38 results on '"Lianfu Chen"'
Search Results
2. Genetic structure and evolutionary diversity of mating-type (MAT) loci in Hypsizygus marmoreus
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Gang Wang, Yuanyuan Wang, Lianfu Chen, Hongbo Wang, Lin Guo, Xuan Zhou, Meijie Dou, Baiyu Wang, Jingxian Lin, Lei Liu, Zhengchao Wang, Youjin Deng, and Jisen Zhang
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Tetrapolar ,Research ,Basidiomycota ,QK1-989 ,Sexual reproduction ,Botany ,Hypsizygus marmoreus ,Agricultural and Biological Sciences (miscellaneous) ,Ecology, Evolution, Behavior and Systematics ,Mating-type - Abstract
The mating compatibility in fungi is generally governed by genes located within a single or two unlinked mating type (MAT) loci. Hypsizygus marmoreus is an edible mushroom in the order Agaricales with a tetrapolar system, which contains two unlinked MAT loci-homeodomain (HD) transcription factor genes and pheromone/pheromone receptor genes (P/R). In this study, we analyzed the genetic structure and diversity of MAT loci in tetrapolar system of H. marmoreus through sequencing of 54 heterokaryon and 8 homokaryon strains. Although within the HD loci, the gene order was conserved, the gene contents were variable, and the HD loci haplotypes were further classified into four types. By analyzing the structure, phylogeny, and the HD transmissibility based on the progeny of these four HD mating-type loci types, we found that they were heritable and tightly linked at the HD loci. The P/R loci genes were found to comprise three pheromone receptors, three pheromones, and two pheromone receptor-like genes. Intra- and inter-specific phylogenetic analyses of pheromone receptors revealed that the STE3 genes were divided into three groups, and we thus theorize that they diverged before speciation. Comparative analysis of the MAT regions among 73 Basidiomycete species indicated that the diversity of HD and P/R loci in Agaricales and Boletales may contribute to mating compatibility. The number of HD genes were not correlated with the tetrapolar or bipolar systems. In H. marmoreus, the expression levels of these genes at HD and P/R loci of compatible strains were found higher than in those of homonuclear/homokaryotic strains, indicating that these mating genes acted as switches for mating processes. Further collinear analysis of HD loci in interspecific species found that HD loci contains conserved recombination hotspots showing major rearrangements in Coprinopsis cinerea and Schizophyllum commune, suggesting different mechanisms for evolution of physically linked MAT loci in these groups. It seems likely that gene rearrangements are common in Agaricales fungi around HD loci. Together, our study provides insights into the genomic basis of mating compatibility in H. marmoreus.
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- 2021
3. First report on the regulation and function of carbon metabolism during large sclerotia formation in medicinal fungus Wolfiporia cocos
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Cong Zhang, Lianfu Chen, Mengting Chen, and Zhangyi Xu
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Genetics ,Microbiology - Published
- 2023
4. Genome-Wide Identification and Expression Analysis of Expansin Gene Family in the Storage Root Development of Diploid Wild Sweetpotato Ipomoea trifida
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Ming Li, Lianfu Chen, Tao Lang, Huijuan Qu, Cong Zhang, Junyan Feng, Zhigang Pu, Meifang Peng, and Honghui Lin
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Genetics ,Ipomoea trifida ,expansin ,evolution ,gene expression ,storage root development ,Genetics (clinical) - Abstract
Expansins play important roles in root growth and development, but investigation of the expansin gene family has not yet been reported in Ipomoea trifida, and little is known regarding storage root (SR) development. In this work, we identified a total of 37 expansins (ItrEXPs) in our previously reported SR-forming I. trifida strain Y22 genome, which included 23 ItrEXPAs, 4 ItrEXPBs, 2 ItrEXLAs and 8 ItrEXLBs. The phylogenetic relationship, genome localization, subcellular localization, gene and protein structure, promoter cis-regulating elements, and protein interaction network were systematically analyzed to reveal the possible roles of ItrEXPs in the SR development of I. trifida. The gene expression profiling in Y22 SR development revealed that ItrEXPAs and ItrEXLBs were down-regulated, and ItrEXPBs were up-regulated while ItrEXLAs were not obviously changed during the critical period of SR expansion, and might be beneficial to SR development. Combining the tissue-specific expression in young SR transverse sections of Y22 and sweetpotato tissue, we deduced that ItrEXLB05, ItrEXLB07 and ItrEXLB08 might be the key genes for initial SR formation and enlargement, and ItrEXLA02 might be the key gene for root growth and development. This work provides new insights into the functions of the expansin gene family members in I. trifida, especially for EXLA and EXLB subfamilies genes in SR development.
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- 2022
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5. A chromosome-level genome assembly of the pollinating fig wasp Valisia javana
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Lianfu Chen, Chao Feng, Rong Wang, Xiaojue Nong, Xiaoxia Deng, Xiaoyong Chen, and Hui Yu
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Wasps ,Genetics ,Animals ,General Medicine ,Ficus ,Symbiosis ,Molecular Biology ,Chromosomes ,Phylogeny - Abstract
Fig wasp has always been thought the species-specific pollinator for their host fig (Moraceae, Ficus) and constitute a model system with its host to study co-evolution and co-speciation. The availability of a high-quality genome will help to further reveal the mechanisms underlying these characteristics. Here, we present a high-quality chromosome-level genome for Valisa javana developed by a combination of PacBio long-read and Illumina short-read. The assembled genome size is 296.34 Mb from 13 contigs with a contig N50 length of 26.76 kb. Comparative genomic analysis revealed expanded and positively selected genes related to biological features that aid fig wasps living in syconium of its highly specific host. Protein-coding genes associated with chemosensory, detoxification and venom genes were identified. Several differentially expressed genes in transcriptome data of V. javana between odor-stimulated samples and the controls have been identified in some olfactory signal transduction pathways, e.g. olfactory transduction, cAMP, cGMP-PKG, Calcim, Ras and Rap1. This study provides a valuable genomic resource for a fig wasp, and sheds insight into further revealing the mechanisms underlying their adaptive traits to their hosts in different places and co-speciation with their host.
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- 2022
6. Genome-Wide Identification and Expression Analysis of Expansin Gene Family in the Storage Root Development of Diploid Wild Sweetpotato
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Ming, Li, Lianfu, Chen, Tao, Lang, Huijuan, Qu, Cong, Zhang, Junyan, Feng, Zhigang, Pu, Meifang, Peng, and Honghui, Lin
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Gene Expression Regulation, Plant ,Ipomoea ,Ipomoea batatas ,Diploidy ,Phylogeny - Abstract
Expansins play important roles in root growth and development, but investigation of the expansin gene family has not yet been reported in
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- 2022
7. Identifying a melanogenesis-related candidate gene by a high-quality genome assembly and population diversity analysis in Hypsizygus marmoreus
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Meijie Dou, Gang Wang, Baogui Xie, Haofeng Wu, Qing Zhang, Jisen Zhang, Hongbo Wang, Weiqi Tang, Jingxian Lin, Xuan Zhou, Zhong-Jian Liu, Lin Guo, Yuanyuan Wang, Liu Lei, Baiyu Wang, Ray Ming, Lianfu Chen, and Zhengchao Wang
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Comparative genomics ,Genetics ,0303 health sciences ,Candidate gene ,education.field_of_study ,Population ,Bulked segregant analysis ,Chromosome ,Genomics ,Sequence Analysis, DNA ,Biology ,Genome ,White (mutation) ,03 medical and health sciences ,0302 clinical medicine ,Genetic variation ,Genome, Fungal ,Agaricales ,education ,Molecular Biology ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
Hypsizygus marmoreus is one of the most important edible fungi in Basidiomycete division and includes white and gray strains. However, very limited knowledge is known about the genomic structures and the genetic basis for the white/gray diversity of this mushroom. Here, we report the near-complete high-quality H. marmoreus genome at the chromosomal level. Comparative genomics analysis indicates that chromosome structures were relatively conserved, and variations in collinearity and chromosome number were mainly attributed by chromosome split/fusion events in Aragicales, whereas the fungi genome experienced many genomic chromosome fracture, fusion, and genomic replication events after the split of Aragicales from Basidiomycetes. Resequencing of 57 strains allows us to classify the population into four major groups and associate genetic variations with morphological features, indicating that white strains were not originated independently. We further generated genetic populations and identified a cytochrome P450 as the candidate causal gene for the melanogenesis in H. marmoreus based on bulked segregant analysis (BSA) and comparative transcriptome analysis. The high-quality H. marmoreus genome and diversity data compiled in this study provide new knowledge and resources for the molecular breeding of H. marmoreus as well as the evolution of Basidiomycete.
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- 2021
8. Methane-Dependent Mineral Reduction by Aerobic Methanotrophs under Hypoxia
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Yeyi Yang, Xuee Wu, Ludmila Chistoserdova, Yue Zheng, Jinhua Li, Feng Zhao, Yan Liu, Baoli Zhu, Wei Qin, Huan Wang, and Lianfu Chen
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0301 basic medicine ,Ecology ,biology ,Phylum ,Health, Toxicology and Mutagenesis ,030106 microbiology ,Hypoxia (environmental) ,010501 environmental sciences ,biology.organism_classification ,01 natural sciences ,Pollution ,Methane ,03 medical and health sciences ,chemistry.chemical_compound ,chemistry ,Environmental chemistry ,Environmental Chemistry ,Proteobacteria ,Waste Management and Disposal ,0105 earth and related environmental sciences ,Water Science and Technology - Abstract
Methanotrophs play an important role in controlling methane balance in the biosphere. For over 100 years, methanotrophs of the Proteobacteria phylum have been studied under oxic conditions, with mo...
