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transcriptome analysis of adipose tissue and muscle of Laiwu and Duroc pigs

Animal Nutrition 2024年第2期17卷 134-143页

作者： Jie Wu Fangyuan Yu Zhaoyang Di Liwen Bian Jie Yang Lina Wang Qingyan Jiang Yulong Yin Lin Zhang National Engineering Research Center for Breeding Swine Industry State Key Laboratory of Swine and Poultry Breeding IndustryGuangdong Laboratory of Lingnan Modern AgricultureGuangdong Provincial Key Laboratory of Animal Nutrition ControlCollege of Animal ScienceSouth China Agricultural University Key Laboratory of Agro-Ecological Processes in Subtropical Region Laboratory of Animal Nutritional Physiology and Metabolic ProcessInstitute of Subtropical AgricultureChinese Academy of Sciences

Fat content is an important trait in pig production. Adipose tissue and muscle are important sites for fat deposition and affect production efficiency and quality. To regulate the fat content in these tissues, we need to understand the mechanisms behind fat deposition. Laiwu pigs, a Chinese indigenous breed, have significantly higher fat content in both adipose tissue and muscle than commercial breeds such as *** this study, we analyzed the transcriptomes in adipose tissue and muscle of 21-d-old Laiwu and Duroc piglets. Results showed that there were 828 and 671 differentially expressed genes(DEG) in subcutaneous adipose tissue(SAT) and visceral adipose tissue(VAT), respectively. Functional enrichment analysis showed that these DEG were enriched in metabolic pathways, especially carbohydrate and lipid metabolism. Additionally, in the longissimus muscle(LM) and psoas muscle(PM), 312 and 335 DEG were identified, demonstrating enrichment in the cell cycle and metabolic pathways. The protein-protein interaction(PPI) networks of these DEG were analyzed and potential hub genes were identified, such as FBP1 and SCD in adipose tissues and RRM2 and GADL1 in muscles. Meanwhile, results showed that there were common DEG between adipose tissue and muscle, such as LDHB, THRSP, and DGAT2. These findings showed that there are significant differences in the transcriptomes of the adipose tissue and muscle between Laiwu and Duroc piglets(P < 0.05), especially in metabolic patterns. This insight serves to advance our comprehensive understanding of metabolic regulation in these tissues and provide targets for fat content regulation.

关键词： Laiwu Duroc Adipose Muscle transcriptome Carbohydrate and lipid metabolism

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transcriptome analysis reveals immune-related genes in tissues of Vibrio anguillarum-infected turbot Scophthalmus maximus

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Journal of Oceanology and Limnology 2024年第1期42卷 332-344页

作者： Yuting SONG Maqsood Ahmed SOOMRO Xianzhi DONG Guobin HU College of Marine Life Sciences Ocean University of ChinaQingdao 266003China Institute of Evolution&Marine Biodiversity Ocean University of ChinaQingdao 266003China Institute of Biophysis Chinese Academy of SciencesBeijing 100101China

Turbot Scophthalmus maximus is an important mariculture fish species with high economic ***,the bacterial diseases caused by Vibrio anguillarum infection bring huge economic losses to the turbot aquaculture *** understand the immune response of the turbot against *** infection and to explore novel immune-related genes,the transcriptome analysis of turbot spleen and gills were conducted after *** *** expressed genes(DEGs)were identified in spleen and gill of the turbot amounted to 17261 and 16436,respectively.A large number of immunerelated DEGs were enriched in cytokine-cytokine receptor interaction signaling pathway,and the others by the kyoto encyclopedia of genes and genomes(KEGG)*** gene ontology(GO)classification analysis revealed that *** infection had the greatest effect on biological processes and cellular *** immune-related DEGs were identified in the spleen(cstl.1,egfl6,lamb21,v2rx4,calcr,and gpr78a)and gills(ghra,sh3gl2a,cst12,inhbaa,cxcl8,and il-1b)by heat *** proteinprotein interaction(PPI)networks were constructed to analyze the immune *** results demonstrate that the maturation and antigen processing of major histocompatibility complex(MHC)class II molecule,and calcitonin-or adrenomedullin-regulated physiological activity were important events in the immunity of turbot against *** *** the gills,the protein interactions in TGF-βsignaling pathway,production of inflammatory factors,and endocytosis regulation were most *** research laid a foundation for discovering novel immune-related genes and enriching the knowledge of immune mechanisms of turbot against *** infection.

