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Gonadal transcriptomic analysis and differentially expressed genes between the testes and ovaries in Trachinotus ovatus

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Aquaculture and Fisheries 2022年第1期7卷 31-39页

作者： Pingping He Peng Zhu Pinyuan Wei Xiaofei Zhuo Yuan Ma Xiaohan Chen Yong Lin Youhou Xu Hui Luo Jinxia Peng Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture Guangxi Academy of Fisheries SciencesNanning530021China Beibu Gulf University Qinzhou535000China College of Animal Science Southwest UniversityChongqing402460China

The Trachinotus ovatus is a popular aquaculture species in *** are no obvious morphological differences between male and female fish,even during maturity,prompting research studies on sex-related features of this *** examine sex determination-and gonadal development-related genes,we conducted transcriptome analysis of the ovaries and testes of ***.A total of 345,972,132 high-quality clean reads were obtained from 12 *** addition,28,137 gonad-expressed unigenes were obtained by mapping the clean reads to the *** reference genome.A total of 8,237 differentially expressed genes(DEGs)were identified between stage I ovaries and testes,including 3,235 testicular upregulated and 5,002 ovarian upregulated ***,13,448 DEGs were obtained between stage III ovarian and testicular libraries,including 7,576 testicular upregulated and 5,872 ovarian upregulated *** DEGs included some sex-determining genes such as sry,dmrt1,and *** between ovarian and testicular libraries were significantly enriched with KEGG pathways that are involved in gonadal development,sex determination,and gonadal ***,10 DEGs(seven testicular upregulated and three ovarian upregulated unigenes)were selected for quantitative real-time PCR *** genes(zinc-binding protein A33-like,pro-opiomelanocortin-like,leucine-rich repeat and transmembrane domain-containing protein 2-like,and forkhead boxC1)showed a specific testicular expression *** gonadally expressed as well as testicular and ovarian DEGs provide useful information for further research on the reproductive biology of ***.

关键词： transcriptome Trachinotus ovatus Gonad High-throughput sequencing RT-qPCR

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Comparison of gene expression responses of zebrafish larvae to Vibrio parahaemolyticus infection by static immersion and caudal vein microinjection

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Aquaculture and Fisheries 2021年第3期6卷 267-276页

作者： Xinya Guo Ce Ji Xuan Du Jianfeng Ren Yao Zu Weiming Li Qinghua Zhang Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Ministry of EducationShanghai Ocean UniversityShanghai201306China International Research Center for Marine Biosciences Ministry of Science and TechnologyShanghai Ocean UniversityShanghai201306China National Pathogen Collection Center for Aquatic Animals Ministry of AgricultureShanghai Ocean UniversityShanghai201306China Department of Fisheries and Wildlife Michigan State UniversityEast LansingMI48824USA

infection model for studying inflammation and the innate immune *** investigated the genes and signaling pathways activated by static immersion and caudal vein microinjection infection using transcriptome profiling and reverse-transcription quantitative PCR(RT-qPCR)to compare the innate immune response in 3 days post-fertilization(dpf)zebrafish larvae infected by Vibrio parahaemolyticus Vp13 *** median lethal dose(LD50)values at 96 h following immersion and microinjection were 3.63×107 CFU/mL and 5.76×102 CFU/nL,*** innate immune response was initiated after 2 h of incubation with the respective LD50 for each infection *** hundred and two genes in the immersion group and 359 genes in the microinjection group were activated and differentially expressed ***-three Gene Ontology(GO)terms and four Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways were significantly enriched in the immersion group,compared with only three GO terms and no KEGG pathways in the microinjection *** genes,tnfb and ccl20a.3,were significantly up-regulated in both *** speculated that immersion infection may affect initial dorsal determination,cytochromes,and fatty acid-binding proteins,as well as inflammation,while microinjection infection may mainly directly affect the immune *** with doses>LD50(1.09×109 CFU/mL and 1.09×103 CFU/nL by immersion and microinjection,respectively)caused more significant up-regulation of il11a,tnfa,tnfb,il1b,ccl34a.4,ccl20a.3,irak3,cxcl18b,and ccl35.1,suggesting that in addition to the classical innate immunity genes tnfa,tnfb,il1b,and il6,the genes il11a,ccl34a.4,ccl20a.3,cxcl18b,and ccl35.1 were also important for defending against Vp13 *** findings highlight the genes involved in the responses of zebrafish to Vp13 infection via different routes and doses,and thus provide the basis for further analyses of immune response signaling pathways.