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- 2020
9. Adaptation of Fig Wasps (Agaodinae) to Their Host Revealed by Large-Scale Transcriptomic Data
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Lianfu Chen, Da-Mien Wong, Bhanumas Chantarasuwan, Xiao-Yong Chen, Simon T. Segar, Hui Yu, and Rong Wang
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Agaonidae ,biology ,Phylogenetic tree ,gene families ,Host (biology) ,Science ,macromolecular substances ,biology.organism_classification ,Article ,Monophyly ,speciation ,Evolutionary biology ,Insect Science ,Gene family ,specific mutualism ,Adaptation ,pollination ecology ,Gene ,Fig wasp - Abstract
Simple Summary Research on fig wasps has made a considerable contribution to the understanding of insect–plant interactions. However, the molecular mechanisms underlying fig wasp host specificity are poorly understood. This study reports on a relatively large-scale transcriptomic dataset of 25 fig wasp species. We outline potential genetic mechanisms underlying the specific host adaptation by investigating changes in a gene family, in evolutionary rates, and in genes under positive selection. The transcriptome datasets reported here (1) provide new insights into the evolutionary diversification and host specificity of fig wasps and (2) contribute to a growing dataset on fig wasp genomics. Abstract Figs and fig wasps are highly species-specific and comprise a model system for studying co-evolution and co-speciation. The evolutionary relationships and molecular adaptations of fig wasps to their fig hosts are poorly understood, and this is in part due to limited sequence data. Here, we present large-scale transcriptomic datasets of 25 fig wasp species with the aim of uncovering the genetic basis for host specificity. Our phylogenetic results support the monophyly of all genera associated with dioecious figs, and two genera associated with monoecious figs, Eupristina and Platyscapa, were revealed to be close relatives. We identified gene loss and gain, potentially rapidly evolving genes, and genes under positive selection. Potentially functional changes were documented and we hypothesize as to how these may determine host specificity. Overall, our study provides new insights into the evolutionary diversification of fig wasps and contributes to our understanding of adaptation in this group.
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- 2021
- Full Text
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10. Precise chemodynamic therapy of cancer by trifunctional bacterium-based nanozymes
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Yanli Zhao, Xuyu Li, Heyou Han, Lianfu Chen, Weiyun Zhang, Jiawei Liu, Zhaoyu Ma, Yue Zheng, Dongdong Wang, Mohamed F. Foda, and School of Physical and Mathematical Sciences
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Tumor targeting ,medicine.medical_treatment ,General Physics and Astronomy ,Catalysis ,Cell Line, Tumor ,Neoplasms ,Chemistry [Science] ,medicine ,Ferroptosis ,General Materials Science ,Interferon gamma ,chemistry.chemical_classification ,Reactive oxygen species ,Bacteria ,biology ,General Engineering ,Cancer ,Hydrogen Peroxide ,Immunotherapy ,medicine.disease ,biology.organism_classification ,chemistry ,Cancer cell ,Cancer research ,Reactive Oxygen Species ,Intracellular ,medicine.drug - Abstract
Chemodynamic therapy (CDT) destroys cancer cells by converting H2O2 or O2 into reactive oxygen species (ROS), but its therapeutic efficacy is restricted by the antioxidant capacity of tumor. Previous solutions focused on strengthening the nanodrugs with the ability to increase ROS production or weaken the antioxidant capacity of cancer cells. Conversely, we here develop a mild nanodrug with negligible side effects. Specifically, the Au@Pt nanozyme decorated on a bacterial surface (Bac-Au@Pt) is reported to achieve precise CDT. Due to the tumor targeting ability of bacteria and catalytic property of Au@Pt nanozyme under acidic conditions, this nanosystem can release ROS to tumor cells effectively. In addition, the interferon gamma released by T cells specifically decreases the intracellular reductants in tumor cells, while having no obvious effect on normal cells. Therefore, a low dose of Bac-Au@Pt achieves a satisfactory therapeutic efficacy to tumor cells and is nontoxic to normal cells even at their acidic components. This nanosystem enables CDT and immunotherapy to mutually benefit and improve by each other, providing a promising strategy to achieve high anticancer efficacy even with a low dose usage. National Research Foundation (NRF) This work was financially supported by the National Natural Science Foundation of China (21778020 and 31950410755), the Sci-Tech Innovation Foundation of Huazhong Agricultural University (2662018PY024), the Fundamental Research Funds for the Central Universities (2662015QD026), and the Science and Technology Major Project of Guangxi (Gui Ke AA18118046). This work is also supported by the Singapore National Research Foundation Investigatorship (NRF-NRFI2018-03).
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- 2021
11. Low host specificity and broad geographical ranges in a community of parasitic non‐pollinating fig wasps (Sycoryctinae; Chalcidoidea)
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Da-Yong Zhang, Hui Yu, Simon T. Segar, Enwei Tian, Tanming Wattana, Xiaoxia Deng, Lianfu Chen, Finn Kjellberg, South China Botanical Garden, Chinese Academy of Sciences [Beijing] (CAS), Beijing Normal University (BNU), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Chinese Academy of Science (CAS), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
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0106 biological sciences ,Range (biology) ,mutualism ,Wasps ,Population ,Biology ,010603 evolutionary biology ,01 natural sciences ,Host Specificity ,Parasitoid ,Pollinator ,Animals ,Parasites ,Pollination ,Symbiosis ,education ,parasitoid ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Local adaptation ,Isolation by distance ,Mutualism (biology) ,education.field_of_study ,[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] ,Ecology ,010604 marine biology & hydrobiology ,Beta-diversity ,population genetics ,15. Life on land ,Ficus ,biology.organism_classification ,[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics ,Biological dispersal ,community assembly ,Animal Science and Zoology ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology - Abstract
Plants, phytophagous insects and their parasitoids form the most diverse assemblages of macroscopic organisms on earth. Enclosed assemblages in particular represent a tractable system for studying community assembly and diversification. Communities associated with widespread plant species are especially suitable as they facilitate a comparative approach. Pantropical fig-wasp communities represent a remarkably well-replicated system, ideal for studying these historical processes. We expect high dispersal ability in non-pollinating fig wasps to result in lower geographical turnover in comparison to pollinating fig wasps. The ability of non-pollinating wasps to utilise a number of hosts (low host specificity) is a key determinant of overall geographical range, with intraspecific competition becoming a constraining factor should diet breadth overlap among species. Finally, we expect conserved community structure throughout the host range. We aim to test these expectations, derived from population genetic and community studies, using the multi-trophic insect community associated with Ficus hirta throughout its 3,500 km range across continental and insular Asia. We collect molecular evidence from one coding mitochondrial gene, one non-coding nuclear gene and multiple microsatellites across 25 geographical sites. Using these data, we establish species boundaries, determine levels of host specificity among non-pollinating fig wasps and quantify geographical variation in community composition. We find low host specificity in two genera of non-pollinating fig wasps. Functional community structure is largely conserved across the range of the host fig, despite limited correspondence between the ranges of non-pollinator and pollinator species. While nine pollinators are associated with Ficus hirta, the two non-pollinator tribes developing in its figs each contained only four species. Contrary to predictions, we find stronger isolation by distance in non-pollinators than pollinators. Long-lived non-pollinators may disperse more gradually and be less reliant on infrequent long-distance dispersal by wind currents. Segregation among non-pollinating species across their range is suggestive of competitive exclusion and we propose that this may be a result of increased levels of local adaptation and moderate, but regular, rates of dispersal. Our findings provide one more example of lack of strict codiversification in the geographical diversification of plant-associated insect communities.
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- 2021
12. Saponins Extracted from Tea (Camellia Sinensis) Flowers Induces Autophagy in Ovarian Cancer Cells
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Yaomin Wang, Yi Charlie Chen, Youying Tu, Lianfu Chen, and Chen Xia
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0301 basic medicine ,MAPK/ERK pathway ,Cell ,genetic processes ,Pharmaceutical Science ,Apoptosis ,Camellia sinensis ,Analytical Chemistry ,0302 clinical medicine ,Drug Discovery ,Chromatography, High Pressure Liquid ,chemistry.chemical_classification ,Ovarian Neoplasms ,food and beverages ,tea (Camellia sinensis) flower ,Cell biology ,medicine.anatomical_structure ,ovarian cancer ,Chemistry (miscellaneous) ,030220 oncology & carcinogenesis ,Molecular Medicine ,Female ,Microtubule-Associated Proteins ,Signal Transduction ,Programmed cell death ,autophagy ,Cell Survival ,Antineoplastic Agents ,Flowers ,complex mixtures ,Article ,lcsh:QD241-441 ,03 medical and health sciences ,lcsh:Organic chemistry ,Downregulation and upregulation ,Cell Line, Tumor ,medicine ,Humans ,natural sciences ,Physical and Theoretical Chemistry ,Protein kinase B ,PI3K/AKT/mTOR pathway ,Reactive oxygen species ,Plant Extracts ,Adenine ,Organic Chemistry ,Autophagy ,fungi ,Saponins ,phytochemicals ,030104 developmental biology ,chemistry ,Lysosomes ,Reactive Oxygen Species - Abstract
Tea flower saponins (TFS) possess effective anticancer properties. The diversity and complexity of TFS increases the difficulty of their extraction and purification from tea flowers. Here, multiple methods including solvent extraction, microporous resin separation and preparative HPLC separation were used to obtain TFS with a yield of 0.34%. Furthermore, we revealed that TFS induced autophagy&mdash, as evidenced by an increase in MDC-positive cell populations and mCherry-LC3B-labeled autolysosomes and an upregulation of LC3II protein levels. 3-MA reversed the decrease in cell viability induced by TFS, showing that TFS induced autophagic cell death. TFS-induced autophagy was not dependent on the Akt/mTOR/p70S6K signaling pathway. TFS-induced autophagy in OVCAR-3 cells was accompanied by ERK pathway activation and reactive oxygen species (ROS) generation. This paper is the first report of TFS-mediated autophagy of ovarian cancer cells. These results provide new insights for future studies of the anti-cancer effects of TFS.