关键词： Scophthalmus maximus Vibrio anguillarum transcriptome differentially expressed genes immune mechanism

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transcriptome Dynamics and Cell Dialogs Between Oocytes and Granulosa Cells in Mouse Follicle Development

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 93-106页

作者： Wenju Liu Chuan Chen Yawei Gao Xinyu Cui Yuhan Zhang Liang Gu Yuanlin He Jing Li Shaorong Gao Rui Gao Cizhong Jiang Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education Orthopaedic Department of Tongji HospitalSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital Shanghai Key Laboratory of Signaling and Disease ResearchSchool of Life Sciences and TechnologyTongji UniversityShanghai 200092China Frontier Science Center for Stem Cell Research Tongji UniversityShanghai 200092China Department of Epidemiology and Biostatistics Jiangsu Key Lab of Cancer BiomarkersPrevention and TreatmentCollaborative Innovation Center for Cancer Personalized MedicineSchool of Public HealthNanjing Medical UniversityNanjing 210029China

The development and maturation of follicles is a sophisticated and multistage *** dynamic gene expression of oocytes and their surrounding somatic cells and the dialogs between these cells are critical to this *** this study,we accurately classified the oocyte and follicle development into nine stages and profiled the gene expression of mouse oocytes and their surrounding granulosa cells and cumulus *** clustering of the transcriptomes showed the trajectories of two distinct development courses of oocytes and their surrounding somatic *** expression changes precipitously increased at Type 4 stage and drastically dropped afterward within both oocytes and granulosa ***,the number of differentially expressed genes between oocytes and granulosa cells dramatically increased at Type 4 stage,most of which persistently passed on to the later ***,cell communications within and between oocytes and granulosa cells became active from Type 4 stage *** dialogs connected oocytes and granulosa cells in both unidirectional and bidirectional ***2/3,TGFBR2/3,INHBA/B,and ACVR1/1B/2B of TGF-βsignaling pathway functioned in the follicle *** signaling pathway regulated the development of granulosa ***,many maternally DNA methylation-or H3K27me3-imprinted genes remained active in granulosa cells but silent in oocytes during ***,Type 4 stage is the key turning point when significant transcription changes diverge the fate of oocytes and granulosa cells,and the cell dialogs become active to assure follicle *** findings shed new insights on the transcriptome dynamics and cell dialogs facilitating the development and maturation of oocytes and follicles.

关键词： Folliculogenesis Oocyte Granulosa cell transcriptome Cell dialog

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transcriptome Analysis of Heterosis in Survival in the Hybrid Progenies of‘Haida No.1’and Orange-Shelled Lines of the Pacific Oyster Crassostrea gigas

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Journal of Ocean University of China 2024年第1期23卷 199-208页

作者： YANG Hang LI Qi Key Laboratory of Mariculture Ministry of EducationOcean University of ChinaQingdao 266003China

Heterosis has been exploited to enhance the yield and adaptability in various shellfish species;however,the molecular basis of it remains *** Pacific oyster Crassostrea gigas is one of the most economically important aquaculture species,and its productive traits can be improved by ***,an intraspecific cross between orange shell(O,10th generation)and‘Haida No.1’(H,13th generation)of *** was performed to assess the heterosis of survival *** rates of hybrid family(OH)and inbred families(HH and OO)were compared at larval stage,and eyed-pediveliger larvae of three families were subjected to transcriptome *** analysis results of best-parent heterosis and mid-parent heterosis showed that the hybrid family exhi-bited a high heterosis in survival relative to the parental *** OH-M(OH ***)and OH-P(OH ***)had 425 and 512 dif-ferentially expressed genes(DEGs),*** enrichment analysis of these DEGs revealed that the significantly enrich-ed genes function in virion binding,C-type lectin receptor signaling pathway,cellular defense response and other immune-related pro-cesses,which involves perlucin-like protein,CD209 antigen-like protein,ZNFX1,caspase-3 and acan *** differentially ex-pressed genes in OH-M and OH-P,together with the immune-related processes mentioned above may play an important role in the larval survival of *** addition,three genes(CYP450,fucolectin and perlucin-like)are associated with the orange shell and low survival of maternal oyster *** findings provide support for the application of hybrid with superior survival and will facilitate the understanding of heterosis formation in the Pacific oyster.

