry, 12 MSDIN genes were shown to produce novel cyclic peptides. To further confirm the results, three of the cyclic peptides were chemically synthesized. The tandem mass spectrometry (MS/MS) spectra of the natural and the synthetic peptides shared a majority of the fragment ions, demonstrating an identical structure between each peptide pair. Collectively, the results suggested that the genome-guided approach is reliable for identifying novel cyclic peptides in Amanita species and that there is a large peptide reservoir in these mushrooms.
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Affiliation(s)
- Shengwen Zhou
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; (S.Z.); (X.L.); (Y.L.); (P.Y.); (Z.L.Y.)
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- School of Life Sciences, Yunnan University, Kunming 650091, Yunnan, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xincan Li
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; (S.Z.); (X.L.); (Y.L.); (P.Y.); (Z.L.Y.)
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunjiao Lüli
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; (S.Z.); (X.L.); (Y.L.); (P.Y.); (Z.L.Y.)
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Li
- Department of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650091, Yunnan, China;
| | - Zuo H. Chen
- College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China;
| | - Pengcheng Yuan
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; (S.Z.); (X.L.); (Y.L.); (P.Y.); (Z.L.Y.)
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- School of Life Sciences, Yunnan University, Kunming 650091, Yunnan, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhu L. Yang
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; (S.Z.); (X.L.); (Y.L.); (P.Y.); (Z.L.Y.)
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Guohong Li
- School of Life Sciences, Yunnan University, Kunming 650091, Yunnan, China;
| | - Hong Luo
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; (S.Z.); (X.L.); (Y.L.); (P.Y.); (Z.L.Y.)
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
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Zhou K, Huang Y, Chen Z, Du X, Qin J, Wen L, Ma H, Pan X, Lin Y. Liver and spleen transcriptome reveals that Oreochromis aureus under long-term salinity stress may cause excessive energy consumption and immune response. FISH & SHELLFISH IMMUNOLOGY 2020; 107:469-479. [PMID: 33181338 DOI: 10.1016/j.fsi.2020.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/14/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
To investigate the physiological responses of Oreochromis aureus to salinity fluctuations at the molecular level. We used RNA-seq to explore the differentially expressed genes (DEGs) in the liver and spleen of O. aureus at 0, 3, 7 and 11 ppt (parts per thousand) salinity levels. Herein, De novo assembly generated 71,009 O. aureus unigenes, of which 34,607 were successfully mapped to the four major databases. A total of 120 shared DEGs were identified in liver and spleen transcripts, of which 83 were up-regulated and 37 were down-regulated. GO and KEGG analysis found a total of 26 significant pathways, mainly including energy metabolism, immune response, ion transporters and signal transduction. The trend module category of DEGs showed that the genes (e.g., FASN, ODC1, CD22, MRC, TRAV and SLC7 family) involved in the change-stable-change (1) and the constant-change categories (2) were highly sensitive to salinity fluctuations, which were of great value for further study. Based on these results, it would help provide basic data for fish salinity acclimation, and provide new insights into evolutionary response of fish to various aquatic environments in the long-term stress adaptation mechanism.
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Affiliation(s)
- Kangqi Zhou
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Yin Huang
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Zhong Chen
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Xuesong Du
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Junqi Qin
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Luting Wen
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Huawei Ma
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China
| | - Xianhui Pan
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
| | - Yong Lin
- Guangxi Key Laboratory for Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, 530021, China.
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He Z, Long P, Fang F, Li S, Zhang P, Chen Z. Diversity of MSDIN family members in amanitin-producing mushrooms and the phylogeny of the MSDIN and prolyl oligopeptidase genes. BMC Genomics 2020; 21:440. [PMID: 32590929 PMCID: PMC7318481 DOI: 10.1186/s12864-020-06857-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/22/2020] [Indexed: 11/14/2022] Open
Abstract
Background Amanitin-producing mushrooms, mainly distributed in the genera Amanita, Galerina and Lepiota, possess MSDIN gene family for the biosynthesis of many cyclopeptides catalysed by prolyl oligopeptidase (POP). Recently, transcriptome sequencing has proven to be an efficient way to mine MSDIN and POP genes in these lethal mushrooms. Thus far, only A. palloides and A. bisporigera from North America and A. exitialis and A. rimosa from Asia have been studied based on transcriptome analysis. However, the MSDIN and POP genes of many amanitin-producing mushrooms in China remain unstudied; hence, the transcriptomes of these speices deserve to be analysed. Results In this study, the MSDIN and POP genes from ten Amanita species, two Galerina species and Lepiota venenata were studied and the phylogenetic relationships of their MSDIN and POP genes were analysed. Through transcriptome sequencing and PCR cloning, 19 POP genes and 151 MSDIN genes predicted to encode 98 non-duplicated cyclopeptides, including α-amanitin, β-amanitin, phallacidin, phalloidin and 94 unknown peptides, were found in these species. Phylogenetic analysis showed that (1) MSDIN genes generally clustered depending on the taxonomy of the genus, while Amanita MSDIN genes clustered depending on the chemical substance; and (2) the POPA genes of Amanita, Galerina and Lepiota clustered and were separated into three different groups, but the POPB genes of the three distinct genera were clustered in a highly supported monophyletic group. Conclusions These results indicate that lethal Amanita species have the genetic capacity to produce numerous cyclopeptides, most of which are unknown, while lethal Galerina and Lepiota species seem to only have the genetic capacity to produce α-amanitin. Additionally, the POPB phylogeny of Amanita, Galerina and Lepiota conflicts with the taxonomic status of the three genera, suggesting that underlying horizontal gene transfer has occurred among these three genera.
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Affiliation(s)
- Zhengmi He
- College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China
| | - Pan Long
- College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China
| | - Fang Fang
- College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China
| | - Sainan Li
- College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China
| | - Ping Zhang
- College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China
| | - Zuohong Chen
- College of Life Science, Hunan Normal University, Lushan Road, Changsha, 410081, China.
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He Y, Zhang CH, Deng WQ, Zhou XY, Li TH, Li CH. Transcriptome sequencing analysis of the MSDIN gene family encoding cyclic peptides in lethal Amanita fuligineoides. Toxicon 2020; 183:61-68. [PMID: 32473253 DOI: 10.1016/j.toxicon.2020.05.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 10/24/2022]
Abstract
Amanita fuligineoides, a lethal mushroom discovered in China, contains abundant cyclic peptide toxins that can cause fatal poisoning. However, the MSDIN gene family encoding for these cyclic peptides in A. fuligineoides has not been systematically studied. In this research, the transcriptome sequencing of A. fuligineoides was performed and its MSDIN family members were analyzed. A total of 4.41 Gb data containing 30833 unigenes was obtained; sequence alignments throughout several databases were done to obtain their functional annotations. Based on these annotations, MSDIN genes were found and verified by RT-PCR. A total of 29 different core peptides were obtained: 3 toxin genes, encoding β-amanitin (β-AMA), phalloidin (PHD), and phallacidin (PCD), and 26 genes encoding unknown cyclic peptides, 20 of which are reported for the first time and may encode for novel cyclic peptides. Analysis of the predicted precursor peptides indicated that octocyclic peptides were the main MSDIN peptides synthesized by A. fuligineoides, accounting for the 45%. A phylogenetic analysis suggested that studied precursor peptides could be clustered into 7 clades, which might represent different functionalities. Results suggested that A. fuligineoides might have a strong capacity to synthesize cyclopeptides, laying the foundation for their excavation and utilization.