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- 2020
13. Standardized Saponin Extract from Baiye No.1 Tea (Camellia sinensis) Flowers Induced S Phase Cell Cycle Arrest and Apoptosis via AKT-MDM2-p53 Signaling Pathway in Ovarian Cancer Cells
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Yon Rojanasakul, Youying Tu, Gary O. Rankin, Yi Charlie Chen, Bo Li, Yuanyuan Wu, Yaomin Wang, Ning Ren, and Lianfu Chen
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Pharmaceutical Science ,A2780/CP70 ovarian cancer cells ,Analytical Chemistry ,S phase cell cycle arrest ,lcsh:QD241-441 ,03 medical and health sciences ,0302 clinical medicine ,lcsh:Organic chemistry ,Drug Discovery ,BTFS ,FADD ,Viability assay ,Physical and Theoretical Chemistry ,Protein kinase B ,030304 developmental biology ,0303 health sciences ,biology ,Chemistry ,Organic Chemistry ,Cyclin-dependent kinase 2 ,apoptosis ,food and beverages ,Molecular biology ,tea (Camellia sinensis) flowers ,Chemistry (miscellaneous) ,Apoptosis ,030220 oncology & carcinogenesis ,Cancer cell ,biology.protein ,Molecular Medicine ,Signal transduction ,Cyclin A2 - Abstract
Ovarian cancer is considered to be one of the most serious malignant tumors in women. Natural compounds have been considered as important sources in the search for new anti-cancer agents. Saponins are characteristic components of tea (Camellia sinensis) flower and have various biological activities, including anti-tumor effects. In this study, a high purity standardized saponin extract, namely Baiye No.1 tea flower saponin (BTFS), which contained Floratheasaponin A and Floratheasaponin D, were isolated from tea (Camellia sinensis cv. Baiye 1) flowers by macroporous resin and preparative liquid chromatography. Then, the component and purity were detected by UPLC-Q-TOF/MS/MS. This high purity BTFS inhibited the proliferation of A2780/CP70 cancer cells dose-dependently, which is evidenced by the inhibition of cell viability, reduction of colony formation ability, and suppression of PCNA protein expression. Further research found BTFS induced S phase cell cycle arrest by up-regulating p21 proteins expression and down-regulating Cyclin A2, CDK2, and Cdc25A protein expression. Furthermore, BTFS caused DNA damage and activated the ATM-Chk2 signaling pathway to block cell cycle progression. Moreover, BTFS trigged both extrinsic and intrinsic apoptosis&mdash, BTFS up-regulated the expression of death receptor pathway-related proteins DR5, Fas, and FADD and increased the ratio of pro-apoptotic/anti-apoptotic proteins of the Bcl-2 family. BTFS-induced apoptosis seems to be related to the AKT-MDM2-p53 signaling pathway. In summary, our results demonstrate that BTFS has the potential to be used as a nutraceutical for the prevention and treatment of ovarian cancer.
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- 2020
14. Standardized Saponin Extract from Baiye No.1 Tea (
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Youying, Tu, Lianfu, Chen, Ning, Ren, Bo, Li, Yuanyuan, Wu, Gary O, Rankin, Yon, Rojanasakul, Yaomin, Wang, and Yi Charlie, Chen
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Ovarian Neoplasms ,Plant Extracts ,Cell Survival ,Proto-Oncogene Proteins c-mdm2 ,tea (Camellia sinensis) flowers ,Apoptosis ,Flowers ,Saponins ,Camellia sinensis ,Article ,A2780/CP70 ovarian cancer cells ,S phase cell cycle arrest ,Gene Expression Regulation ,Cell Line, Tumor ,Proliferating Cell Nuclear Antigen ,S Phase Cell Cycle Checkpoints ,Humans ,Female ,BTFS ,Tumor Suppressor Protein p53 ,Oleanolic Acid ,Cyclin A2 ,Proto-Oncogene Proteins c-akt ,Cyclin-Dependent Kinase Inhibitor p27 ,Signal Transduction - Abstract
Ovarian cancer is considered to be one of the most serious malignant tumors in women. Natural compounds have been considered as important sources in the search for new anti-cancer agents. Saponins are characteristic components of tea (Camellia sinensis) flower and have various biological activities, including anti-tumor effects. In this study, a high purity standardized saponin extract, namely Baiye No.1 tea flower saponin (BTFS), which contained Floratheasaponin A and Floratheasaponin D, were isolated from tea (Camellia sinensis cv. Baiye 1) flowers by macroporous resin and preparative liquid chromatography. Then, the component and purity were detected by UPLC-Q-TOF/MS/MS. This high purity BTFS inhibited the proliferation of A2780/CP70 cancer cells dose-dependently, which is evidenced by the inhibition of cell viability, reduction of colony formation ability, and suppression of PCNA protein expression. Further research found BTFS induced S phase cell cycle arrest by up-regulating p21 proteins expression and down-regulating Cyclin A2, CDK2, and Cdc25A protein expression. Furthermore, BTFS caused DNA damage and activated the ATM-Chk2 signaling pathway to block cell cycle progression. Moreover, BTFS trigged both extrinsic and intrinsic apoptosis—BTFS up-regulated the expression of death receptor pathway-related proteins DR5, Fas, and FADD and increased the ratio of pro-apoptotic/anti-apoptotic proteins of the Bcl-2 family. BTFS-induced apoptosis seems to be related to the AKT-MDM2-p53 signaling pathway. In summary, our results demonstrate that BTFS has the potential to be used as a nutraceutical for the prevention and treatment of ovarian cancer.
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- 2020
15. Purified Tea (Camellia sinensis (L.) Kuntze) Flower Saponins Induce the p53-Dependent Intrinsic Apoptosis of Cisplatin-Resistant Ovarian Cancer Cells
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Lianfu Chen, Gary O. Rankin, Ning Ren, Yi Charlie Chen, Youying Tu, and Bo Li
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0301 basic medicine ,endocrine system diseases ,Chakasaponin I ,Apoptosis ,Mass Spectrometry ,lcsh:Chemistry ,0302 clinical medicine ,tea flower saponins ,lcsh:QH301-705.5 ,Spectroscopy ,Caspase ,Ovarian Neoplasms ,biology ,Molecular Structure ,General Medicine ,Computer Science Applications ,ovarian cancer ,030220 oncology & carcinogenesis ,Female ,p53 pathway ,medicine.drug ,Signal Transduction ,DNA damage ,Cell Survival ,Poly ADP ribose polymerase ,Flowers ,Catalysis ,Article ,Inorganic Chemistry ,03 medical and health sciences ,intrinsic apoptosis ,Cell Line, Tumor ,medicine ,Humans ,Physical and Theoretical Chemistry ,Molecular Biology ,Cell Proliferation ,Cisplatin ,Tea ,Organic Chemistry ,Intrinsic apoptosis ,Cancer ,Saponins ,medicine.disease ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,Drug Resistance, Neoplasm ,Cancer research ,biology.protein ,Tumor Suppressor Protein p53 ,Ovarian cancer ,DNA Damage - Abstract
Ovarian cancer is currently ranked at fifth in cancer deaths among women. Patients who have undergone cisplatin-based chemotherapy can experience adverse effects or become resistant to treatment, which is a major impediment for ovarian cancer treatment. Natural products from plants have drawn great attention in the fight against cancer recently. In this trial, purified tea (Camellia sinensis (L.) Kuntze) flower saponins (PTFSs), whose main components are Chakasaponin I and Chakasaponin IV, inhibited the growth and proliferation of ovarian cancer cell lines A2780/CP70 and OVCAR-3. Flow cytometry, caspase activity and Western blotting analysis suggested that such inhibitory effects of PTFSs on ovarian cancer cells were attributed to the induction of cell apoptosis through the intrinsic pathway rather than extrinsic pathway. The p53 protein was then confirmed to play an important role in PTFS-induced intrinsic apoptosis, and the levels of its downstream proteins such as caspase families, Bcl-2 families, Apaf-1 and PARP were regulated by PTFS treatment. In addition, the upregulation of p53 expression by PTFSs were at least partly induced by DNA damage through the ATM/Chk2 pathway. The results help us to understand the mechanisms underlying the effects of PTFSs on preventing and treating platinum-resistant ovarian cancer.