关键词： Crassostrea gigas survival rate heterosis transcriptome

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transcriptome analysis suggests broad jejunal alterations in Linghu’s obesity-diarrhea syndrome:A pilot study

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World Journal of Gastroenterology 2024年第21期30卷 2777-2792页

作者： Xiao-Tong Niu Xiang-Yao Wang Yan Wang Ke Han Nan Ru Jing-Yuan Xiang En-Qiang Linghu Medical School of Chinese PLA Chinese PLA General HospitalBeijing 100853China Department of Gastroenterology The First Medical Center of Chinese PLA General HospitalBeijing 100853China School of Medicine Nankai UniversityTianjin 300071China

BACKGROUND Obesity is associated with a significantly increased risk for chronic diarrhea,which has been proposed as Linghu’s obesity-diarrhea syndrome(ODS);however,its molecular mechanisms are largely *** To reveal the transcriptomic changes in the jejunum involved in *** In a cohort of 6 ODS patients(JOD group),6 obese people without diarrhea(JO group),and 6 healthy controls(JC group),high-throughput sequencing and bioinformatics analyses were performed to identify jejunal mucosal mRNA expression alterations and dysfunctional biological *** another cohort of 16 ODS patients(SOD group),16 obese people without diarrhea(SO group),and 16 healthy controls(SC group),serum diamine oxidase(DAO)and D-lactate(DLA)concentrations were detected to assess changes in intestinal barrier *** The gene expression profiles of jejunal mucosa in the JO and JC groups were similar,with only 1 differentially expressed gene(DEG).The gene expression profile of the JOD group was significantly changed,with 411 DEGs compared with the JO group and 211 DEGs compared with the JC group,129 of which *** enrichment analysis of these DEGs showed that the biological processes such as digestion,absorption,and transport of nutrients(especially lipids)tended to be up-regulated in the JOD group,while the biological processes such as rRNA processing,mitochondrial translation,antimicrobial humoral response,DNA replication,and DNA repair tended to be down-regulated in the JOD *** DEGs(CDT1,NHP2,EXOSC5,EPN3,NME1,REG3A,PLA2G2A,and PRSS2)may play a key regulatory role in the pathological process of ODS,and their expression levels were significantly decreased in ODS patients(P<0.001).In the second cohort,compared with healthy controls,the levels of serum intestinal barrier function markers(DAO and D-LA)were significantly increased in all obese individuals(P<0.01),but were higher in the SOD group than in the SO group(P<0.001).CONCLUSION Compared with health

关键词： Obesity Chronic diarrhea Jejunum transcriptome Intestinal barrier

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Physiological,transcriptome and gene functional analysis provide novel sights into cadmium accumulation and tolerance mechanisms in kenaf

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Journal of Environmental Sciences 2024年第3期137卷 500-514页

作者： Shan Cao Meng Wang Jiao Pan Dengjie Luo Samavia Mubeen Caijin Wang Jiao Yue Xia Wu Qijing Wu Hui Zhang Canni Chen Muzammal Rehman Sichen Xie Ru Li Peng Chen Guangxi Key Laboratory of Agro-environment and Agric-products safety Key Laboratory of Plant Genetics and BreedingCollege of AgricultureGuangxi UniversityNanning 530004China State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China