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Affiliation(s)
- Yong He
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Cheng-Hua Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Wang-Qiu Deng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Xiao-Yun Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
| | - Tai-Hui Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Chuan-Hua Li
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.
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Disclosure of the Molecular Mechanism of Wheat Leaf Spot Disease Caused by Bipolaris sorokiniana through Comparative Transcriptome and Metabolomics Analysis. Int J Mol Sci 2019; 20:ijms20236090. [PMID: 31816858 PMCID: PMC6929001 DOI: 10.3390/ijms20236090] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/24/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
Wheat yield is greatly reduced because of the occurrence of leaf spot diseases. Bipolaris sorokiniana is the main pathogenic fungus in leaf spot disease. In this study, B. sorokiniana from wheat leaf (W-B. sorokiniana) showed much stronger pathogenicity toward wheat than endophytic B. sorokiniana from Pogostemon cablin (P-B. sorokiniana). The transcriptomes and metabolomics of the two B. sorokiniana strains and transcriptomes of B. sorokiniana-infected wheat leaves were comparatively analyzed. In addition, the expression levels of unigenes related to pathogenicity, toxicity, and cell wall degradation were predicted and validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis. Results indicated that pathogenicity-related genes, especially the gene encoding loss-of-pathogenicity B (LopB) protein, cell wall-degrading enzymes (particularly glycosyl hydrolase-related genes), and killer and Ptr necrosis toxin-producing related unigenes in the W-B. sorokiniana played important roles in the pathogenicity of W-B. sorokiniana toward wheat. The down-regulation of cell wall protein, photosystem peptide, and rubisco protein suggested impairment of the phytosynthetic system and cell wall of B. sorokiniana-infected wheat. The up-regulation of hydrolase inhibitor, NAC (including NAM, ATAF1 and CUC2) transcriptional factor, and peroxidase in infected wheat tissues suggests their important roles in the defensive response of wheat to W-B. sorokiniana. This is the first report providing a comparison of the transcriptome and metabolome between the pathogenic and endophytic B. sorokiniana strains, thus providing a molecular clue for the pathogenic mechanism of W-B. sorokiniana toward wheat and wheat's defensive response mechanism to W-B. sorokiniana. Our study could offer molecular clues for controlling the hazard of leaf spot and root rot diseases in wheat, thus improving wheat yield in the future.
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Lüli Y, Cai Q, Chen ZH, Sun H, Zhu XT, Li X, Yang ZL, Luo H. Genome of lethal Lepiota venenata and insights into the evolution of toxin-biosynthetic genes. BMC Genomics 2019; 20:198. [PMID: 30849934 PMCID: PMC6408872 DOI: 10.1186/s12864-019-5575-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/28/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Genomes of lethal Amanita and Galerina mushrooms have gradually become available in the past ten years; in contrast the other known amanitin-producing genus, Lepiota, is still vacant in this aspect. A fatal mushroom poisoning case in China has led to acquisition of fresh L. venenata fruiting bodies, based on which a draft genome was obtained through PacBio and Illumina sequencing platforms. Toxin-biosynthetic MSDIN family and Porlyl oligopeptidase B (POPB) genes were mined from the genome and used for phylogenetic and statistical studies to gain insights into the evolution of the biosynthetic pathway. RESULTS The analysis of the genome data illustrated that only one MSDIN, named LvAMA1, exits in the genome, along with a POPB gene. No POPA homolog was identified by direct homology searching, however, one additional POP gene, named LvPOPC, was cloned and the gene structure determined. Similar to ApAMA1 in A. phalloides and GmAMA1 in G. marginata, LvAMA1 directly encodes α-amanitin. The two toxin genes were mapped to the draft genome, and the structures analyzed. Furthermore, phylogenetic and statistical analyses were conducted to study the evolution history of the POPB genes. Compared to our previous report, the phylogenetic trees unambiguously showed that a monophyletic POPB lineage clearly conflicted with the species phylogeny. In contrast, phylogeny of POPA genes resembled the species phylogeny. Topology and divergence tests showed that the POPB lineage was robust and these genes exhibited significantly shorter genetic distances than those of the house-keeping rbp2, a characteristic feature of genes with horizontal gene transfer (HGT) background. Consistently, same scenario applied to the only MSDIN, LvAMA1, in the genome. CONCLUSIONS To the best of our knowledge, this is the first reported genome of Lepiota. The analyses of the toxin genes indicate that the cyclic peptides are synthesized through a ribosomal mechanism. The toxin genes, LvAMA1 and LvPOPB, are not in the vicinity of each other. Phylogenetic and evolutionary studies suggest that HGT is the underlining cause for the occurrence of POPB and MSDIN in Amanita, Galerina and Lepiota, which are allocated in three distantly-related families.
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Affiliation(s)
- Yunjiao Lüli
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qing Cai
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Zuo H. Chen
- College of Life Science, Hunan Normal University, Changsha, 410081 China
| | - Hu Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Xue-Tai Zhu
- College of Life Sciences, Northwest Normal University, Lanzhou, 730030 China
| | - Xuan Li
- Department of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, 650091 Yunnan China
| | - Zhu L. Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
| | - Hong Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan China
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Mei X, Liu Y, Huang H, Du F, Huang L, Wu J, Li Y, Zhu S, Yang M. Benzothiazole inhibits the growth of Phytophthora capsici through inducing apoptosis and suppressing stress responses and metabolic detoxification. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 154:7-16. [PMID: 30765059 DOI: 10.1016/j.pestbp.2018.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/21/2018] [Accepted: 12/10/2018] [Indexed: 05/22/2023]
Abstract
Benzothiazole (BZO) is an antimicrobial secondary metabolite volatilized by many plants and microbes. However, the mechanism of BZO against phytopathogens is still unclear. Here, we found that BZO has antimicrobial activity against the oomycete pathogen Phytophthora capsici. Transcriptome and proteome analyses demonstrated that BZO significantly suppressed the expression of genes and proteins involved in morphology, abiotic stress defense and detoxification, but induced the activity of apoptosis. Annexin V-FITC/PI staining confirmed that the process of apoptosis was significantly induced by BZO at concentration of 150 mg L-1. FITC-phalloidin actin-cytoskeleton staining combined with hyphal cell wall staining and hyphal ultrastructure studies further confirmed that BZO disrupted the cell membrane and hyphal morphology through disrupting the cytoskeleton, eventually inhibiting the growth of hyphae. These data demonstrated that BZO has multiple modes of action and may act as potential leading compound for the development of new oomycete fungicides. These results also showed that the combination of transcriptomic and proteomic approaches was a useful method for exploring the novel antifungal mechanisms of natural compounds.