关键词： Immersion Microinjection transcriptome Vibrio parahaemolyticus Zebrafish

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Combined analysis of transcriptomics and metabolomics revealed complex metabolic genes for diterpenoids biosynthesis in different organs of Anoectochilus roxburghii

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Chinese Herbal Medicines 2023年第2期15卷 298-309页

作者： Yicong Wei Jiayuan Zhang Keming Qi Ye Li Ying Chen College of Pharmacy Fujian University of Traditional Chinese MedicineFuzhou 350122China College of Landscape and Architecture Fujian Agriculture and Forestry UniversityFuzhou 350002China

Objective:Diterpenoids with a wide variety of biological activities from Anoectochilus roxburghii,a precious medicinal plant,are important active ***,due to the lack of genetic information on the metabolic process of diterpenoids in ***,the genes involved in the molecular regulation mechanism of diterpenoid metabolism are still *** study revealed the complex metabolic genes for diterpenoids biosynthesis in different organs of *** by combining analysis of transcriptomics and ***:The differences in diterpenoid accumulation in roots,stems and leaves of *** were analyzed by metabonomic analysis,and its metabolic gene information was obtained by transcriptome ***,the molecular mechanism of differential diterpenoid accumulation in different organs of *** was analyzed from the perspective of gene expression ***:A total of 296 terpenoid metabolites were identified in the five terpenoid metabolic pathways in *** were 38,34,and 18 diterpenoids with different contents between roots and leaves,between leaves and stems,and between roots and stems,***-nine metabolic enzyme genes with 883 unigenes in the diterpenoid synthesis process were identified,and the DXS and FDPS in the terpenoid backbone biosynthesis stage and CPA,GA20ox,GA3ox,GA2ox,and MAS in the diterpenoid biosynthesis stage were predicted to be the key metabolic enzymes for the accumulation of *** addition,14 key transcription factor coding genes were predicted to be involved in the regulation of the diterpenoid *** expression of genes such as GA2ox,MAS,CPA,GA20ox and GA3ox might be activated by some of the 14 transcription *** transcription factor NTF-Y and PRE6 were predicted to be the most important transcription ***:This study determined 29 metabolic enzyme genes and predicted 14 transcription factors involved in the molecular regulation

关键词： Anoectochilus roxburghii(Wall.)Lindl. diterpenoid metabolic pathway leaves metabolomics roots stems transcriptome

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Molecular aspects of eye development and regeneration in the Australian redclaw crayfish,Cherax quadricarinatus

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Aquaculture and Fisheries 2019年第1期4卷 27-36页

作者： Tomer Ventura Michael J.Stewart Jennifer C.Chandler Bronwyn Rotgans Abigail Elizur Alex W.Hewitt GeneCology Research Centre Faculty of ScienceHealthEducation and EngineeringUniversity of the Sunshine CoastSunshine CoastQueensland 4556Australia Lions Eye Institute University of Western AustraliaPerthWestern Australia 6330Australia School of Medicine Menzies Institute for Medical ResearchUniversity of TasmaniaHobartTasmania 7005Australia

The compound eye evolved over 500 million years ago and enables mosaic vision in most arthropod *** molecular regulation of the development of the compound eye has been primarily studied in the fruit fly Drosophila ***,due to the nature of holometabolous insects halting growth after their terminal metamorphosis into the adult form,they lack the capacity to ***,unlike holometabolous insects,continue to grow during adulthood,achieved through regular shedding of their exoskeleton,in a cyclic process known as *** therefore offers crustaceans as a highly suitable model to study ocular regeneration in the adult arthropod *** have assessed the regenerative capacity of the retinal section of the Cherax quadricarinatus(red-claw crayfish)eye,following ablation and successive post-metamorphic *** work then provides a transcriptomic description of the outer,pigmented retinal tissue(the ommatidia and lamina ganglionaris)and the basal,non-pigmented neuroendocrine ocular tissue(the X-organ Sinus Gland complex,hemiellipsoid body and optic nerve).Using comparative analysis,we identified all the transcripts in the *** ocular transcriptome that are known to function in compound eye development in *** and uniquely transcribed genes of the retina are described,suggesting proposed mechanisms that may regulate ocular regeneration in decapod *** research exemplifies the application *** holds as an optimal model to study the regulation of ocular *** in-depth transcriptomic analyses are now required,sampled throughout the regeneration process to better define the regulatory mechanism.