Kenaf is considered to have great potential for remediation of heavy metals in ***,studies on molecular mechanisms of root Cd accumulation and tolerance are still *** this study,two differently tolerant kenaf cultivars were selected as materials and the physiological and transcriptomic effects were evaluated under Cd *** study showed that 200μmol/L CdCl_(2) treatment triggered the reactive oxygen species(ROS)explosion and membrane lipid *** with the Cd-sensitive cultivar‘Z',the Cd-tolerant cultivar‘F'was able to resist oxidative stress in cells by producing higher antioxidant enzyme activities and increasing the contents of ascorbic acid(AsA)and glutathione(GSH).The root cell wall of‘F'exhibited higher polysaccharide contents under Cd treatment,providing more Cd-binding *** were 3,439 differentially expressed genes(DEGs)that were co-regulated by Cd treatment in two *** biosynthesis and plant hormone signal transduction pathways were significantly enriched by functional annotation *** associated with pectin,cellulose,and hemi-cellulose metabolism were involved in Cd chelation of root cell wall;V-ATPases,ABCC3 and Narmp3 could participated in vacuolar compartmentalization of Cd;PDR1 was responsible for Cd effux;the organic acid transporters contributed to the absorption of Cd in *** genes might have played key roles in kenaf Cd tolerance and Cd ***,HcZIP2 was identified to be involved in Cd uptake and transport in *** findings provide a deeper understanding of the molecular pathways underlying Cd accumulation and detoxification mechanisms in kenaf.

关键词： Kenaf Cd stress Physiological transcriptome HcZIP2

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Comparative transcriptome analysis reveals key genes and pathways in response to Alternaria alternata apple pathotype infection

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Horticultural Plant Journal 2024年第3期10卷 641-656页

作者： Kai Liu Zhaolin Liang An Yang Jiadi Yan Peihua Cong Xiaolei Han Caixia Zhang Key Laboratory of Horticultural Crop Germplasm Utilization of the Ministry of Agriculture and Rural Affairs(MOA) Research Institute of PomologyChinese Academy of Agricultural SciencesXingchengLiaoning 125100China

Apple leaf spot,caused by the Alternaria alternata apple pathotype(AAAP),is an important fungal disease of *** understand the molecular basis of resistance and pathogenesis in apple leaf spot,the transcriptomes of two apple cultivars‘Hanfu'(HF)(resistant)and‘Golden Delicious'(GD)(susceptible)were analyzed at 0,6,18,24 and 48 h after AAAP inoculation by *** each time point,a large number of significantly differentially expressed genes(DEGs)were screened between AAAP-inoculated and uninoculated apple *** of the common DEGs at four time points revealed significant differences in the resistance of‘HF'and‘GD'apple to AAAP ***,RNL,and JA signal-related genes were upregulated in both cultivars to restrict AAAP ***,genes encoding CNLs,TNLs,WRKYs,and AP2s were only activated in‘HF'as part of the resistance response,of which,some play major roles in the regulation of ET and SA signal *** analysis showed that many DEGs with opposite expression trends in the two hosts may play important regulatory roles in response to AAAP *** expression of one such gene MdERF110 in‘GD'apple leaves improved AAAP ***,this study highlights the reasons for differential resistance to AAAP infection between‘HF'and‘GD'apples which can theoretically assist the molecular breeding of disease-resistant apple crops.

关键词： Apple transcriptome Alternaria alternata apple pathotype Infection Defense response

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A transcriptome Analysis of Neural Tissue of Litopenaeus vannamei After Acute Exposure to Alexandrium pacificum

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Journal of Ocean University of China 2024年第2期23卷 529-538页

作者： YANG Huijie HUANG Xianghu MA Yukun HU Zhangxi ZHANG Ning LI Changling ZHANG Yulei Department of Aquaculture College of FisheriesGuangdong Ocean UniversityZhanjiang 524088China Guangdong Laboratory of Marine Ecology Environment Monitoring and Warning Zhanjiang 524088China

Alexandrium pacificum(***)is a typical paralytic shellfish poisonous *** algal blooms(HABs)caused by this species can bring serious environmental problems and economic losses to the aquaculture *** this study,transcriptome sequencing and analyses were performed on the neural tissue of Litopenaeus vannamei(***)after acute exposure to *** disrupted solution for 72 h,and differentially expressed genes(DEGs)were *** results showed that,compared with the control samples,300 DEGs were identified in the experimental group,of which 194 were up-regulated,and 106 *** gene ontology(GO)functional enrichment analysis showed that DEGs were significantly enriched in the cortical cytoskeleton organization,troponin complex,amylo-alpha-1,6-glucosidase and thymidine *** encyclopedia of genes and genomes(KEGG)enrichment analysis found that DEGs were mainly enriched in the oxidative phosphorylation process,intercellular tight junctions and *** results showed that the proteoglycans,signaling pathways,and various metabolic processes that regulate cell proliferation,differentiation,and apoptosis all played an essential role in the response of *** to *** toxins.