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Affiliation(s)
- Xinyue Mei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; College of Resources and Environment, Yunnan Agricultural University, Kunming, Yunnan Province, China
| | - Yixiang Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Fei Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Lanlin Huang
- College of Resources and Environment, Yunnan Agricultural University, Kunming, Yunnan Province, China
| | - Jiaqing Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Yiwen Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Shusheng Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China.
| | - Min Yang
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
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Yang R, Li J, Zhang H, Yang F, Wu Z, Zhuo X, An X, Cheng Z, Zeng Q, Luo Q. Transcriptome Analysis and Functional Identification of Xa13 and Pi-ta Orthologs in Oryza granulata. THE PLANT GENOME 2018; 11:170097. [PMID: 30512031 DOI: 10.3835/plantgenome2017.11.0097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nees & Arn. ex Watt, a perennial wild rice species with a GG genome, preserves many important genes for cultivated rice ( L.) improvement. At present, however, no genetic resource is available for studying . Here, we report 91,562 high-quality transcripts of assembled de novo. Moreover, comparative transcriptome analysis revealed that 1311 single-copy orthologous pairs shared by and (Zoll. & Moritzi) Baill. that may have undergone adaptive evolution. We performed an analysis of the genes potentially involved in plant-pathogen interactions to explore the molecular basis of disease resistance, and isolated the full-length cDNAs of () and () orthologs from . The overexpression of in Nipponbare and functional characterization showed enhanced the resistance of transgenic Nipponbare to rice blast resulting from the presence of the gene. , an alternatively spliced transcript of the blast resistance gene in encodes a 1024-amino acid polypeptide with a C-terminal thioredoxin domain. This study provides an important resource for functional and evolutionary studies of the genus .
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16
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Wang Q, Chen M, Zhang W. A two-component signal transduction system contributes to the virulence of Riemerella anatipestifer. J Vet Sci 2018; 19:260-270. [PMID: 29284206 PMCID: PMC5879074 DOI: 10.4142/jvs.2018.19.2.260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/25/2017] [Accepted: 11/24/2017] [Indexed: 11/20/2022] Open
Abstract
Similar to other studies of bacterial pathogens, current studies of the pathogenesis of Riemerella anatipestifer (RA) are focused mainly on in vitro culture conditions. To elucidate further the pathogenesis of RA in vivo, bacterial RNA was extracted from overnight tryptic soy broth cultures (in vitro) and from the blood of infected ducks (in vivo) for comparative RNA sequencing analysis. In total, 682 upregulated genes were identified in vivo. Among the upregulated genes, a signal transduction response regulator (ArsR) and a signal transduction histidine kinase (SthK) were predicted to be located on the same operon. A mutant was constructed by deletion of both of these genes. Duck infection tests showed that genes ArsR and SthK were related to the virulence of the pathogen in vivo. Differentially expressed genes identified by comparison of in vitro and in vivo conditions provided an insight into the physiological process of RA infection and provided an opportunity to identify additional virulence factors.
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Affiliation(s)
- Qing Wang
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mianmian Chen
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Zhang
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Tiwari B, Kalim S, Tyagi N, Kumari R, Bangar P, Barman P, Kumar S, Gaikwad A, Bhat KV. Identification of genes associated with stress tolerance in moth bean [ Vigna aconitifolia (Jacq.) Marechal], a stress hardy crop. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:551-561. [PMID: 30042612 PMCID: PMC6041239 DOI: 10.1007/s12298-018-0525-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 12/15/2017] [Accepted: 03/14/2018] [Indexed: 05/24/2023]
Abstract
Moth bean is the most drought and heat tolerant cultigens among Asian Vigna. We performed comparative transcriptome analysis of moth bean cultivar "Marumoth" under control and stress condition. De novo transcriptome assembly was carried out by using Velvet followed by Oases softwares. Differential expression analyses, SSR identification and validation and mapping of pathways and transcription factors were conducted. A total of 179,979 and 201,888 reads were generated on Roche 454 platform and 48,617,205 and 45,449,053 reads were generated on ABI Solid platform for the control and stressed samples. Combined assembly from Roche and ABI Solid platforms generated 16,090 and 15,096 transcripts for control and stressed samples. We found 1287 SSRs and 5606 transcripts involved in 179 pathways. The 55 transcription factor families represented 19.42% of total mothbean transcripts. In expression profiling, ten transcripts were found to be up-regulated and 41 down-regulated while 490 showed no major change under moisture stress condition. Stress inducible genes like Catalase, Cyt P450 monooxygenase, heat shock proteins (HSP 90 and HSP 70), oxidoreductase, protein kinases, dehydration responsive protein (DRP), universal stress protein and ferridoxin NADH oxidoreductase genes were up-regulated in stressed sample. Genes which might be involved in moisture stress tolerance in moth bean were identified and these might be useful for stress tolerance breeding in moth bean and other related crops.
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Affiliation(s)
- Bhavana Tiwari
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Neetu Tyagi
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ratna Kumari
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Pooja Bangar
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Paramananda Barman
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ambika Gaikwad
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - K. V. Bhat
- Genomic Resources Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Ye W, Zhang W, Liu T, Huang Z, Zhu M, Chen Y, Li H, Li S. De Novo Transcriptome Sequencing of the Deep-Sea-Derived Fungus Dichotomomyces cejpii and Analysis of Gliotoxin Biosynthesis Genes. Int J Mol Sci 2018; 19:E1910. [PMID: 29966253 PMCID: PMC6073683 DOI: 10.3390/ijms19071910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/17/2018] [Accepted: 06/26/2018] [Indexed: 12/03/2022] Open
Abstract
Gliotoxin, produced by fungi, is an epipolythiodioxopiperazine (ETP) toxin with bioactivities such as anti-liver fibrosis, antitumor, antifungus, antivirus, antioxidation, and immunoregulation. Recently, cytotoxic gliotoxins were isolated from a deep-sea-derived fungus, Dichotomomyces cejpii. However, the biosynthetic pathway for gliotoxins in D. cejpii remains unclear. In this study, the transcriptome of D. cejpii was sequenced using an Illumina Hiseq 2000. A total of 19,125 unigenes for D. cejpii were obtained from 9.73 GB of clean reads. Ten genes related to gliotoxin biosynthesis were annotated. The expression levels of gliotoxin-related genes were detected through quantitative real-time polymerase chain reaction (qRT-PCR). The GliG gene, encoding a glutathione S-transferase (DC-GST); GliI, encoding an aminotransferase (DC-AI); and GliO, encoding an aldehyde reductase (DC-AR), were cloned and expressed, purified, and characterized. The results suggested the important roles of DC-GST, DC-AT, and DC-AR in the biosynthesis of gliotoxins. Our study on the genes related to gliotoxin biosynthesis establishes a molecular foundation for the wider application of gliotoxins from D. cejpii in the biomedical industry in the future.
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Affiliation(s)
- Wei Ye
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Taomei Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Zilei Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Muzi Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Yuchan Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Haohua Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
| | - Saini Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Yuexiu District, Guangzhou 510070, China.
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Molecular cloning and the expression pattern of AePOPB involved in the α-amanitin biosynthesis in Amanita exitialis fruiting bodies. Gene 2018; 662:123-130. [PMID: 29627524 DOI: 10.1016/j.gene.2018.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 04/02/2018] [Accepted: 04/04/2018] [Indexed: 12/31/2022]
Abstract
Amanita exitialis Zhu L. Yang & T. H. Li is the species responsible for the largest number of mushroom-associated human poisonings and fatalities in South China due to its lethal cyclic peptide toxins. Prolyl oligopeptidase B (POPB) is considered a key enzyme in the production of the highly toxic cyclic peptide α-amanitin. However, the POPB gene of A. exitialis has not been studied. In the present study we cloned and sequenced the full-length A. exitialis POPB (AePOPB) gene. The aim was to verify the gene structure and functions of AePOPB. The full-length sequence of AePOPB is 3144 bp, including 18 exons encoding 730 aa, and the advanced structure is very similar to that of the previously reported POPB in Galerina marginata (GmPOPB). The amino acid sequence of AePOPB is highly homologous with those from other amanitin-producing lethal mushrooms, implying that AePOPB may have a similar role in the biosynthesis of cyclic peptide toxins. Expression levels of AePOPB were detectable in all parts and developmental stages of the fruiting bodies, and AePOPB was expressed more strongly at early development stages (early and late elongation stages). At early and late elongation stages, the expression peaks occurred in the stipe, whereas at early and late mature stages, the expression peaks occurred in the pileus. The expression patterns of AePOPB in different stages and different parts of the fruiting bodies were highly consistent with those of Aeα-AMA, which is required for α-amanitin accumulation. These results indicate that AePOPB should be involved in the α-amanitin biosynthesis in A. exitialis.