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- 2020
16. Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes
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Ma Xiaolong, Wei Liu, Fang Shu, Yinbing Bian, Lianfu Chen, Qianqian Zhang, and Yingli Cai
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0301 basic medicine ,Mitochondrial DNA ,Nuclear gene ,Population ,Genomics ,Biology ,Catalysis ,Article ,Inorganic Chemistry ,nuclear genome ,lcsh:Chemistry ,03 medical and health sciences ,mitochondrial orf ,Ascomycota ,Genome Size ,Gene Expression Regulation, Fungal ,morchella crassipes ,Gene family ,heterothallism ,Heterothallic ,Physical and Theoretical Chemistry ,education ,Molecular Biology ,Gene ,mating type ,lcsh:QH301-705.5 ,Spectroscopy ,Phylogeny ,Genetics ,education.field_of_study ,Whole Genome Sequencing ,Organic Chemistry ,Intron ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,Molecular Sequence Annotation ,General Medicine ,030108 mycology & parasitology ,Computer Science Applications ,030104 developmental biology ,Morchella crassipes ,lcsh:Biology (General) ,lcsh:QD1-999 ,mitochondrial genome ,Genome, Mitochondrial ,Genome, Fungal - Abstract
Morchella crassipes (Vent.) Pers., a typical yellow morel species with high economic value, is mainly distributed in the low altitude plains of Eurasia. However, rare research has been performed on its genomics and polarity, thus limiting its research and development. Here, we reported a fine physical map of the nuclear genome at the subchromosomal-scale and the complete mitochondrial genome of M. crassipes. The complete size of the nuclear genome was 56.7 Mb, and 23 scaffolds were assembled, with eight of them being complete chromosomes. A total of 11,565 encoding proteins were predicted. The divergence time analysis showed that M. crassipes representing yellow morels differentiated with black morels at ~33.98 Mya (million years), with 150 gene families contracted and expanded in M. crassipes versus the two black morels (M. snyderi and M. importuna). Furthermore, 409 CAZYme genes were annotated in M. crassipes, containing almost all plant cell wall degrading enzymes compared with the mycorrhizal fungi (truffles). Genomic annotation of mating type loci and amplification of the mating genes in the monospore population was conducted, the results indicated that M. crassipes is a heterothallic fungus. Additionally, a complete circular mitochondrial genome of M. crassipes was assembled, the size reached as large as 531,195 bp. It can be observed that the strikingly large size was the biggest up till now, coupled with 14 core conserved mitochondrial protein-coding genes, two rRNAs, 31 tRNAs, 51 introns, and 412 ncORFs. The total length of intron sequences accounted for 53.67% of the mitochondrial genome, with 19 introns having a length over 5 kb. Particularly, 221 of 412 ncORFs were distributed within 51 introns, and the total length of the ncORFs sequence accounted for 40.83% of the mitochondrial genome, and 297 ncORFs had expression activity in the mycelium stage, suggesting their potential functions in M. crassipes. Meanwhile, there was a high degree of repetition (51.31%) in the mitochondria of M. crassipes. Thus, the large number of introns, ncORFs and internal repeat sequences may contribute jointly to the largest fungal mitochondrial genome to date. The fine physical maps of nuclear genome and mitochondrial genome obtained in this study will open a new door for better understanding of the mysterious species of M. crassipes.
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- 2020
17. Conversion of biomass waste to multi-heteroatom-doped carbon networks with high surface area and hierarchical porosity for advanced supercapacitors
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Shuijin Lei, Wei Zhou, Peiqin Deng, Baochang Cheng, Yanhe Xiao, Wei Wang, Xiuling Ou, and Lianfu Chen
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Supercapacitor ,Materials science ,Mechanical Engineering ,Heteroatom ,chemistry.chemical_element ,Biomass ,02 engineering and technology ,Electrolyte ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Capacitance ,0104 chemical sciences ,chemistry ,Chemical engineering ,Mechanics of Materials ,General Materials Science ,0210 nano-technology ,Porosity ,Current density ,Carbon - Abstract
Carbon represents one of the most prominent materials for energy applications. It is always desirable to achieve high value-added carbon materials from biomass wastes. Herein, the advanced carbon materials with multi-heteroatom-doping, high surface area and hierarchical porosity are prepared by hydrothermal conversion and post-activation of silkworm excrement, an agricultural waste. Owing to their unique composition and porosity, the carbon networks show a specific capacitance as high as 412 F g−1 in 6M KOH electrolyte at a current density of 0.5 A g−1. The symmetric supercapacitor device can deliver a high energy density up to 28.78 Wh kg−1 at a power density of 300 W kg−1 with a wide voltage window of 2.0 V in 1M Na2SO4 aqueous electrolyte. It also exhibits superb cycling stability with a capacitance retention of 92.9% for 10000 cycles. This work demonstrates a facile and eco-friendly strategy to transform biomass wastes into superior carbon electrode materials for high-performance supercapacitors.
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- 2018
18. Tetra-heteroatom self-doped carbon nanosheets derived from silkworm excrement for high-performance supercapacitors
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Lianfu Chen, Peiqin Deng, Yan Liu, Yanhe Xiao, Shuijin Lei, Wei Lu, Linfeng Fei, Wei Zhou, and Baochang Cheng
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Supercapacitor ,Materials science ,Renewable Energy, Sustainability and the Environment ,Carbonization ,Heteroatom ,Energy Engineering and Power Technology ,chemistry.chemical_element ,02 engineering and technology ,Electrolyte ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Capacitance ,Energy storage ,0104 chemical sciences ,Chemical engineering ,chemistry ,Electrical and Electronic Engineering ,Physical and Theoretical Chemistry ,0210 nano-technology ,Pyrolysis ,Carbon - Abstract
Carbon materials are deemed to be competitive candidate electrode materials for energy storage systems. It is still a great challenge to explore advanced carbon-based electrode materials for high-performance supercapacitors by a facile, economical and efficient method. In this work, N-, P-, S-, O-self-doped carbon nanosheets with high surface area and well-developed porosity are successfully prepared by pyrolysis carbonization and post KOH activation from silkworm excrement, a novel abundant, low-cost and eco-friendly agricultural waste. Thanks to their unique multi-heteroatom doping and porous structure, the obtained carbon materials exhibit high charge storage capacity with a specific capacitance of 401 F g−1 at a current density of 0.5 A g−1 in 6 M KOH and good cycling stability with a capacitance retention of 93.8% over 10000 cycles. A symmetric supercapacitor device using 1 M Na2SO4 aqueous solution as the electrolyte can deliver a specific capacitance of 41.7 F g−1 at a current density of 0.5 A g−1, and a high energy density of 23.17 Wh kg−1 at a power density of 500 W kg−1 with a wide voltage window of 2.0 V. This work develops a new strategy to produce favorable carbon-based electrode materials for supercapacitors with high electrochemical performances.
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- 2018
19. Fabrication of Bi19S27I3 nanorod cluster films for enhanced photodetection performance
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Lianfu Chen, Baochang Cheng, Jinsong Xiong, Xiuling Ou, Yanhe Xiao, Yueling Xu, Yutao Yan, and Shuijin Lei
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Photocurrent ,Materials science ,Absorption spectroscopy ,business.industry ,Photodetector ,02 engineering and technology ,Photodetection ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Inorganic Chemistry ,Optoelectronics ,Direct and indirect band gaps ,Nanorod ,0210 nano-technology ,business ,Absorption (electromagnetic radiation) ,Visible spectrum - Abstract
Thin-film photodetectors built from one-dimensional nanostructures have attracted extensive attention due to their significance in basic scientific research and potential technological applications. It is still desirable to develop new materials with a wide response range for application in photodetectors. In this work, a Bi19S27I3 nanorod cluster film has been successfully fabricated on various rigid substrates by a facile solvothermal method. The component nanorods exhibit an oriented growth along the [001] direction. The UV-Vis-NIR absorption spectrum shows a continuous strong absorption spanning the whole visible light to near-infrared region and presents a direct band gap of 0.83 eV for the prepared Bi19S27I3 nanorod clusters. The spectral photoresponse of the Bi19S27I3-based photodetector device demonstrates a broad photoresponse ranging from ultraviolet to near infrared. The photocurrent results reveal that the photodetector exhibits a more sensitive response towards near-infrared light than visible light. Furthermore, the photodetector based on the Bi19S27I3 nanorod cluster film shows significantly enhanced photodetection performance compared to Bi19S27I3 nanorod powder. The photocurrent and on-off ratio of the prepared nanorod cluster film are respectively up to 400 times and several times higher than those of the powder sample. The on-off ratios are about 265 and 66 under NIR illumination and 48 and 11 under visible light for the film and powder samples, respectively. These results suggest a great potential application of the prepared Bi19S27I3 nanorod cluster film in optoelectronic devices.
