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Full-Length Transcriptome Analysis of the Pituitary of Pre-Matured and Artificially Matured Female Japanese Eel(Anguilla japonica) 认领 引用
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作者 GAO Yu LI Jiangling +10 位作者 FENG Zhenguang HUANG Mingxi LI Wen XU Ruihan CHEN Ruoxue BAN Yu LIANG Jingjie HUANG Yan XIE Yangjie CHEN Jianchun CHEN Tiansheng 《Journal of Ocean University of China》 SCIE CAS CSCD 2026年第3期1041-1054,共14页
The Japanese eel(Anguilla japonica)is a catadromous migratory fish with a high economic value.The gonads of captive eels do not mature naturally.Under artificial maturation,the hypothalamic-pituitary-gonadal(HPG)axis ... The Japanese eel(Anguilla japonica)is a catadromous migratory fish with a high economic value.The gonads of captive eels do not mature naturally.Under artificial maturation,the hypothalamic-pituitary-gonadal(HPG)axis is activated,and the maturation coefficient of the gonads increased significantly.Prior research investigations into Japanese eel breeding have primarily focused on elucidating the mechanisms underlying gonadal development.However,the problems plaguing the artificial breeding of Japanese eels have remained unsolved.Additionally,the insights into the molecular mechanisms within the pituitary,which acts as an upstream regulatory hub,and its impact on ovarian development are limited.To address these,the pre-matured pituitary(PP)and artificially matured pituitary(AP)tissues from female Japanese eels were subjected to transcriptomics using a method combining PacBio Iso-seq with Illumina RNA-Seq.PacBio sequencing produced 19576 filtered consensus sequences from PP and 39828 from AP.Then,we predicted gene regulatory elements such as alternative polyadenylation,transcription factors,and long noncoding RNAs.A total of 3016 differentially expressed genes(DEGs)were identified based on the Illumina RNA-seq data.Further gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed.Several DEGs that were upregulated in the pituitary were identified.These genes,including nr5a2,pgr,greb1,smad4,bmp5,ar,lhb,adcy5,and tgfbr3,most likely regulate downstream gonadal development via the pituitary.In conclusion,this study obtained the differential expression and full-length transcriptomes of the pituitary in the pre-matured and artificially matured female Japanese eel.These results offer substantial evidence for developing more efficient sex hormones during the captive breeding of eels,while also furnishing a scientific basis for the conservation of eel resources. 展开更多
关键词 Anguilla japonica pituitary transcriptome analysis gonad maturation
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A genome-wide association study integrated with transcriptome analysis to identify boron efficiency-related candidate genes and favorable haplotypes in Brassica napus L. 认领 引用
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作者 Ziwei Zhang Haoqiang Zhai +2 位作者 Yingpeng Hua Sheliang Wang Fangsen Xu 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2026年第7期2723-2738,共16页
Rapeseed(Brassica napus L.)is a major oil crop worldwide that is vigorously promoted for cultivation in China.Boron(B)is an essential micronutrient for plant growth and development.However,the agricultural soils in ra... Rapeseed(Brassica napus L.)is a major oil crop worldwide that is vigorously promoted for cultivation in China.Boron(B)is an essential micronutrient for plant growth and development.However,the agricultural soils in rapeseed planting areas often show either B deficiency or severe B deficiency.Increasing the resistance to B deficiency is a pivotal goal in the breeding of rapeseed,yet the genetic basis for variations in B efficiency-related traits remains unclear.In this study,a natural population with 391 rapeseed accessions and a nutrient solution system were used to investigate B efficiency-related traits,including relative root length(RRL),shoot dry weight(SDW),root dry weight(RDW),and B efficiency coefficient(BEC),all of which exhibited extensive phenotypic variations under B deficiency.Through a genome-wide association study(GWAS)of B efficiency-related traits using high-density SNP markers obtained from whole-genome resequencing,106 significantly associated SNPs were identified by employing both the general linear model and the mixed linear model.Among these SNP loci,two prominent SNP clusters were detected on chrA03:14,087,835-14,764,672 and chrC03:20,110,319-22,135,492at low B levels across three repeated experiments of multiple traits.Integrating those results with a transcriptome analysis,four genes exhibiting higher differentially expressed fold-change along with favorable haplotypes within the promoter or coding region,BnaA03g29020D,BnaA03g29440D,BnaC03g33010D,and BnaC03g34490D,were identified as candidate genes that could potentially be involved in efficient B utilization,and their favorable haplotypes were found to improve seedling growth and productivity under B deficiency.Considering the lack of B mineral resources in China,the rapid and accurate identification of more B-efficient alleles and studying the genetic mechanism underlying crop responses to B deficiency have important theoretical and practical significance for cultivating B-efficient varieties and maintaining green,sustainable agriculture. 展开更多
关键词 rapeseed boron deficiency GWAS transcriptomic analysis favorable haplotypes B efficiency
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Comparative transcriptome analysis identifies key regulators of nitrogen use efficiency in chrysanthemum 认领 引用 被引量：1