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Sun J, Niu YM, Zhang YT, Li HJ, Yin Y, Zhang YZ, Ma PB, Zhou J, Huang L, Zhang HS, Sun CY. Toxicity and toxicokinetics of Amanita exitialis in beagle dogs. Toxicon 2018; 143:59-67. [DOI: 10.1016/j.toxicon.2018.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/01/2017] [Accepted: 01/11/2018] [Indexed: 11/25/2022]
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Chen C, Li Q, Wang Q, Lu D, Zhang H, Wang J, Fu R. Transcriptional profiling provides new insights into the role of nitric oxide in enhancing Ganoderma oregonense resistance to heat stress. Sci Rep 2017; 7:15694. [PMID: 29146915 PMCID: PMC5691203 DOI: 10.1038/s41598-017-15340-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/26/2017] [Indexed: 12/18/2022] Open
Abstract
Ganoderma is well known for its use in traditional Chinese medicine and is widely cultivated in China, Korea, and Japan. Increased temperatures associated with global warming are negatively influencing the growth and development of Ganoderma. Nitric oxide is reported to play an important role in alleviating fungal heat stress (HS). However, the transcriptional profiling of Ganoderma oregonense in response to HS, as well as the transcriptional response regulated by NO to cope with HS has not been reported. We used RNA-Seq technology to generate large-scale transcriptome data from G. oregonense mycelia subjected to HS (32 °C) and exposed to concentrations of exogenous NO. The results showed that heat shock proteins (HSPs), "probable stress-induced proteins", and unigenes involved in "D-amino-acid oxidase activity" and "oxidoreductase activity" were significantly up-regulated in G. oregonense subjected to HS (P < 0.05). The significantly up-regulated HSPs, "monooxygenases", "alcohol dehydrogenase", and "FAD/NAD(P)-binding domain-containing proteins" (P < 0.05) regulated by exogenous NO may play important roles in the enhanced HS tolerance of G. oregonense. These results provide insights into the transcriptional response of G. oregonense to HS and the mechanism by which NO enhances the HS tolerance of fungi at the gene expression level.
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Affiliation(s)
- Cheng Chen
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, P.R. China
| | - Qiang Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
| | - Qiangfeng Wang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Daihua Lu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, P.R. China
| | - Hong Zhang
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, P.R. China. .,Sichuan Academy of Agricultural Sciences, 20 # Jingjusi Rd, Chengdu, 610066, Sichuan, China.
| | - Jian Wang
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, P.R. China
| | - Rongtao Fu
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, P.R. China
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22
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Sun J, Li HJ, Zhang HS, Zhang YZ, Xie JW, Ma PB, Guo C, Sun CY. Investigating and analyzing three cohorts of mushroom poisoning caused by Amanita exitialis in Yunnan, China. Hum Exp Toxicol 2017; 37:665-678. [PMID: 28830233 DOI: 10.1177/0960327117721960] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Amanita exitialis is a lethal mushroom found in China. Knowledge regarding taxonomic characterization, toxin detection, general poisoning conditions, clinical manifestations, laboratory examinations, and clinical treatments for this species is currently lacking. We investigated three A. exitialis mushroom poisoning cohorts in Yunnan Province in 2014 and 2015, involving 10 patients. Mushroom samples were identified by morphological and molecular studies. Ultra performance liquid chromatography-electrospray ionization tandem mass spectrometry was used to detect the peptide toxins in the mushroom samples. Epidemiological information, clinical data, and results of laboratory examinations were collected and analyzed. The mushroom samples were all identified as A. exitialis. The average toxin concentration decreased from the cap to the stipe to the volva, and the average concentration of the peptide toxins decreased in the order of α-amanitin > phallacidin > β-amanitin > γ-amanitin. The latency period between ingestion and the onset of symptoms was 13.9 ± 2.1 h, and the time from ingestion to hospitalization was 49.6 ± 8.5 h. The most common symptoms were nausea and vomiting (100%). Four patients died from fulminant hepatic failure. Laboratory examinations showed that the alanine transaminase, aspartate transaminase, prothrombin time, and activated partial thromboplastin time levels peaked on the third day post-ingestion. Total bilirubin and direct bilirubin values peaked on day 7. The death group and the survival group had a similar variation trend of serological indexes, but the death group had a greater change. A. exitialis is an extremely dangerous mushroom and there is a need to educate the public to avoid picking and eating wild mushrooms that have not been definitively identified.
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Affiliation(s)
- J Sun
- 1 National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.,2 Yinchuan City Centre for Disease Control and Prevention, Ningxia, People's Republic of China
| | - H-J Li
- 1 National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - H-S Zhang
- 1 National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Y-Z Zhang
- 1 National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - J-W Xie
- 3 State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing, People's Republic of China
| | - P-B Ma
- 1 National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - C Guo
- 4 Tengchong Centre for Disease Control and Prevention, Yunnan, People's Republic of China
| | - C Y Sun
- 1 National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
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23
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Guo P, Qi YP, Yang LT, Lai NW, Ye X, Yang Y, Chen LS. Root Adaptive Responses to Aluminum-Treatment Revealed by RNA-Seq in Two Citrus Species With Different Aluminum-Tolerance. FRONTIERS IN PLANT SCIENCE 2017; 8:330. [PMID: 28337215 PMCID: PMC5340773 DOI: 10.3389/fpls.2017.00330] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/24/2017] [Indexed: 05/02/2023]
Abstract
Seedlings of aluminum (Al)-tolerant Citrus sinensis and Al-intolerant Citrus grandis were fertigated daily with nutrient solution containing 0 and 1.0 mM AlCl3●6H2O for 18 weeks. The Al-induced decreases of biomass and root total soluble proteins only occurred in C. grandis, demonstrating that C. sinensis had higher Al-tolerance than C. grandis. Under Al-treatment, C. sinensis roots secreted more citrate and malate than C. grandis ones; less Al was accumulated in C. sinenis than in C. grandis leaves. The Al-induced reduction of phosphorus was lesser in C. sinensis roots and leaves than in C. grandis ones, whereas the Al-induced increase of sulfur was greater in C. sinensis roots and leaves. Using RNA-seq, we isolated 1905 and 2670 differentially expressed genes (DEGs) from Al-treated C. sinensis than C. grandis roots, respectively. Among these DEGs, only 649 DEGs were shared by the two species. Further analysis suggested that the following several aspects conferred C. sinensis higher Al-tolerance: (a) Al-treated C. sinensis seedlings had a higher external Al detoxification capacity via enhanced Al-induced secretion of organic acid anions, a higher antioxidant capacity and a more efficient chelation system in roots; (b) Al-treated C. sinensis seedlings displayed a higher level of sulfur in roots and leaves possibly due to increased uptake and decreased export of sulfur and a higher capacity to maintain the cellular phosphorus homeostasis by enhancing phosphorus acquisition and utilization; (c) Cell wall and cytoskeleton metabolism, energy and carbohydrate metabolism and signal transduction displayed higher adaptative responses to Al in C. sinensis than in C. grandis roots; (d) More upregulated than downregulated genes related to fatty acid and amino acid metabolisms were isolated from Al-treated C. sinensis roots, but the reverse was the case for Al-treated C. grandis roots. These results provide a platform for further investigating the roles of genes possibly responsible for citrus Al-tolerance.