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- 2018
20. Comparative secretomic analysis of lignocellulose degradation by Lentinula edodes grown on microcrystalline cellulose, lignosulfonate and glucose
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Lianlian Yan, Yuhua Gong, Yan Zhou, Wei Liu, Yinbing Bian, Yingli Cai, Yue Hu, and Lianfu Chen
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Proteomics ,0301 basic medicine ,Glycoside Hydrolases ,Shiitake Mushrooms ,Biophysics ,Lignocellulosic biomass ,Cellulase ,Polysaccharide ,Lignin ,Biochemistry ,03 medical and health sciences ,chemistry.chemical_compound ,Hydrolysis ,Cellulose ,chemistry.chemical_classification ,Laccase ,biology ,biology.organism_classification ,Microcrystalline cellulose ,Glucose ,030104 developmental biology ,Lentinula ,chemistry ,biology.protein - Abstract
Lentinula edodes has the potential to degrade woody and nonwoody lignocellulosic biomass. However, the mechanism of lignocellulose degradation by L. edodes is unclear. The aim of this work is to explore the profiling of soluble secreted proteins involved in lignocellulose degradation in L. edodes. For that, we compared the secretomes of L. edodes grown on microcrystalline cellulose, cellulose with lignosulfonate and glucose. Based on nanoliquid chromatography coupled with tandem mass spectrometry of whole-protein hydrolysate, 230 proteins were identified. Label-free proteomic analysis showed that the most abundant carbohydrate-active enzymes involved in polysaccharide hydrolysis were endo-β-1,4-glucanase, α-galactosidase, polygalacturonase and glucoamylase in both cellulosic secretomes. In contrast, enzymes involved in lignin degradation were most abundant in glucose culture, with laccase 1 being the predominant protein (13.13%). When the cellulose and cellulose with lignosulfonate secretomes were compared, the abundance of cellulases and hemicellulases was higher in cellulose with lignosulfonate cultures, which was confirmed by enzyme activity assays. In addition, qRT-PCR analysis demonstrated that the expression levels of genes encoding cellulases and hemicellulases were significantly increased (by 32.2- to 1166.7-fold) when L. edodes was grown in cellulose with lignosulfonate medium. Biological significance In this article, the secretomes of L. edodes grown on three different carbon sources were compared. The presented results revealed the profiling of extracellular enzymes involved in lignocellulose degradation, which is helpful to further explore the mechanism of biomass bioconversion by L. edodes.
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- 2017
21. A novel fluffy nanostructured 3D network of Ni(C7H4O5) for supercapacitors
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Lianfu Chen, Yanhe Xiao, Baochang Cheng, Shuijin Lei, Qiulin Chen, and Peiqin Deng
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Supercapacitor ,Chemistry ,Scanning electron microscope ,General Chemical Engineering ,Nanotechnology ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Capacitance ,Energy storage ,0104 chemical sciences ,Amorphous solid ,Chemical engineering ,Electrode ,Electrochemistry ,0210 nano-technology ,Current density ,Power density - Abstract
Supercapacitors have raised considerable research interest in recent years due to their extensive potential application in next-generation energy storage. It is always of great importance to develop new electrode materials for supercapacitors so far. In this research, nickel gallate complex (Ni(C7H4O5)) nanostructures are successfully grown on nickel foam by a facile hydrothermal route, which can be directly used as the electrodes for supercapacitors. X-ray diffraction patterns show that the sample is amorphous. The scanning electron microscopy images reveal that the products consist of novel fluffy 3D network with a mass of fibers. The electrochemical measurements demonstrate that the prepared Ni(C7H4O5) electrode possesses the specific capacitance of 3.688 F cm−2 (1229.3 F g−1) at a current density of 9 mA cm−2 (3 A g−1). It presents an excellent cycling stability with a capacitance retention of 87.9% after 5000 cycles even at a very high current density of 40 mA cm−2. An asymmetric supercapacitor device is assembled using the Ni(C7H4O5) sample as positive electrode and activated carbon as negative one. A high gravimetric capacitance of 71.4 F g−1 at a current density of 0.5 A g−1 can be achieved. The fabricated device delivers the highest energy density of 23.8 W h kg−1 at a power density of 388.2 W kg−1 with a voltage window of 1.55 V. This strategy should be extended to other organometallic compounds for supercapacitors.
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- 2017
22. Direct growth of nickel terephthalate on Ni foam with large mass-loading for high-performance supercapacitors
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Baochang Cheng, Xiuling Ou, Lianfu Chen, Peiqin Deng, Wei Wang, Shuijin Lei, Yanhe Xiao, and Qiulin Chen
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Supercapacitor ,Materials science ,Renewable Energy, Sustainability and the Environment ,Nanotechnology ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Electrochemistry ,01 natural sciences ,Capacitance ,Energy storage ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Chemical engineering ,Electrode ,Polyaniline ,General Materials Science ,0210 nano-technology ,Current density ,Power density - Abstract
It is always of great significance to explore novel electrode materials for supercapacitors, one of the next-generation energy storage devices. In this work, we have successfully fabricated a nickel terephthalate (Ni–Tp) complex on Ni foam with high mass-loading via a facile hydrothermal route, which can be directly used as an electrode for supercapacitors. More significantly, the electrochemical properties would be substantially improved by the electrochemical deposition of polyaniline (PANI) nanofibers on the surface. The resulting Ni–Tp/PANI electrode shows much higher specific capacitance, rate capability and cycling stability than the pristine Ni–Tp electrode. The electrochemical measurements demonstrate that the obtained Ni–Tp/PANI electrode possesses a specific capacitance of 10.327 F cm−2 (938.845 F g−1) at a current density of 20 mA cm−2 (1.818 A g−1) and cycling stability with a capacitance retention of 85.4% after 3000 cycles at a current density of 50 mA cm−2. An asymmetric supercapacitor is constructed by integrating the Ni–Tp/PANI sample as the positive electrode and activated carbon as the negative electrode. The fabricated device can reach a specific capacitance of 59.498 F g−1 at a current density of 0.556 A g−1 (10 mA cm−2) and an energy density of 19.853 W h kg−1 at a power density of 430.556 W kg−1 with a voltage window of 1.55 V. For the achieved high electrochemical performance, Ni–Tp can be expected to be a favorable candidate for supercapacitors.
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- 2017
23. The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences
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Yingli Cai, Ma Xiaolong, Lianfu Chen, Qianqian Zhang, Fang Shu, Yinbing Bian, and Wei Liu
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Mitochondrial DNA ,Interspersed repeat ,02 engineering and technology ,Biochemistry ,Homing endonuclease ,03 medical and health sciences ,Open Reading Frames ,Ascomycota ,Structural Biology ,Group I catalytic intron ,Molecular Biology ,Gene ,Phylogeny ,030304 developmental biology ,Repetitive Sequences, Nucleic Acid ,Genetics ,0303 health sciences ,biology ,Intron ,Molecular Sequence Annotation ,General Medicine ,Group II intron ,Ribosomal RNA ,021001 nanoscience & nanotechnology ,Introns ,Mitochondria ,Genome, Mitochondrial ,biology.protein ,0210 nano-technology - Abstract
The complete mitochondrial genome of Morchella importuna, the famous edible and medicinal mushroom, was assembled as a 272,238 bp single circular dsDNA. As the largest mitogenome among fungi, it exhibits several distinct characteristics. The mitogenome of M. importuna encoded 14 core conserved mitochondrial protein-coding genes and 151 mitochondrial non-conserved open reading frames (ncORFs) were predicted, of which 61 were annotated as homing endonuclease genes, and 108 were confirmed to be expressed during the vegetative growth stages of M. importuna. In addition, 34 introns were identified in seven core genes (cob, cox1, cox2, cox3, nad1, nad4 and nad5) and two rRNA genes (rrnS and rrnL) with a length from 383 bp to 7453 bp, and eight large introns with a length range of 2340 bp to 7453 bp contained multiple intronic mtORFs. Moreover, 34 group I (IA, IB, IC1, IC2, ID and derived group I introns) and four group II intron domains were identified for the 34 introns, including five hybrid ones. Furthermore, the M. importuna mitogenome showed the presence of about 18.7% mitogenomic interspersed repeats. These and the aforementioned ncORFs and introns, contributed to the enlarged size of the mitogenome.
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- 2019
24. Multiple parapatric pollinators have radiated across a continental fig tree displaying clinal genetic variation
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Enwei Tian, Da-Yong Zhang, Wattana Tanming, Lianfu Chen, Stephen G. Compton, Linna Zheng, Finn Kjellberg, Xiaoxia Deng, Hui Yu, Yufen Cheng, Wei Wu, South China Botanical Garden, The Chinese Academy of Sciences, Beijing Normal University (BNU), University of Leeds, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Beijing Normal University, Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud])
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0106 biological sciences ,0301 basic medicine ,Reproductive Isolation ,Pollination ,plant growth form ,mutualism ,Wasps ,Ficus ,Genes, Insect ,Parapatric speciation ,010603 evolutionary biology ,01 natural sciences ,Trees ,03 medical and health sciences ,Pollinator ,Genetics ,Animals ,14. Life underwater ,Agaonidae ,dispersal ,Ecology, Evolution, Behavior and Systematics ,Asia, Southeastern ,Isolation by distance ,biology ,Ecology ,DNA, Chloroplast ,Genetic Variation ,15. Life on land ,[SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics ,biology.organism_classification ,Co-evolution ,030104 developmental biology ,speciation ,Biological dispersal ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,gene flow ,Fig wasp ,Microsatellite Repeats ,[SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis - Abstract
International audience; The ways that plant-feeding insects have diversified are central to our understanding of terrestrial ecosystems. Obligate nursery pollination mutualisms provide highly relevant model systems of how plants and their insect associates have diversified and the over 800 species of fig trees (Ficus) allow comparative studies. Fig trees can have one or more pollinating fig wasp species (Agaonidae) that breed within their figs, but factors influencing their number remain to be established. In some widely distributed fig trees, the plants form populations isolated by large swathes of sea, and the different populations are pollinated by different wasp species. Other Ficus species with continuous distributions may present genetic signatures of isolation by distance, suggesting more limited pollinator dispersal, which may also facilitate pollinator speciation. We tested the hypothesis that Ficus hirta, a species for which preliminary data showed genetic isolation by distance, would support numerous pollinator species across its range. Our results show that across its range F. hirta displays clinal genetic variation and is pollinated by nine parapatric species of Valisia. This is the highest number of pollinators reported to date for any Ficus species, and it is the first demonstration of the occurrence of parapatric pollinator species on a fig host displaying continuous genetic structure. Future comparative studies across Ficus species should be able to establish the plant traits that have driven the evolution of pollinator dispersal behaviour, pollinator speciation and host plant spatial genetic structure.