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作者 Lijiao Ge Weihao Miao +8 位作者 Kuolin Duan Tong Sun Xinyan Fang Zhiyong Guan Jiafu Jiang Sumei Chen Weimin Fang Fadi Chen Shuang Zhao 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2025年第1期176-195,共20页
Nitrogen(N)is a limiting factor that determines the yield and quality of chrysanthemum.Genetic variation in N use efficiency(NUE)has been reported among chrysanthemum genotypes.We performed a transcriptome analysis of... Nitrogen(N)is a limiting factor that determines the yield and quality of chrysanthemum.Genetic variation in N use efficiency(NUE)has been reported among chrysanthemum genotypes.We performed a transcriptome analysis of two chrysanthemum genotypes,'Nannonglihuang'(LH,N-efficient genotype)and'Nannongxuefeng"(XF,N-inefficient genotype),under low N(0.4 mmol L-1N)and normal N(8 mmol L-1N)treatments for 15 d and an N recovery treatment for 12 h(low N treatment for 15 d and then normal N treatment for 12 h)to understand the genetic factors impacting NUE in chrysanthemum.The two genotypes exhibited contrasting responses to the different N treatments.The N-efficient genotype LH had significant superiority in agronomic traits,N accumulation and glutamine synthase activity under both normal N and low N treatments.Low N treatment promoted root growth in LH,but inhibited root growth in XF.Transcriptome analysis revealed that the low N treatment increased the expression of some N metabolism genes,genes related to auxin and abscisic acid signal transduction in the roots of both genotypes,as well as genes related to gibberellin signal transduction in roots of LH.The N recovery treatment just increased the expression of genes related to cytokinin signal transduction in roots of LH.The expression levels of the NRT2.1,AMT1.1,and Gln1 genes related to gibberellin and cytokinin signal transduction were higher in roots of LH than in XF under different N treatments,suggesting that the genes related to N metabolism and hormone(auxin,abscisic acid,gibberellin,and cytokinin)signal transduction in roots of LH are more sensitive to different N treatments than those of XF.Co-expression network analysis(WGCNA)also identified hub genes like bZIP43,bHLH93,NPF6.3,IBR10,MYB62,PP2C,PP2C06 and NLP7,which may be the key regulators of N-mediated responses in chrysanthemum and play crucial roles in enhancing NUE and resistance to low N stress in the N-efficient chrysanthemum genotype.These results revealed the key factors involved in regulating NUE in chrysanthemum at the genetic level,which provides new insights into the complex mechanism of efficient nitrogen utilization in chrysanthemum,and can be useful for the improvement and breeding of high NUE chrysanthemum genotypes. 展开更多
关键词 chrysanthemum genotype NUE gene expression transcriptome analysis
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Global Transcriptome Analysis of Rice Seedlings in Response to Extracellular ATP 认领 引用 被引量：1
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作者 Chaemyeong LIM Sae Hyun LEE +7 位作者 Haeun LEE So-Yon PARK Kiyoon KANG Hyeryung YOON Tae-Jin YANG Gary STACEY Nam-Chon PAEK Sung-Hwan CHO 《Rice science》 SCIE CSCD 2025年第3期380-399,共20页
Herbivorous insects and pathogens cause severe damage to rice tissues,affecting yield and grain quality.Damaged cells trigger downstream defense responses through various signals.Extracellular ATP(eATP),a signaling mo... Herbivorous insects and pathogens cause severe damage to rice tissues,affecting yield and grain quality.Damaged cells trigger downstream defense responses through various signals.Extracellular ATP(eATP),a signaling molecule released during mechanical cell damage,is considered a constitutive damage-associated molecular pattern(DAMP),which is crucial for initiating plant defense responses.Thus,understanding how rice plants cope with DAMPs such as eATP is essential.Here,we found that exogenous ATP affected rice growth and development,cell wall composition,chloroplast development,and cell death.Subsequent global transcriptome analysis revealed that several pathways were involved in the eATP response,including genes related to cell surface receptors,cell wall organization,chlorophyll biosynthesis,heat and temperature stimulation,epigenetic regulation,and reactive oxygen species metabolism.Cell surface receptors,including members of the lectin receptor-like kinases(LecRKs),were found to participate in the eATP response.We further investigated ATP-induced genes in T-DNA activation mutants of OsLecRKs,demonstrating their involvement in eATP signaling in rice.This study confirms a DAMP-mediated transcriptional response in plants and provides novel candidates for advancing resistant rice breeding against insect herbivores and pathogens. 展开更多
关键词 extracellular ATP damage-associated molecular pattern RNA-sequencing transcriptome analysis rice
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Transcriptome Analysis of the Susceptibility to High Temperature of the Tetraploid Pacific Oyster Crassostrea gigas 认领 引用
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作者 BAI Xianchao ZHOU Yaru +3 位作者 BI Wenlong HU Hong XU Chengxun LI Qi 《Journal of Ocean University of China》 SCIE CAS CSCD 2025年第3期721-734,共14页