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Affiliation(s)
- Peng Guo
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yi-Ping Qi
- Institute of Materia Medica, Fujian Academy of Medical SciencesFuzhou, China
| | - Lin-Tong Yang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Ning-Wei Lai
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xin Ye
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yi Yang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Li-Song Chen
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
- The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
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24
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Ye W, Liu T, Zhu M, Zhang W, Li H, Huang Z, Li S. De Novo Transcriptome Analysis of Plant Pathogenic Fungus Myrothecium roridum and Identification of Genes Associated with Trichothecene Mycotoxin Biosynthesis. Int J Mol Sci 2017; 18:E497. [PMID: 28245611 PMCID: PMC5372513 DOI: 10.3390/ijms18030497] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 12/20/2022] Open
Abstract
Myrothecium roridum is a plant pathogenic fungus that infects different crops and decreases the yield of economical crops, including soybean, cotton, corn, pepper, and tomato. Until now, the pathogenic mechanism of M. roridum has remained unclear. Different types of trichothecene mycotoxins were isolated from M. roridum, and trichothecene was considered as a plant pathogenic factor of M. roridum. In this study, the transcriptome of M. roridum in different incubation durations was sequenced using an Illumina Hiseq 2000. A total of 35,485 transcripts and 25,996 unigenes for M. roridum were obtained from 8.0 Gb clean reads. The protein-protein network of the M. roridum transcriptome indicated that the mitogen-activated protein kinases signal pathway also played an important role in the pathogenicity of M. roridum. The genes related to trichothecene biosynthesis were annotated. The expression levels of these genes were also predicted and validated through quantitative real-time polymerase chain reaction. Tri5 gene encoding trichodiene synthase was cloned and expressed, and the purified trichodiene synthase was able to catalyze farnesyl pyrophosphate into different kinds of sesquiterpenoids.Tri4 and Tri11 genes were expressed in Escherichia coli, and their corresponding enzymatic properties were characterized. The phylogenetic tree of trichodiene synthase showed a great discrepancy between the trichodiene synthase from M. roridum and other species. Our study on the genes related to trichothecene biosynthesis establishes a foundation for the M. roridum hazard prevention, thus improving the yields of economical crops.
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Affiliation(s)
- Wei Ye
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
| | - Taomei Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
| | - Muzi Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
| | - Haohua Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
| | - Zilei Huang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
| | - Saini Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, No. 100 Xianlie Middle Road, Yuexiu District, Guangzhou 510070, China.
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25
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Pulman JA, Childs KL, Sgambelluri RM, Walton JD. Expansion and diversification of the MSDIN family of cyclic peptide genes in the poisonous agarics Amanita phalloides and A. bisporigera. BMC Genomics 2016; 17:1038. [PMID: 27978833 PMCID: PMC5159998 DOI: 10.1186/s12864-016-3378-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/05/2016] [Indexed: 11/24/2022] Open
Abstract
Background The cyclic peptide toxins of Amanita mushrooms, such as α-amanitin and phalloidin, are encoded by the “MSDIN” gene family and ribosomally biosynthesized. Based on partial genome sequence and PCR analysis, some members of the MSDIN family were previously identified in Amanita bisporigera, and several other members are known from other species of Amanita. However, the complete complement in any one species, and hence the genetic capacity for these fungi to make cyclic peptides, remains unknown. Results Draft genome sequences of two cyclic peptide-producing mushrooms, the “Death Cap” A. phalloides and the “Destroying Angel” A. bisporigera, were obtained. Each species has ~30 MSDIN genes, most of which are predicted to encode unknown cyclic peptides. Some MSDIN genes were duplicated in one or the other species, but only three were common to both species. A gene encoding cycloamanide B, a previously described nontoxic cyclic heptapeptide, was also present in A. phalloides, but genes for antamanide and cycloamanides A, C, and D were not. In A. bisporigera, RNA expression was observed for 20 of the MSDIN family members. Based on their predicted sequences, novel cyclic peptides were searched for by LC/MS/MS in extracts of A. phalloides. The presence of two cyclic peptides, named cycloamanides E and F with structures cyclo(SFFFPVP) and cyclo(IVGILGLP), was thereby demonstrated. Of the MSDIN genes reported earlier from another specimen of A. bisporigera, 9 of 14 were not found in the current genome assembly. Differences between previous and current results for the complement of MSDIN genes and cyclic peptides in the two fungi probably represents natural variation among geographically dispersed isolates of A. phalloides and among the members of the poorly defined A. bisporigera species complex. Both A. phalloides and A. bisporigera contain two prolyl oligopeptidase genes, one of which (POPB) is probably dedicated to cyclic peptide biosynthesis as it is in Galerina marginata. Conclusion The MSDIN gene family has expanded and diverged rapidly in Amanita section Phalloideae. Together, A. bisporigera and A. phalloides are predicted to have the capacity to make more than 50 cyclic hexa-, hepta-, octa-, nona- and decapeptides. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3378-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jane A Pulman
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,Center for Genomics-Enabled Plant Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,Center for Genomics-Enabled Plant Science, Michigan State University, East Lansing, MI, 48824, USA
| | - R Michael Sgambelluri
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Jonathan D Walton
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.
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26
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Ye W, Wu H, He X, Wang L, Zhang W, Li H, Fan Y, Tan G, Liu T, Gao X. Transcriptome Sequencing of Chemically Induced Aquilaria sinensis to Identify Genes Related to Agarwood Formation. PLoS One 2016; 11:e0155505. [PMID: 27182594 PMCID: PMC4868263 DOI: 10.1371/journal.pone.0155505] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 04/30/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Agarwood is a traditional Chinese medicine used as a clinical sedative, carminative, and antiemetic drug. Agarwood is formed in Aquilaria sinensis when A. sinensis trees are threatened by external physical, chemical injury or endophytic fungal irritation. However, the mechanism of agarwood formation via chemical induction remains unclear. In this study, we characterized the transcriptome of different parts of a chemically induced A. sinensis trunk sample with agarwood. The Illumina sequencing platform was used to identify the genes involved in agarwood formation. METHODOLOGY/PRINCIPAL FINDINGS A five-year-old Aquilaria sinensis treated by formic acid was selected. The white wood part (B1 sample), the transition part between agarwood and white wood (W2 sample), the agarwood part (J3 sample), and the rotten wood part (F5 sample) were collected for transcriptome sequencing. Accordingly, 54,685,634 clean reads, which were assembled into 83,467 unigenes, were obtained with a Q20 value of 97.5%. A total of 50,565 unigenes were annotated using the Nr, Nt, SWISS-PROT, KEGG, COG, and GO databases. In particular, 171,331,352 unigenes were annotated by various pathways, including the sesquiterpenoid (ko00909) and plant-pathogen interaction (ko03040) pathways. These pathways were related to sesquiterpenoid biosynthesis and defensive responses to chemical stimulation. CONCLUSIONS/SIGNIFICANCE The transcriptome data of the different parts of the chemically induced A. sinensis trunk provide a rich source of materials for discovering and identifying the genes involved in sesquiterpenoid production and in defensive responses to chemical stimulation. This study is the first to use de novo sequencing and transcriptome assembly for different parts of chemically induced A. sinensis. Results demonstrate that the sesquiterpenoid biosynthesis pathway and WRKY transcription factor play important roles in agarwood formation via chemical induction. The comparative analysis of the transcriptome data of agarwood and A. sinensis lays the foundation for elucidating the mechanism of agarwood formation via chemical induction, and thus, enables future improvements in agarwood quality while protecting endangered wild A. sinensis.