关键词： Ocular development Regeneration Compound eye Crustacean Cherax quadricarinatus transcriptome

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Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium

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Cell Regeneration 2022年第1期11卷 172-187页

作者： Haonan Li Xiaodan Wang Yalong Wang Mengxian Zhang Fan Hong Hong Wang Along Cui Jianguo Zhao Weizhi Ji Ye-Guang Chen The State Key Laboratory of Membrane Biology Tsinghua-Peking Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing 100084China Guangzhou Institutes of Biomedicine and Health Chinese Academy of SciencesGuangzhou Science ParkGuangzhou 510530China Guangzhou Laboratory Guangzhou 510005China State Key Laboratory of Primate Biomedical Research Institute of Primate Translational MedicineKunming University of Science and TechnologyKunming 650500YunnanChina State Key Laboratory of Stem cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China

Animal models are widely used for biomedical studies and drug *** small intestine plays key roles in nutrient absorption,hormone secretion,microbiota defense and drug absorption and *** the intestinal structure of mammals is conserved,the differences on epithelial cell composition,functional assignments and drug absorption among mammals are largely ***,cross-species analysis of single-cell transcriptomic atlas of the ileum epithelium from mouse,rat,pig,macaque and human reveals the conserved and differential cell types and functions among species,identifies a new CA7+cell type in pig,macaque and human ileum,uncovers the distinct expression pattern in enterocytes,enteroendocrine cells and Paneth cells,and defines the conserved and species-specific intestinal stem cell signature *** examination of drug absorption across species suggests that drug metabolism in mouse ileum is closer to human while drug transport in macaque ileum is more similar to ***,our data provide the comprehensive information about cell composition and functional assignments in five species,and offer the valuable guidance for animal model selection and drug testing.

关键词： scRNA-seq transcriptome Ileum Monkey Pig Rat CA7 cells

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Transcriptomic analysis of wheat reveals possible resistance mechanism mediated by Yr10 to stripe rust

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Stress Biology 2023年第1期3卷 477-494页

作者： Zhongyi Wu Gaohua Zhang Ran Zhao Qi Gao Jinchen Zhao Xiaoxu Zhu Fangyan Wang Zhensheng Kang Xiaojing Wang State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences Northwest A&F UniversityYangling 712100ShaanxiChina State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection Northwest A&F UniversityYangling 712100ShaanxiChina State Key Laboratory of Crop Stress Biology for Arid Areas and College of Natural Resources and Environment Northwest A&F UniversityYangling 712100ShaanxiChina

Stripe rust,caused by Puccinia striiformis ***(Pst),is a catastrophic disease that threatens global wheat ***10 is a race-specific all-stage disease resistance gene in ***,the resistance mechanism of Yr10 is poorly ***,to elucidate the potential molecular mechanism mediated by Yr10,transcriptomic sequencing was performed at 0,18,and 48 h post-inoculation(hpi)of compatible wheat Avocet S(AvS)and incompatible near-isogenic line(NIL)AvS+Yr10 inoculated with Pst race ***,227,208,and 4050 differentially expressed genes(DEGs)were identified at 0,18,and 48 hpi between incompatible and compatible *** response of Yr10 to stripe rust involved various processes and activities,as indicated by the results of Gene Ontology(GO)enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway ***,the response included photosynthesis,defense response to fungus,metabolic processes related to salicylic acid(SA)and jasmonic acid(JA),and activities related to reactive oxygen species(ROS).Ten candidate genes were selected for qRT-PCR verification and the results showed that the transcriptomic data was *** the functional analysis of candidate genes by the virus-induced gene silencing(VIGS)system,it was found that the gene TaHPPD(4-hydroxyphenylpyruvate dioxygenase)negatively regulated the resistance of wheat to stripe rust by affecting SA signaling,pathogenesis-related(PR)gene expression,and ROS *** study provides insight into Yr10-mediated resistance in wheat.