关键词： Litopenaeus vannamei Alexandrium pacificum paralytic shellfish poisoning transcriptome nerve

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Investigating the Impact of Ocean Acidification on Anti-Stress Mechanisms in Sepia esculenta Larvae Based on transcriptome Profiling

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Journal of Ocean University of China 2024年第4期23卷 1054-1066页

作者： WANG Yongjie LIU Xiumei LV Tingjin WANG Weijun SUN Guohua YANG Jianmin LI Zan School of Agriculture Ludong UniversityYantai 264025China College of Life Sciences Yantai UniversityYantai 264005China Yantai Institute of Marine Economy Yantai 264003China

With the rapid development of oil,energy,power and other industries,CO_(2) emissions rise sharply,which will cause a large amount of CO_(2) in the air be absorbed by the ocean and lead to ocean *** growth and development of organisms can be seriously affected by acidified *** esculenta is a mollusk with high nutritional and economic value and is widely cultured in offshore waters of *** are the early life forms of the organism and are more vulnerable to changes in the external *** low pH will lead to some adverse reactions in larvae,which will affect metabolism,immune response and other life *** this study,we sequenced the transcriptome of *** subjected to acidified seawater stress and identified 1072differentially expressed genes(DEGs).The detected atypical expression of DEGs substantiates cellular malformation and translocation in *** under low pH ***,this also substantiates the notable impact of ocean acidification on *** DEGs were used for functional enrichment analysis of GO and KEGG,and the top twenty items of the biological process classification in GO terms and 11 KEGG signaling pathways were significantly ***,the constructed proteinprotein interaction network(PPI)was used to analyze protein-protein interactions,and 12 key DEGs and 3 hub genes were *** reliability of 12 genes was verified by quantitative RT-PCR.A comprehensive analysis of the KEGG signaling pathway and PPI revealed that ocean acidification leads to abnormalities in lipid metabolism in *** larvae,which can lead to cancer development and metastasis,accompanied by some degree of *** results of the study will help to further investigate the physiological processes of *** when stimulated by ocean acidification,and provide a reference to cope with the captive breeding of *** affected by acidification.

关键词： Sepia esculenta ocean acidification protein-protein interaction network transcriptome immunity

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Comparative transcriptome Analysis of Shell-Matrix-Protein Genes and Observation of the Shell Microstructure in the Deep-Sea Clam Calyptogena marissinica

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Journal of Ocean University of China 2024年第3期23卷 797-810页

作者： SHI Yu LIU Dongting YAO Gaoyou HE Maoxian CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology Guangdong Provincial Key Laboratory of Applied Marine BiologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou 510301China Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou) Guangzhou 511458China University of Chinese Academy of Sciences Beijing 100049China

The deep-sea clam Calyptogena marissinica is widely distributed in the Haima cold seep ecosystem on the northwes-tern slope of the South China Sea with low pH values,low temperature and high *** information is available on the biomineralization of this *** this research,we generated a comprehensive transcript dataset of ***’s mantle tissue,and a total of 19821 unigenes were *** shell matrix proteins(SMP)-related genes were *** qPCR results showed that four out of six prismatic matrix genes(MSP2,MSP5,prisilkin-39,and shematrin),four out of the six nacreous matrix genes(perlucin,pif,pif97,and papilin),and two extrapallial fluid proteins(SPARC and calmodulin)were significantly expressed in the *** the nacreous and the prismatic layers are chrysanthemum-shaped,which are stacked on the top of each other to form a laminated nacreous *** alignment and phylogenetic analysis of MSP-5,Prisilkin-39,Perlucin,and Pif homologues showed that some amino acids of *** that differed from those detected in other molluscs may cause the different shape of the nacreous and prismatic layers,but do not lead to a change in the species’evolutionary *** results indicated the conservation of the functions of SMP-related genes in ***,and the specific shape of the prismatic and nacreous layers of this deep-sea mollusc,which will contribute to the research on the molecular regulation mechanisms of biomineralization in *** and provide a new perspective to investigate biomineralization in deep-sea clams in general.

关键词： transcriptome biomineralization mantle tissue shell Calyptogena marissinica

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