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Affiliation(s)
- Wei Ye
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China
| | - Hongqing Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China
| | - Xin He
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China
- Guangdong Pharmaceutical University, Guangzhou, 510060, China
| | - Lei Wang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China
- Inner Mongolia Medical University, Hohhot, 010110, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China
- * E-mail: (WMZ); (XXG)
| | - Haohua Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China
| | - Yunfei Fan
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China
| | - Guohui Tan
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China
| | - Taomei Liu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, 510070, China
| | - Xiaoxia Gao
- Guangdong Pharmaceutical University, Guangzhou, 510060, China
- * E-mail: (WMZ); (XXG)
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Su X, Li Q, Chen S, Dong C, Hu Y, Yin L, Yang J. Analysis of the transcriptome of Isodon rubescens and key enzymes involved in terpenoid biosynthesis. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1146086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Xiuhong Su
- Pharmacognosy Discipline, College of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Qinglei Li
- Pharmacognosy Discipline, College of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Suiqing Chen
- Pharmacognosy Discipline, College of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Chengming Dong
- Pharmacognosy Discipline, College of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Yuansen Hu
- Department of Microbiology, College of Bioengineering, Henan University of Technology, Zhengzhou, Henan, China
| | - Lei Yin
- Pharmacognosy Discipline, College of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Jingfan Yang
- Pharmacognosy Discipline, College of Pharmacy, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
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28
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Liu CH, Fan C. De novo Transcriptome Assembly of Floral Buds of Pineapple and Identification of Differentially Expressed Genes in Response to Ethephon Induction. FRONTIERS IN PLANT SCIENCE 2016; 7:203. [PMID: 26955375 PMCID: PMC4767906 DOI: 10.3389/fpls.2016.00203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 02/05/2016] [Indexed: 05/11/2023]
Abstract
A remarkable characteristic of pineapple is its ability to undergo floral induction in response to external ethylene stimulation. However, little information is available regarding the molecular mechanism underlying this process. In this study, the differentially expressed genes (DEGs) in plants exposed to 1.80 mL·L(-1) (T1) or 2.40 mL·L(-1) ethephon (T2) compared with Ct plants (control, cleaning water) were identified using RNA-seq and gene expression profiling. Illumina sequencing generated 65,825,224 high-quality reads that were assembled into 129,594 unigenes with an average sequence length of 1173 bp. Of these unigenes, 24,775 were assigned to specific KEGG pathways, of which metabolic pathways and biosynthesis of secondary metabolites were the most highly represented. Gene Ontology (GO) analysis of the annotated unigenes revealed that the majority were involved in metabolic and cellular processes, cell and cell part, catalytic activity and binding. Gene expression profiling analysis revealed 3788, 3062, and 758 DEGs in the comparisons of T1 with Ct, T2 with Ct, and T2 with T1, respectively. GO analysis indicated that these DEGs were predominantly annotated to metabolic and cellular processes, cell and cell part, catalytic activity, and binding. KEGG pathway analysis revealed the enrichment of several important pathways among the DEGs, including metabolic pathways, biosynthesis of secondary metabolites and plant hormone signal transduction. Thirteen DEGs were identified as candidate genes associated with the process of floral induction by ethephon, including three ERF-like genes, one ETR-like gene, one LTI-like gene, one FT-like gene, one VRN1-like gene, three FRI-like genes, one AP1-like gene, one CAL-like gene, and one AG-like gene. qPCR analysis indicated that the changes in the expression of these 13 candidate genes were consistent with the alterations in the corresponding RPKM values, confirming the accuracy and credibility of the RNA-seq and gene expression profiling results. Ethephon-mediated induction likely mimics the process of vernalization in the floral transition in pineapple by increasing LTI, FT, and VRN1 expression and promoting the up-regulation of floral meristem identity genes involved in flower development. The candidate genes screened can be used in investigations of the molecular mechanisms of the flowering pathway and of various other biological mechanisms in pineapple.
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Affiliation(s)
- Chuan-He Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Key Laboratory of South Subtropical Fruit Biology, Genetic Resource Utilization Ministry of AgricultureGuangzhou, China
- *Correspondence: Chuan-He Liu
| | - Chao Fan
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural SciencesGuangzhou, China
- Key Laboratory of South Subtropical Fruit Biology, Genetic Resource Utilization Ministry of AgricultureGuangzhou, China
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Zhang K, Luo L, Chen X, Hu M, Hu Q, Gong L, Weng Q. Molecular Effects of Irradiation (Cobalt-60) on the Control of Panonychus citri (Acari: Tetranychidae). Int J Mol Sci 2015; 16:26964-77. [PMID: 26569230 PMCID: PMC4661862 DOI: 10.3390/ijms161126004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/21/2015] [Accepted: 11/02/2015] [Indexed: 11/16/2022] Open
Abstract
The effective dose of irradiation to control pest mites in quarantine has been studied extensively, but the molecular mechanisms underlying the effects of the irradiation on mites are largely unknown. In this study, exposure to 400 Gy of γ rays had significant (p < 0.05) effects on the adult survival, fecundity and egg viability of Panonychus citri. The irradiation caused the degradation of the DNA of P. citri adults and damaged the plasma membrane system of the egg, which led to condensed nucleoli and gathered yolk. Additionally, the transcriptomes and gene expression profiles between irradiated and non-irradiated mites were compared, and three digital gene expression libraries were assembled and analyzed. The differentially expressed genes were putatively involved in apoptosis, cell death and the cell cycle. Finally, the expression profiles of some related genes were studied using quantitative real-time PCR. Our study provides valuable information on the changes in the transcriptome of irradiated P. citri, which will facilitate a better understanding of the molecular mechanisms that cause the sterility induced by irradiation.
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Affiliation(s)
- Ke Zhang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education of China, South China Agricultural University, Guangzhou 510642, China.
| | - Lingyan Luo
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education of China, South China Agricultural University, Guangzhou 510642, China.
| | - Xieting Chen
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education of China, South China Agricultural University, Guangzhou 510642, China.
| | - Meiying Hu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education of China, South China Agricultural University, Guangzhou 510642, China.
| | - Qiongbo Hu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education of China, South China Agricultural University, Guangzhou 510642, China.
| | - Liang Gong
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Qunfang Weng
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education of China, South China Agricultural University, Guangzhou 510642, China.
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De novo transcriptome analysis of Inonotus baumii by RNA-seq. J Biosci Bioeng 2015; 121:380-4. [PMID: 26493632 DOI: 10.1016/j.jbiosc.2015.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 08/24/2015] [Accepted: 09/05/2015] [Indexed: 01/24/2023]
Abstract
Inonotus baumii, a basidiomycete white rot fungus, has been widely used as traditional herbal medicine in China, Korea, Japan and other Asian countries for many years. Its extract is of great medicinal importance and plays a valuable role in the immune response and disease resistance. However, limited genetic resources for I. baumii have hindered exploration of this species. In order to gain a molecular understanding of this fungus, Illumina high-throughput technology was used to sequence and analyze the transcriptome of I. baumii, and 280,691 contigs, 43,890 scaffolds and 30,051 unigenes were obtained. Additionally, based on similarity search with known proteins, unigenes were annotated with gene descriptions, gene ontology (GO), clusters of orthologous group (COG), and database of protein families (Pfam) terms. According to the annotation of unigenes, a total of 12 candidate genes involved in the triterpenoid biosynthesis pathway and 21 putative FOLymes (fungal oxidative lignin enzymes) and 176 CAZymes (carbohydrate-active enzymes) were obtained using homology-based BlastX. Moreover, for better understanding of the transcripts function, the BlastX algorithm was used to search for homologous sequences against the Yeast genome. This is the first study on transcriptome analyses of I. baumii, which provided a dataset for functional gene mining and laid a basis for further functional genomics studies of I. baumii.