关键词： transcriptome Yr10 Virus-induced gene silencing system (VIGS)system 4-hydroxyphenylpyruvate dioxygenase HPPD

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Molecular and physiological responses to salt stress in salinity-sensitive and tolerant Hibiscus rosa-sinensis cultivars

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Molecular Horticulture 2023年第1期3卷 1-18页

作者： Alice Trivellini Giulia Carmassi Guido Scatena Paolo Vernieri Antonio Ferrante Department of Agriculture Food and EnvironmentUniversity of PisaPisaItaly Italian Institute for Environmental Protection and Research–ISPRA Via del Cedro 3857122 LeghornItaly Department of Agricultural and Environmental Sciences Universita Degli Studi Di MilanoVia Celoria 220133 MilanItaly

Ornamental plants are used to decorate urban and peri-urban areas,and during their cultivation or utilisation,they can be exposed to abiotic *** is an abiotic stress factor that limits plant growth and reduces the ornamental value of sensitive *** this study,transcriptomic analysis was conducted to identify genes associated with tolerance or sensitivity to salinity in two hibiscus(Hibiscus rosa-sinensis L.)cultivars,‘Porto’and‘Sunny wind’.The physiological and biochemical parameters of plants exposed to 50,100,or 200 mM NaCl and water(control)were *** treatments were applied for six *** four weeks,differences between cultivars were clearly evident and‘Porto’was more tolerant than‘Sunny wind’.The tolerant cultivar showed lower electrolyte leakage and ABA concentrations,and higher proline content in the *** of Na in different organs was lower in the flower organs of‘Porto’.At the molecular level,several differential expressed genes were observed between the cultivars and flower *** the highly expressed DEGs,coat protein,alcohol dehydrogenase,and AP2/EREBP transcription factor *** the downregulated genes,GH3 and NCED were the most *** differential expression of these genes may explain the salt stress tolerance of‘Porto’.

关键词： Flower ABA Ion leakage Petals Proline transcriptome

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Transcriptomic response of Pinus massoniana to infection stress from the pine wood nematode Bursaphelenchus xylophilus

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Stress Biology 2023年第1期3卷 534-545页

作者： Yibo An Yongxia Li Ling Ma Dongzhen Li Wei Zhang Yuqian Feng Zhenkai Liu Xuan Wang Xiaojian Wen Xingyao Zhang Key Laboratory of Forest Protection of National Forestry and Grassland Administration Ecology and Nature Conservation InstituteChinese Academy of Forestryl00091BeijingChina Co-Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry UniversityNanjing 210037China Chongqing Forestry Investment and Development Co. Ltd.National Forestry and Grassland National Reserve Forest Engineering Technology Research CenterChongqing 401120China Northeast Forestry University College of ForestryHarbin 150040China

The pinewood nematode(PWN)Bursaphelenchus xylophilus is a forestry quarantine pest and causes an extremely dangerous forest disease that is spreading *** to the complex pathogenic factors of pine wood nematode disease,the pathogenesis is still *** ultimately invades a host and causes ***,little is known about the defence-regulating process of host pine after infection by *** at the molecular ***,we wanted to understand how Pinus massoniana regulates its response to invasion by *** were artificially inoculated with *** solution,while those without *** solution were used as *** inoculated with *** solution for 0 h,6 h,24 h,and 120 h was subjected to highthroughput sequencing to obtain transcriptome *** various time points(0 h,6 h,24 h,120 h),gene transcription was measured in *** inoculated with *** different time points,*** gene transcription differed significantly,with a response to early invasion by *** to Gene Ontology(GO)classification and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis,*** response to PWN invasion involves a wide range of genes,including plant hormone signal transformation,flavonoid biosynthesis,amino sugar and nucleoside sugar metabolism,and MAPK signalling *** them,inoculation for 120 hours had the greatest impact on differential ***,weighted gene coexpression network analysis(WGCNA)was used to analyse transcriptional regulation of *** after PWN *** results showed that the core gene module of *** responding to PWN was“MEmagenta”,enriched in oxidative phosphorylation,amino sugar and nucleotide sugar metabolism,and the MAPK signalling *** family transcription factors with the highest number of changes between infected and healthy pine trees accounted for 20.4% of the total differentially expressed tran