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- 2019
25. Comparative transcriptomics reveals potential genes involved in the vegetative growth of Morchella importuna
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Yingli Cai, Yinbing Bian, Wei Liu, Peixin He, and Lianfu Chen
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Genetics ,Sclerotium ,biology ,Morchella importuna ,Environmental Science (miscellaneous) ,Morchella ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,Transcriptome ,Open reading frame ,ORFS ,Gene ,Mycelium ,Biotechnology - Abstract
True morels (Morchella spp.) are edible, medicinal mushrooms which have recently been artificially cultivated in China but stable production remains a problem. Here, we describe complete and comprehensive transcriptome of Morchella importuna at the stages of vegetative mycelium (VM), initial sclerotium (IS) and mature sclerotium (MS) by deep transcriptional sequencing and de novo assembly for the first time and which will potentially provide useful information for improving its cultivation. A total of 26,496 genes were identified with a contig N50 length of 1763 bp and an average length of over 1064 bp. Additionally, 11,957 open reading frames (ORFs) were predicted and 9676 of them (80.9%) were annotated. The 2605 differentially expressed genes (DEGs) identified by gene expression clustering were mainly involved with energy metabolism and could be divided into three broad clusters, of which genes in cluster_1 and cluster_2 were involved in the metabolic process of carbohydrate, polysaccharide, hydrolase, caprolactam, beta-galactosidase, and disaccharide, respectively. Genes in cluster_3 were the largest category, mainly identified with the catalytic activity and transporter activity. Overall, the enzymes involved in the carbohydrate metabolism were highly expressed, and the CAZyme (carbohydrate-active enzyme) genes were significantly expressed within cluster_3. For expression verification, 16 CAZYme genes were selected for qRT-PCR, and the results suggested that the catabolism of carbohydrates occurs mainly in the vegetative mycelium stage, and the anabolism of the energy-rich substances is the main event of mycelial growth and sclerotial morphogenesis of M. importuna.
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- 2019
26. Comparative transcriptomics reveals potential genes involved in the vegetative growth of
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Wei, Liu, Yingli, Cai, Peixin, He, Lianfu, Chen, and Yinbing, Bian
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Original Article - Abstract
True morels (Morchella spp.) are edible, medicinal mushrooms which have recently been artificially cultivated in China but stable production remains a problem. Here, we describe complete and comprehensive transcriptome of Morchella importuna at the stages of vegetative mycelium (VM), initial sclerotium (IS) and mature sclerotium (MS) by deep transcriptional sequencing and de novo assembly for the first time and which will potentially provide useful information for improving its cultivation. A total of 26,496 genes were identified with a contig N50 length of 1763 bp and an average length of over 1064 bp. Additionally, 11,957 open reading frames (ORFs) were predicted and 9676 of them (80.9%) were annotated. The 2605 differentially expressed genes (DEGs) identified by gene expression clustering were mainly involved with energy metabolism and could be divided into three broad clusters, of which genes in cluster_1 and cluster_2 were involved in the metabolic process of carbohydrate, polysaccharide, hydrolase, caprolactam, beta-galactosidase, and disaccharide, respectively. Genes in cluster_3 were the largest category, mainly identified with the catalytic activity and transporter activity. Overall, the enzymes involved in the carbohydrate metabolism were highly expressed, and the CAZyme (carbohydrate-active enzyme) genes were significantly expressed within cluster_3. For expression verification, 16 CAZYme genes were selected for qRT-PCR, and the results suggested that the catabolism of carbohydrates occurs mainly in the vegetative mycelium stage, and the anabolism of the energy-rich substances is the main event of mycelial growth and sclerotial morphogenesis of M. importuna. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-019-1614-y) contains supplementary material, which is available to authorized users.
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- 2018
27. Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)
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Qiang Gao, Lianfu Chen, Chunhai Chen, Songbo Wang, Xiaochuan Liu, Chengcheng Shi, Sining Wang, Shancen Zhao, Lichao Li, Zehui Jiang, Zhimin Gao, Hansheng Zhao, Le Wang, Wei Yang, Yongfeng Lou, Huayu Sun, Huanming Yang, Hao Xu, Hailin Zhang, Xianqiang Zhou, Chi Zhang, Yihong Yang, Benhua Fei, Jiongliang Wang, and Yan-Li Wei
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0301 basic medicine ,Bamboo ,Sequence assembly ,Health Informatics ,Computational biology ,Poaceae ,Genome ,Lignin ,Chromosomes, Plant ,Evolution, Molecular ,03 medical and health sciences ,Gene Expression Regulation, Plant ,evolution ,Gene family ,Gene ,genome ,biology ,Research ,Alternative splicing ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Molecular Sequence Annotation ,Genomics ,biology.organism_classification ,Computer Science Applications ,Alternative Splicing ,030104 developmental biology ,Phyllostachys edulis ,annotation ,moso bamboo ,transcriptome ,Genome, Plant ,Reference genome - Abstract
Background Bamboo is one of the most important nontimber forestry products worldwide. However, a chromosome-level reference genome is lacking, and an evolutionary view of alternative splicing (AS) in bamboo remains unclear despite emerging omics data and improved technologies. Results Here, we provide a chromosome-level de novo genome assembly of moso bamboo (Phyllostachys edulis) using additional abundance sequencing data and a Hi-C scaffolding strategy. The significantly improved genome is a scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version. A total of 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,711 unique AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and Pacific Biosciences sequencing platforms. Through comparisons with orthologous genes in related plant species, we observed that the AS genes are concentrated among more conserved genes that tend to accumulate higher transcript levels and share less tissue specificity. Furthermore, gene family expansion, abundant AS, and positive selection were identified in crucial genes involved in the lignin biosynthetic pathway of moso bamboo. Conclusions These fundamental studies provide useful information for future in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo.
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- 2018
28. Opposite Polarity Monospore Genome De Novo Sequencing and Comparative Analysis Reveal the Possible Heterothallic Life Cycle of Morchella importuna
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Yinbing Bian, Yingli Cai, Qianqian Zhang, Wei Liu, and Lianfu Chen
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0106 biological sciences ,0301 basic medicine ,Mating type ,gene expansion and contraction ,Biology ,01 natural sciences ,Genome ,Catalysis ,Article ,Inorganic Chemistry ,lcsh:Chemistry ,Evolution, Molecular ,03 medical and health sciences ,Ascomycota ,Gene Expression Regulation, Fungal ,heterothallism ,Heterothallic ,Physical and Theoretical Chemistry ,KEGG ,Molecular Biology ,Gene ,lcsh:QH301-705.5 ,mating type ,Spectroscopy ,Phylogeny ,Genetics ,Life Cycle Stages ,Phylogenetic tree ,Gene Expression Profiling ,Organic Chemistry ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Morchella importuna ,Molecular Sequence Annotation ,General Medicine ,Genomics ,Morchella ,Computer Science Applications ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,DNA Transposable Elements ,Ploidy ,Genome, Fungal ,transcriptome ,010606 plant biology & botany - Abstract
Morchella is a popular edible fungus worldwide due to its rich nutrition and unique flavor. Many research efforts were made on the domestication and cultivation of Morchella all over the world. In recent years, the cultivation of Morchella was successfully commercialized in China. However, the biology is not well understood, which restricts the further development of the morel fungus cultivation industry. In this paper, we performed de novo sequencing and assembly of the genomes of two monospores with a different mating type (M04M24 and M04M26) isolated from the commercially cultivated strain M04. Gene annotation and comparative genome analysis were performed to study differences in CAZyme (Carbohydrate-active enzyme) enzyme content, transcription factors, duplicated sequences, structure of mating type sites, and differences at the gene and functional levels between the two monospore strains of M. importuna. Results showed that the de novo assembled haploid M04M24 and M04M26 genomes were 48.98 and 51.07 Mb, respectively. A complete fine physical map of M. importuna was obtained from genome coverage and gene completeness evaluation. A total of 10,852 and 10,902 common genes and 667 and 868 endemic genes were identified from the two monospore strains, respectively. The Gene Ontology (GO) and KAAS (KEGG Automatic Annotation Serve) enrichment analyses showed that the endemic genes performed different functions. The two monospore strains had 99.22% collinearity with each other, accompanied with certain position and rearrangement events. Analysis of complete mating-type loci revealed that the two monospore M. importuna strains contained an independent mating-type structure and remained conserved in sequence and location. The phylogenetic and divergence time of M. importuna was analyzed at the whole-genome level for the first time. The bifurcation time of morel and tuber was estimated to be 201.14 million years ago (Mya), the two monospore strains with a different mating type represented the evolution of different nuclei, and the single copy homologous genes between them were also different due to a genetic differentiation distance about 0.65 Mya. Compared with truffles, M. importuna had an extension of 28 clusters of orthologous genes (COGs) and a contraction of two COGs. The two different polar nuclei with different degrees of contraction and expansion suggested that they might have undergone different evolutionary processes. The different mating-type structures, together with the functional clustering and enrichment analysis results of the endemic genes of the two different polar nuclei, imply that M. importuna might be a heterothallic fungus and the interaction between the endemic genes may be necessary for its complete life history. Studies on the genome of M. importuna facilitate a better understanding of morel biology and evolution.