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Kanth BK, Kumari S, Choi SH, Ha HJ, Lee GJ. Generation and analysis of expressed sequence tags (ESTs) of Camelina sativa to mine drought stress-responsive genes. Biochem Biophys Res Commun 2015; 467:83-93. [PMID: 26410535 DOI: 10.1016/j.bbrc.2015.09.116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 09/21/2015] [Indexed: 01/02/2023]
Abstract
Camelina sativa is an oil-producing crop belonging to the family of Brassicaceae. Due to exceptionally high content of omega fatty acid, it is commercially grown around the world as edible oil, biofuel, and animal feed. A commonly referred 'false flax' or gold-of-pleasure Camelina sativa has been interested as one of biofuel feedstocks. The species can grow on marginal land due to its superior drought tolerance with low requirement of agricultural inputs. This crop has been unexploited due to very limited transcriptomic and genomic data. Use of gene-specific molecular markers is an important strategy for new cultivar development in breeding program. In this study, Illumina paired-end sequencing technology and bioinformatics tools were used to obtain expression profiling of genes responding to drought stress in Camelina sativa BN14. A total of more than 60,000 loci were assembled, corresponding to approximately 275 K transcripts. When the species was exposed to 10 kPa drought stress, 100 kPa drought stress, and rehydrated conditions, a total of 107, 2,989, and 982 genes, respectively, were up-regulated, while 146, 3,659, and 1189 genes, respectively, were down-regulated compared to control condition. Some unknown genes were found to be highly expressed under drought conditions, together with some already reported gene families such as senescence-associated genes, CAP160, and LEA under 100 kPa soil water condition, cysteine protease, 2OG, Fe(II)-dependent oxygenase, and RAD-like 1 under rehydrated condition. These genes will be further validated and mapped to determine their function and loci. This EST library will be favorably applied to develop gene-specific molecular markers and discover genes responsible for drought tolerance in Camelina species.
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Affiliation(s)
| | - Shipra Kumari
- Chungnam National University, Yuseong-gu, Daejeon, 305-764, Republic of Korea
| | - Seo Hee Choi
- Chungnam National University, Yuseong-gu, Daejeon, 305-764, Republic of Korea
| | - Hye-Jeong Ha
- Chungnam National University, Yuseong-gu, Daejeon, 305-764, Republic of Korea
| | - Geung-Joo Lee
- Chungnam National University, Yuseong-gu, Daejeon, 305-764, Republic of Korea.
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Abstract
Over the last three decades, transcriptomic studies of venom gland cells have continuously evolved, opening up new possibilities for exploring the molecular diversity of animal venoms, a prerequisite for the discovery of new drug candidates and molecular phylogenetics. The molecular complexity of animal venoms is much greater than initially thought. In this review, we describe the different technologies available for transcriptomic studies of venom, from the original individual cloning approaches to the more recent global Next Generation Sequencing strategies. Our understanding of animal venoms is evolving, with the discovery of complex and diverse bio-optimized cocktails of compounds, including mostly peptides and proteins, which are now beginning to be studied by academic and industrial researchers.
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Zhang J, Ren A, Chen H, Zhao M, Shi L, Chen M, Wang H, Feng Z. Transcriptome analysis and its application in identifying genes associated with fruiting body development in basidiomycete Hypsizygus marmoreus. PLoS One 2015; 10:e0123025. [PMID: 25837428 PMCID: PMC4383556 DOI: 10.1371/journal.pone.0123025] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/05/2015] [Indexed: 02/06/2023] Open
Abstract
To elucidate the mechanisms of fruit body development in H. marmoreus, a total of 43609521 high-quality RNA-seq reads were obtained from four developmental stages, including the mycelial knot (H-M), mycelial pigmentation (H-V), primordium (H-P) and fruiting body (H-F) stages. These reads were assembled to obtain 40568 unigenes with an average length of 1074 bp. A total of 26800 (66.06%) unigenes were annotated and analyzed with the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Eukaryotic Orthologous Group (KOG) databases. Differentially expressed genes (DEGs) from the four transcriptomes were analyzed. The KEGG enrichment analysis revealed that the mycelium pigmentation stage was associated with the MAPK, cAMP, and blue light signal transduction pathways. In addition, expression of the two-component system members changed with the transition from H-M to H-V, suggesting that light affected the expression of genes related to fruit body initiation in H. marmoreus. During the transition from H-V to H-P, stress signals associated with MAPK, cAMP and ROS signals might be the most important inducers. Our data suggested that nitrogen starvation might be one of the most important factors in promoting fruit body maturation, and nitrogen metabolism and mTOR signaling pathway were associated with this process. In addition, 30 genes of interest were analyzed by quantitative real-time PCR to verify their expression profiles at the four developmental stages. This study advances our understanding of the molecular mechanism of fruiting body development in H. marmoreus by identifying a wealth of new genes that may play important roles in mushroom morphogenesis.
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Affiliation(s)
- Jinjing Zhang
- College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People’s Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ang Ren
- College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China
| | - Hui Chen
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People’s Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Mingwen Zhao
- College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China
| | - Liang Shi
- College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China
| | - Mingjie Chen
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People’s Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hong Wang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People’s Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhiyong Feng
- College of Life Science, Nanjing Agricultural University, Key Laboratory of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, Nanjing, Jiangsu, China
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, the People’s Republic of China, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Huang Y, Wu X, Jian D, Zhan Y, Fan G. De novo transcriptome analysis of a medicinal fungi Phellinus linteus and identification of SSR markers. BIOTECHNOL BIOTEC EQ 2015; 29:395-403. [PMID: 26019658 PMCID: PMC4434122 DOI: 10.1080/13102818.2015.1008228] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/18/2014] [Indexed: 10/27/2022] Open
Abstract
The aim of this study was to facilitate gene discovery for functional genome studies and to identify simple sequence repeat (SSR) markers for molecular-assisted selection in Phellinus linteus. The transcriptome of Phellinus linteus was sequenced using а high-throughput RNA sequencing system - the Illumina Hiseq 2000. A total of 16,383,818 clean sequencing reads, 35,532 contigs and 25,811 unigenes were postulated. Based on similarity searches with known proteins, 19,350 genes (74.97% of the unigenes) were annotated. In the present research, 19,266, 10,978 and 7831 unigenes were mapped in Nr, Swiss-Prot and clusters of orthologous groups (COG) classifications, respectively. Of all unigenes, 6845 were categorized into three functional groups, namely biological process, cellular components and molecular function and 11,088 were annotated to 108 pathways by searching the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 1129 SSRs were identified in these unigenes. In addition, 23 candidate genes, potentially involved in sterol biosynthesis, were identified and were worthy of further investigation.