关键词： Pinus massoniana Bursaphelenchus xylophilus transcriptome WGCNA

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Function and molecular mechanism analysis of CaLasSDE460 effector involved in the pathogenesis of“Candidatus Liberibacter asiaticus”in citrus

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Molecular Horticulture 2023年第1期3卷 197-213页

作者： Shuai Wang Meixia Du Liting Dong Rongrong Qu Danlu Ran Juanjuan Ma Xuefeng Wang Lanzhen Xu Weimin Li Yongrui He Xiuping Zou Integrative Science Center of Germplasm Creation in Western China(CHONGQING)Science City Citrus Research InstituteSouthwest University/National Citrus Engineering Research CenterChongqingPeople’s Republic of China Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural AffairsBeijing University of AgricultureBeijingPeople’s Republic of China

Citrus Huanglongbing(HLB),caused by Candidatus Liberibacter asiaticus(CaLas),is the most serious disease ***460 was previously characterized as a potential virulence factor of ***,the function and mechanism of CaLasSDE460 involved in CaLas against citrus is still ***,we showed that transgenic expression of CaLasSDE460 in Wanjincheng oranges(*** Osbeck)contributed to the early growth of CaLas and the development of *** the temperature increased from 25℃to 32℃,CaLas growth and symptom development in transgenic plants were slower than those in WT ***-seq analysis of transgenic plants showed that CaLasSDE460 affected multiple biological *** 25℃,transcription activities of the“Protein processing in endoplasmic reticulum”and“Cyanoamino acid metabolism”pathways increased while transcription activities of many pathways decreased at 32℃.124 and 53 genes,separately annotated to plant-pathogen interaction and MAPK signaling pathways,showed decreased expression at 32℃,compared with these(38 for plant-pathogen interaction and 17 for MAPK signaling)at 25℃.Several important genes(MAPKKK14,HSP70b,NCED3 and WRKY33),remarkably affected by CaLasSDE460,were ***,our data suggested that CaLasSDE460 participated in the pathogenesis of CaLas through interfering transcription activities of citrus defense response and this interfering was temperature-dependent.

关键词： Citrus HLB CaLasSDE460 transcriptome Ectopic expression

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Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approach

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Aquaculture and Fisheries 2019年第1期4卷 37-42页

作者： Frederico M.Batista Allison M.Churcher Manuel Manchado Alexandra Leitao Deborah M.Power Centro de Cieencias do Mar(CCMAR) Universidade do AlgarveCampus de Gambelas8005-139 FaroPortugal Instituto Portugues do Mar e da Atmosfera Estaçao Experimental de Moluscicultura de TaviraPortugal Department of Biosciences College of ScienceSwansea UniversitySwanseaSA28PPWalesUnited Kingdom IFAPA Centro El Toruno Junta de AndalucíaCamino Tiro Pichon sn11500 El Puerto de Santa MaríaCadizSpain Environmental Science Center(ESC) Qatar UniversityP.O.Box 2713 DohaQatar

The grooved carpet-shell clam Ruditapes decussatus is native to the Northern Atlantic and Mediterranean Sea and has a high commercial *** is one of the main native bivalve species cultured in *** main objective of the present study was to gain further insights into the immunological repertoire of *** through a transcriptomic *** mantle samples of eight *** individuals were sequenced using Illumina platform.A total of 67132 contigs with more than 800 bp were *** annotation of these contigs revealed 146 immune-related *** gene families in which the highest number of immune-related genes was observed were:C1q domain-containing proteins(63),tumor necrosis factors(15)and toll-like receptors(TLRs,10).A total of 5359 putative single nucleotide polymorphisms(SNPs)were identified in the 146 immune-related *** density of SNPs ranged between 0.04 and 7.92 SNPs/100 *** highest and the lowest SNP density were observed in genes of the C1q domain-containing protein *** to the importance of TLRs in innate immunity,we focused our attention on these membrane *** TLRs were identified based on protein domain *** analysis revealed that *** TLRs were diverse and only 3 showed orthology with TLRs of known immune functions in other bivalve ***,our analysis suggests that lineage restricted-expansions of TLRs occurred in all mollusc taxa analysed including in venerids.

关键词： Ruditapes decussatus transcriptome Immune genes Toll-like receptors

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