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- 2018
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29. The chromosome-level genome assemblies of two rattans (Calamus simplicifolius and Daemonorops jenkinsiana)
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Kai Han, Jingjing Shi, Guangyi Fan, Kebin Yang, Xuemeng Shan, Hansheng Zhao, Sining Wang, Lianfu Chen, Chengcheng Shi, Shancen Zhao, Aiqin Feng, Qiang Gao, Chunhai Chen, Songbo Wang, Zhimin Gao, Xiurong Xu, Jiongliang Wang, Hao Xu, Zehui Jiang, Chi Zhang, Shijie Hao, Huayu Sun, Xin Liu, Rongsheng Li, and Benhua Fei
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0301 basic medicine ,Germplasm ,Genome evolution ,Daemonorops jenkinsiana ,Plant genetics ,rattan ,Health Informatics ,Data Note ,Genome ,Chromosomes, Plant ,03 medical and health sciences ,Gene ,Calamus simplicifolius ,biology ,Chromosome ,biology.organism_classification ,Computer Science Applications ,030104 developmental biology ,annotation ,Calamus ,Evolutionary biology ,whole-genome sequencing ,genome assembly ,Genome, Plant ,Reference genome - Abstract
Background Calamus simplicifolius and Daemonorops jenkinsiana are two representative rattans, the most significant material sources for the rattan industry. However, the lack of reference genome sequences is a major obstacle for basic and applied biology on rattan. Findings We produced two chromosome-level genome assemblies of C. simplicifolius and D. jenkinsiana using Illumina, Pacific Biosciences, and Hi-C sequencing data. A total of ∼730 Gb and ∼682 Gb of raw data covered the predicted genome lengths (∼1.98 Gb of C. simplicifolius and ∼1.61 Gb of D. jenkinsiana) to ∼372 × and ∼426 × read depths, respectively. The two de novo genome assemblies, ∼1.94 Gb and ∼1.58 Gb, were generated with scaffold N50s of ∼160 Mb and ∼119 Mb in C. simplicifolius and D. jenkinsiana, respectively. The C. simplicifolius and D. jenkinsiana genomes were predicted to harbor 51,235 and 53,342 intact protein-coding gene models, respectively. Benchmarking Universal Single-Copy Orthologs evaluation demonstrated that genome completeness reached 96.4% and 91.3% in the C. simplicifolius and D. jenkinsiana genomes, respectively. Genome evolution showed that four Arecaceae plants clustered together, and the divergence time between the two rattans was ∼19.3 million years ago. Additionally, we identified 193 and 172 genes involved in the lignin biosynthesis pathway in the C. simplicifolius and D. jenkinsiana genomes, respectively. Conclusions We present the first de novo assemblies of two rattan genomes (C. simplicifolius and D. jenkinsiana). These data will not only provide a fundamental resource for functional genomics, particularly in promoting germplasm utilization for breeding, but also serve as reference genomes for comparative studies between and among different species.
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- 2018
30. Fabrication of Bi
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Yutao, Yan, Yueling, Xu, Shuijin, Lei, Xiuling, Ou, Lianfu, Chen, Jinsong, Xiong, Yanhe, Xiao, and Baochang, Cheng
- Abstract
Thin-film photodetectors built from one-dimensional nanostructures have attracted extensive attention due to their significance in basic scientific research and potential technological applications. It is still desirable to develop new materials with a wide response range for application in photodetectors. In this work, a Bi
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- 2018
31. Hierarchical BiF3–Bi2NbO5F Core–Shell Structure and Its Application in the Photosensitized Degradation of Rhodamine B under Visible Light Irradiation
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Baochang Cheng, Shuijin Lei, Jianliang Zhou, Xijie Gao, Yutao Yan, Chuanning Wang, Lianfu Chen, Yanhe Xiao, and Di Cheng
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Materials science ,Scanning electron microscope ,Band gap ,Analytical chemistry ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,chemistry.chemical_compound ,General Energy ,chemistry ,Chemical engineering ,Transmission electron microscopy ,Photocatalysis ,Rhodamine B ,Physical and Theoretical Chemistry ,Photodegradation ,Ethylene glycol ,Powder diffraction - Abstract
Catalytic photodegradation has been found to be a versatile, low-cost, and green technology for environmental decontamination. Bismuth-based compounds have attracted a lot of attention for their efficient photocatalytic properties. It is always of great importance to develop new catalysts in the photodegradation field. In this research, hierarchical porous BiF3–Bi2NbO5F core–shell structures have been successfully prepared via a simple solvothermal route. A possible growth mechanism for the core–shell structure was proposed based on time-dependent-evolution experiments. X-ray powder diffraction was used to determine the phase composition. Scanning electron microscopy and transmission electron microscopy were employed to characterize the morphologies of the as-prepared samples. Experiments demonstrated that the volume ratio of ethylene glycol to water played a determinative role in the final morphology of the products. The band gap of the as-prepared BiF3–Bi2NbO5F composite was estimated to about 3.47 eV. ...
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- 2014
32. Regularized multivariate regression models with skew-t error distributions
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Mehdi Maadooliat, Lianfu Chen, and Mohsen Pourahmadi
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Statistics and Probability ,Multivariate statistics ,Multivariate analysis ,Applied Mathematics ,Matrix t-distribution ,Estimator ,Cross-validation ,Statistics::Computation ,Bayesian multivariate linear regression ,Linear regression ,Statistics ,Statistics::Methodology ,Applied mathematics ,Statistics, Probability and Uncertainty ,Likelihood function ,Mathematics - Abstract
We consider regularization of the parameters in multivariate linear regression models with the errors having a multivariate skew-t distribution. An iterative penalized likelihood procedure is proposed for constructing sparse estimators of both the regression coefficient and inverse scale matrices simultaneously. The sparsity is introduced through penalizing the negative log-likelihood by adding L1-penalties on the entries of the two matrices. Taking advantage of the hierarchical representation of skew-t distributions, and using the expectation conditional maximization (ECM) algorithm, we reduce the problem to penalized normal likelihood and develop a procedure to minimize the ensuing objective function. Using a simulation study the performance of the method is assessed, and the methodology is illustrated using a real data set with a 24-dimensional response vector. & 2014 Elsevier B.V. All rights reserved.
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- 2014
33. An improved constraint method in Optimal Estimation of CH4 from GOSAT SWIR observations
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Mingmin Zou, Lianfu Chen, Meng Fan, Shenshen Li, and Jinhua Tao
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- 2016
34. Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation
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Yingli Cai, Yinbing Bian, Yuhua Gong, G. P. Wang, Yin Liu, Wei Liu, Zhangyi Xu, Xiaolong Ma, Mengpei Guo, Yang Xiao, Lianfu Chen, Xiaoyu Lei, and Yan Zhou
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0301 basic medicine ,Gene Expression ,lcsh:Medicine ,Lignin ,Database and Informatics Methods ,chemistry.chemical_compound ,lcsh:Science ,Phylogeny ,Mycelium ,chemistry.chemical_classification ,Mushroom ,Multidisciplinary ,biology ,Organic Compounds ,Fungal genetics ,High-Throughput Nucleotide Sequencing ,food and beverages ,Genomics ,Genomic Databases ,Edible mushroom ,Chemistry ,Lentinula ,Physical Sciences ,Genome, Fungal ,Research Article ,Shiitake Mushrooms ,Mycology ,Cellulase ,Research and Analysis Methods ,Polysaccharide ,Fungal Proteins ,03 medical and health sciences ,Botany ,Genetics ,Fungal Genetics ,Cellulose ,Fungal Genomics ,Sequence Assembly Tools ,Organic Chemistry ,lcsh:R ,Organisms ,Fungi ,Chemical Compounds ,Biology and Life Sciences ,Computational Biology ,Genome Analysis ,biology.organism_classification ,Biological Databases ,030104 developmental biology ,chemistry ,biology.protein ,lcsh:Q - Abstract
Lentinula edodes, one of the most popular, edible mushroom species with a high content of proteins and polysaccharides as well as unique aroma, is widely cultivated in many Asian countries, especially in China, Japan and Korea. As a white rot fungus with lignocellulose degradation ability, L. edodes has the potential for application in the utilization of agriculture straw resources. Here, we report its 41.8-Mb genome, encoding 14,889 predicted genes. Through a phylogenetic analysis with model species of fungi, the evolutionary divergence time of L. edodes and Gymnopus luxurians was estimated to be 39 MYA. The carbohydrate-active enzyme genes in L. edodes were compared with those of the other 25 fungal species, and 101 lignocellulolytic enzymes were identified in L. edodes, similar to other white rot fungi. Transcriptome analysis showed that the expression of genes encoding two cellulases and 16 transcription factor was up-regulated when mycelia were cultivated for 120 minutes in cellulose medium versus glucose medium. Our results will foster a better understanding of the molecular mechanism of lignocellulose degradation and provide the basis for partial replacement of wood sawdust with agricultural wastes in L. edodes cultivation.