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Affiliation(s)
- Yating Huang
- Department of Forest Bioengineering, College of Life Science, Northeast Forestry University , Harbin , P.R. China
| | - Xiaoqiu Wu
- Department of Forest Bioengineering, College of Life Science, Northeast Forestry University , Harbin , P.R. China
| | - Duan Jian
- Department of Forest Bioengineering, College of Life Science, Northeast Forestry University , Harbin , P.R. China
| | - Yaguang Zhan
- Department of Forest Bioengineering, College of Life Science, Northeast Forestry University , Harbin , P.R. China
| | - Guizhi Fan
- Department of Forest Bioengineering, College of Life Science, Northeast Forestry University , Harbin , P.R. China
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Luo H, Hong SY, Sgambelluri RM, Angelos E, Li X, Walton JD. Peptide macrocyclization catalyzed by a prolyl oligopeptidase involved in α-amanitin biosynthesis. ACTA ACUST UNITED AC 2014; 21:1610-7. [PMID: 25484237 DOI: 10.1016/j.chembiol.2014.10.015] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/08/2014] [Accepted: 10/22/2014] [Indexed: 11/29/2022]
Abstract
Amatoxins are ribosomally encoded and posttranslationally modified peptides that account for the majority of fatal mushroom poisonings of humans. A representative amatoxin is the bicyclic octapeptide α-amanitin, formed via head-to-tail macrocyclization, which is ribosomally biosynthesized as a 35-amino acid propeptide in Amanita bisporigera and in the distantly related mushroom Galerina marginata. Although members of the prolyl oligopeptidase (POP) family of serine proteases have been proposed to play a role in α-amanitin posttranslational processing, the exact mechanistic details are not known. Here, we show that a specific POP (GmPOPB) is required for toxin maturation in G. marginata. Recombinant GmPOPB catalyzed two nonprocessive reactions: hydrolysis at an internal Pro to release the C-terminal 25-mer from the 35-mer propeptide and transpeptidation at the second Pro to produce the cyclic octamer. On the other hand, we show that GmPOPA, the putative housekeeping POP of G. marginata, behaves like a conventional POP.
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Affiliation(s)
- Hong Luo
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Sung-Yong Hong
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - R Michael Sgambelluri
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Evan Angelos
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Xuan Li
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Jonathan D Walton
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
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Zhenzhen X, Ling X, Dengdong W, Chao F, Qiongyu L, Zihao L, Xiaochun L, Yong Z, Shuisheng L, Haoran L. Transcriptome analysis of the Trachinotus ovatus: identification of reproduction, growth and immune-related genes and microsatellite markers. PLoS One 2014; 9:e109419. [PMID: 25303650 PMCID: PMC4193775 DOI: 10.1371/journal.pone.0109419] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 08/31/2014] [Indexed: 12/25/2022] Open
Abstract
Background The Trachinotus ovatus (Teleostei, Carangidae) is an economically important marine fish species in the world. However, the lack of genomic information regarding this species limits our understanding of the genetics and biological mechanisms in Trachinotus ovatus. In this study, high throughput transcriptome sequencing was used to obtain comprehensive genomic information in Trachinotus ovatus. Principal Findings Transcriptome sequencing was performed by using Illumina paired-end sequencing technology. The 98,534,862 high quality reads were yielded, and were de novo assembled into 156,094 unigenes with an average sequence length of 1179 bp. Transcriptome annotation revealed that 75,586 and 67,923 unigenes were functionally annotated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 67,923 unigenes were grouped into 25 Cluster of Orthologous Groups (COG) functional categories, 37,976 unigenes were clustered into 61 Gene Ontology (GO) terms, and 38,172 unigenes were assigned to 275 different Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Based on the transcriptome dataset, a large number of unigenes associated with reproduction, growth and immunity were identified. Furthermore, a total number of 38,794 simple sequence repeats (SSRs) were discovered and 16 polymorphic loci were characterized in Trachinotus ovatus. Conclusion/Significance The present study is the first transcriptome analysis of a fish species belonging to the genus Trachinotus and provides a valuable genomic resource for novel gene discovery, gene expression and regulation studies, and the identification of genetic markers in Trachinotus ovatus and the other fish of the genus Trachinotus.
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Affiliation(s)
- Xie Zhenzhen
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xiao Ling
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wang Dengdong
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Fang Chao
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Liu Qiongyu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Li Zihao
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Liu Xiaochun
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhang Yong
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- * E-mail: (LSS); (LHR)
| | - Li Shuisheng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- * E-mail: (LSS); (LHR)
| | - Lin Haoran
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- College of Ocean, Hainan University, Haikou, Hainan, China
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Amin S, Prentis PJ, Gilding EK, Pavasovic A. Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of de novo assemblers. BMC Res Notes 2014; 7:488. [PMID: 25084827 PMCID: PMC4124492 DOI: 10.1186/1756-0500-7-488] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 07/25/2014] [Indexed: 01/22/2023] Open
Abstract
Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms.
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Affiliation(s)
| | | | | | - Ana Pavasovic
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, GPO Box 2434, Brisbane, Qld 4001, Australia.
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Molecular cloning of α-amanitin and characterization of its expression pattern in different parts and development stages of Amanita exitialis fruitbody. Mycol Prog 2014. [DOI: 10.1007/s11557-014-0988-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Armengaud J, Trapp J, Pible O, Geffard O, Chaumot A, Hartmann EM. Non-model organisms, a species endangered by proteogenomics. J Proteomics 2014; 105:5-18. [PMID: 24440519 DOI: 10.1016/j.jprot.2014.01.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 12/24/2013] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED Previously, large-scale proteomics was possible only for organisms whose genomes were sequenced, meaning the most common model organisms. The use of next-generation sequencers is now changing the deal. With "proteogenomics", the use of experimental proteomics data to refine genome annotations, a higher integration of omics data is gaining ground. By extension, combining genomic and proteomic data is becoming routine in many research projects. "Proteogenomic"-flavored approaches are currently expanding, enabling the molecular studies of non-model organisms at an unprecedented depth. Today draft genomes can be obtained using next-generation sequencers in a rather straightforward way and at a reasonable cost for any organism. Unfinished genome sequences can be used to interpret tandem mass spectrometry proteomics data without the need for time-consuming genome annotation, and the use of RNA-seq to establish nucleotide sequences that are directly translated into protein sequences appears promising. There are, however, certain drawbacks that deserve further attention for RNA-seq to become more efficient. Here, we discuss the opportunities of working with non-model organisms, the proteomic methods that have been used until now, and the dramatic improvements proffered by proteogenomics. These put the distinction between model and non-model organisms in great danger, at least in terms of proteomics! BIOLOGICAL SIGNIFICANCE Model organisms have been crucial for in-depth analysis of cellular and molecular processes of life. Focusing the efforts of thousands of researchers on the Escherichia coli bacterium, Saccharomyces cerevisiae yeast, Arabidopsis thaliana plant, Danio rerio fish and other models for which genetic manipulation was possible was certainly worthwhile in terms of fundamental and invaluable biological insights. Until recently, proteomics of non-model organisms was limited to tedious, homology-based techniques, but today draft genomes or RNA-seq data can be straightforwardly obtained using next-generation sequencers, allowing the establishment of a draft protein database for any organism. Thus, proteogenomics opens new perspectives for molecular studies of non-model organisms, although they are still difficult experimental organisms. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France.
| | - Judith Trapp
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France; Irstea, UR MALY, F-69626 Villeurbanne, France
| | - Olivier Pible
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France
| | | | | | - Erica M Hartmann
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France
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