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- 2016
35. A novel cysteine desulfurase influencing organosulfur compounds in Lentinula edodes
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Salam A. Ibrahim, Wen Huang, Hong Yang, Ying Liu, Lianfu Chen, Xiaoyu Lei, and Yinbing Bian
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chemistry.chemical_classification ,Multidisciplinary ,biology ,Sulfur Compounds ,Cysteine desulfurase ,Molecular Sequence Data ,Shiitake Mushrooms ,Lyases ,Sulfoxide ,Lyase ,biology.organism_classification ,Article ,Substrate Specificity ,chemistry.chemical_compound ,Carbon-Sulfur Lyases ,Lentinula ,Enzyme ,chemistry ,Biochemistry ,Cysteine desulfurase activity ,Pyridoxal Phosphate ,Amino Acid Sequence ,Organosulfur compounds ,Cysteine - Abstract
Organosulfur compounds are the basis for the unique aroma of Lentinula edodes and cysteine sulfoxide lyase (C-S lyase) is the key enzyme in this trait. The enzyme from Alliium sativum has been crystallized and well-characterized; however, there have been no reports of the characterization of fungi C-S lyase at the molecular level. We identified a L. edodes C-S lyase (Lecsl), cloned a gene of Csl encoded Lecsl and then combined modeling, simulations and experiments to understand the molecular basis of the function of Lecsl. Our analysis revealed Lecsl to be a novel cysteine desulfurase and not a type of cysteine sulfoxide lyase. The pyridoxal-5-phosphate (PLP) molecule bonded tightly to Lecsl to form a Lecsl-PLP complex. Moreover, the Lecsl had one active center that served to bind two kinds of substrates, S-methyl-L-cysteine sulfoxide and L-cysteine and had both cysteine sulfoxide lyase and cysteine desulfurase activity. We found that the amino acid residue Asn393 was essential for the catalytic activity of Lecsl and that the gene Csl encoded a novel cysteine desulfurase to influence organosulfur compounds in L. edodes. Our results provide a new insight into understanding the formation of the unique aroma of L. edodes.
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- 2014
36. A genome-wide association scan for rheumatoid arthritis data by Hotelling's T2tests
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Ming Zhong, Lianfu Chen, Ruzong Fan, Wei Vivien Chen, and Christopher I. Amos
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Genetics ,0303 health sciences ,Candidate gene ,business.industry ,Chromosome 9 ,Single-nucleotide polymorphism ,Locus (genetics) ,General Medicine ,01 natural sciences ,General Biochemistry, Genetics and Molecular Biology ,010104 statistics & probability ,03 medical and health sciences ,Proceedings ,Genotype ,Medicine ,SNP ,0101 mathematics ,Allele ,business ,Gene ,030304 developmental biology - Abstract
We performed a genome-wide association scan on the North American Rheumatoid Arthritis Consortium (NARAC) data using Hotelling's T 2 tests, i.e., T H based on allele coding and T G based on genotype coding. The objective was to identify associations between single-nucleotide polymorphisms (SNPs) or markers and rheumatoid arthritis. In specific candidate gene regions, we evaluated the performance of Hotelling's T 2 tests. Then Hotelling's T 2 tests were used as a tool to identify new regions that contain SNPs showing strong associations with disease. As expected, the strongest association evidence was found in the region of the HLA-DRB1 locus on chromosome 6. In the region of the TRAF1-C5 genes, we identified two SNPs, rs2900180 and rs3761847, with the largest and the second largest T H and T G scores among all SNPs on chromosome 9. We also identified one SNP, rs2476601, in the region of the PTPN22 gene that had the largest T H score and the second largest T G score among all SNPs on chromosome 1. In addition, SNPs with the largest T H score on each chromosome were identified. These SNPs may be located in the regions of genes that have modest effects on rheumatoid arthritis. These regions deserve further investigation.
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- 2009
37. De Novo Assembly of Auricularia polytricha Transcriptome Using Illumina Sequencing for Gene Discovery and SSR Marker Identification
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Yan Zhou, Xiuzhi Fan, Lianfu Chen, and Yinbing Bian
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lcsh:Medicine ,Gene Expression ,Sequence assembly ,Genomics ,Mycology ,Biology ,Microbiology ,Transcriptomes ,Fungal Proteins ,Transcriptome ,Genome Analysis Tools ,Gene Expression Regulation, Fungal ,Molecular Cell Biology ,KEGG ,lcsh:Science ,Genetic Association Studies ,Illumina dye sequencing ,Expressed Sequence Tags ,Genetics ,Fungal protein ,Expressed sequence tag ,Multidisciplinary ,Basidiomycota ,lcsh:R ,Fungi ,Microbial Growth and Development ,Computational Biology ,food and beverages ,Molecular Sequence Annotation ,Functional Genomics ,lcsh:Q ,Genome Expression Analysis ,Functional genomics ,Metabolic Networks and Pathways ,Research Article ,Microsatellite Repeats - Abstract
Auricularia polytricha (Mont.) Sacc., a type of edible black-brown mushroom with a gelatinous and modality-specific fruiting body, is in high demand in Asia due to its nutritional and medicinal properties. Illumina Solexa sequenceing technology was used to generate very large transcript sequences from the mycelium and the mature fruiting body of A. polytricha for gene discovery and molecular marker development. De novo assembly generated 36,483 ESTs with an N50 length of 636 bp. A total of 28,108 ESTs demonstrated significant hits with known proteins in the nr database, and 94.03% of the annotated ESTs showed the greatest similarity to A. delicata, a related species of A. polytricha. Functional categorization of the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed the conservation of genes involved in various biological processes in A. polytricha. Gene expression profile analysis indicated that a total of 2,057 ESTs were differentially expressed, including 1,020 ESTs that were up-regulated in the mycelium and 1,037 up-regulated in the fruiting body. Functional enrichment showed that the ESTs associated with biosynthesis, metabolism and assembly of proteins were more active in fruiting body development. The expression patterns of homologous transcription factors indicated that the molecular mechanisms of fruiting body formation and development were not exactly the same as for other agarics. Interestingly, an EST encoding tyrosinase was significantly up-regulated in the fruiting body, indicating that melanins accumulated during the processes of the formation of the black-brown color of the fruiting body in A. polytricha development. In addition, a total of 1,715 potential SSRs were detected in this transcriptome. The transcriptome analysis of A. polytricha provides valuable sequence resources and numerous molecular markers to facilitate further functional genomics studies and genetic researches on this fungus.
- Published
- 2014
38. Comparative genome analysis identifies two large deletions in the genome of highly-passaged attenuated Streptococcus agalactiae strain YM001 compared to the parental pathogenic strain HN016
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Lianfu Chen, Aiying Lei, Ting Huang, Liping Li, Xi Gan, Rui Wang, Ming Chen, Yan Huang, Wanwen Liang, and Fuguang Luo
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Sequence analysis ,Virulence attenuation ,Virulence ,Single-nucleotide polymorphism ,Biology ,medicine.disease_cause ,Genome ,Microbiology ,Streptococcus agalactiae ,Streptococcal Infections ,medicine ,Genetics ,Animals ,Humans ,Genetic variation ,Gene ,Mastitis, Bovine ,Prophage ,Phylogeny ,Sequence Deletion ,Comparative Genomic Hybridization ,Virulence factors ,Food Microbiology ,Cattle ,Female ,GC-content ,Genome, Bacterial ,Research Article ,Tilapia ,Biotechnology - Abstract
Background Streptococcus agalactiae (S. agalactiae), also known as group B Streptococcus (GBS), is an important pathogen for neonatal pneumonia, meningitis, bovine mastitis, and fish meningoencephalitis. The global outbreaks of Streptococcus disease in tilapia cause huge economic losses and threaten human food hygiene safety as well. To investigate the mechanism of S. agalactiae pathogenesis in tilapia and develop attenuated S. agalactiae vaccine, this study sequenced and comparatively analyzed the whole genomes of virulent wild-type S. agalactiae strain HN016 and its highly-passaged attenuated strain YM001 derived from tilapia. Methods We performed Illumina sequencing of DNA prepared from strain HN016 and YM001. Sequencedreads were assembled and nucleotide comparisons, single nucleotide polymorphism (SNP) , indels were analyzed between the draft genomes of HN016 and YM001. Clustered regularly interspaced short palindromic repeats (CRISPRs) and prophage were detected and analyzed in different S. agalactiae strains. Results The genome of S. agalactiae YM001 was 2,047,957 bp with a GC content of 35.61 %; it contained 2044 genes and 88 RNAs. Meanwhile, the genome of S. agalactiae HN016 was 2,064,722 bp with a GC content of 35.66 %; it had 2063 genes and 101 RNAs. Comparative genome analysis indicated that compared with HN016, YM001 genome had two significant large deletions, at the sizes of 5832 and 11,116 bp respectively, resulting in the deletion of three rRNA and ten tRNA genes, as well as the deletion and functional damage of ten genes related to metabolism, transport, growth, anti-stress, etc. Besides these two large deletions, other ten deletions and 28 single nucleotide variations (SNVs) were also identified, mainly affecting the metabolism- and growth-related genes. Conclusions The genome of attenuated S. agalactiae YM001 showed significant variations, resulting in the deletion of 10 functional genes, compared to the parental pathogenic strain HN016. The deleted and mutated functional genes all encode metabolism- and growth-related proteins, not the known virulence proteins, indicating that the metabolism- and growth-related genes are important for the pathogenesis of S. agalactiae. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2026-y) contains supplementary material, which is available to authorized users.
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