Tetraploid oysters frequently exhibit growth and survival rates inferior to diploid and triploid oysters.Tetraploid Pacific oysters(Crassostrea gigas)are pivotal as broodstock in the triploid C.gigas industry.However,... Tetraploid oysters frequently exhibit growth and survival rates inferior to diploid and triploid oysters.Tetraploid Pacific oysters(Crassostrea gigas)are pivotal as broodstock in the triploid C.gigas industry.However,the high mortality of tetraploid C.gigas has occurred in production practice with the increasing temperature.The transcriptional patterns of high temperature-susceptible and-tolerant tetraploid C.gigas were compared in response to prolonged thermal treatment.The H was defined as oysters that have not been thermally treated.The susceptible and tolerant oysters after thermal treatment were designed as TS and TH,respectively.The survival rate of tetraploid C.gigas was low(6.33%±2.87%)after thermal treatment.A total of 5147,5250,and 433 differentially expressed genes(DEGs)were detected in TS vs.TH,TS vs.H,and TH vs.H groups,respectively.Functional enrichment analysis indicated that DEGs were notably enriched in various pathways,including the NF-kappa B signaling pathway,apoptosis,TNF signaling pathway,and arginine and proline metabolism,across both TS vs.TH and TS vs.H groups.Among the DEGs under thermal treatment in susceptible oysters,the translation regulation genes like eIF2a kinase 1,eIF2a kinase 3,MKNK1,and ATF-4 exhibited differential expressions.Susceptible oysters displayed a higher number of differentially expressed IAP genes compared to tolerant oysters,while the expression pattern of HSP genes differed between susceptible and tolerant oysters.This study underscores the contrasting response of susceptible and tolerant tetraploid C.gigas to thermal treatment,suggesting that high temperature-susceptible tetraploid C.gigas may be more responsive to rapid alterations in immune response and apoptosis compared to high temperature-tolerant tetraploid C.gigas.It is necessary to improve the high temperature tolerance of tetraploid C.gigas by selective breeding to promote the development of the triploid industry. 展开更多
关键词 Crassostrea gigas tetraploid thermal treatment survival rate transcriptome analysis
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Transcriptome analysis revealed the molecular mechanism by which Chrysanthemum naktongense roots respond to low-concentration lanthanum treatment 认领 引用
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作者 Yaohui Gao Ruiqing Zhang +3 位作者 Ning Xu Ying Song Shiao Chen Miao He 《Ornamental Plant Research》 2025年第1期394-405,共12页
Chrysanthemum naktongense(C.naktongense)is widely distributed in northern China,and has high biomass and strong resistance.Lanthanum is a nonessential heavy metal element in plants,and it affects C.naktongense growth ... Chrysanthemum naktongense(C.naktongense)is widely distributed in northern China,and has high biomass and strong resistance.Lanthanum is a nonessential heavy metal element in plants,and it affects C.naktongense growth and development at high concentrations.Roots are important organs in C.naktongense in terms of plant response to lanthanum treatment.The molecular mechanisms of C.naktongense root response to lanthanum treatment over different durations have not been clarified.The whole roots of C.naktongense were sampled after lanthanum treatment for 0,24,and 72 h.A total of 5,451 differentially expressed genes(1,954 DEGs upregulated and 1,943 downregulated),were identified via RNA-seq.GO enrichment analysis of the top 20 genes revealed that many upregulated DEGs related to biological processes such as secondary metabolic processes and hormone metabolic processes were significantly(p<0.05)enriched.The concentration analysis results of the top 20 KEGG pathways revealed that many of the upregulated DEGs that were significantly(p<0.05)enriched were related to the plant hormone signal transduction pathway.This may be the key to root response to lanthanum treatment.Furthermore,we identified and analyzed 16 CnHsp70s by bioinformatics,the results of qRT-PCR and RNA-seq indicated numerous Hsp70 genes were upregulated under the two durations of treatment,and these genes can serve as good candidates for lanthanum-enriching genes.This study presents a new molecular mechanism by which C.naktongense responds to lanthanum treatment,laying a foundation for the targeted breeding of ornamental flowers in lanthanum-containing soil. 展开更多
关键词 heavy metal element molecular mechanisms Root response Lanthanum treatment Transcriptome analysis Hormone metabolic processes chrysanthemum naktongense cnaktongense Chrysanthemum naktongense
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Physiological and transcriptome analysis of Roucongbing disease in Chinese bayberry(Morella rubra Sieb.et Zucc) 认领 引用
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作者 Li Sun Yetong Qi +4 位作者 Yang Zhang Zheping Yu Xiliang Zheng Xingjiang Qi Shuwen Zhang 《Fruit Research》 2025年第1期234-243,共10页
Chinese bayberry(Morella rubra Sieb.et Zucc)is a characteristic fruit of China with high nutritional value.The frequent occurrence of Roucongbing disease in bayberry fruits has been a major problem affecting productio... Chinese bayberry(Morella rubra Sieb.et Zucc)is a characteristic fruit of China with high nutritional value.The frequent occurrence of Roucongbing disease in bayberry fruits has been a major problem affecting production and marketing in recent years.Unfortunately,the causes and the response mechanisms of this disease are still unclear,which makes it extremely difficult to prevent and treat.In this study,the overall nutrient content between diseased trees and control(non-diseased)trees were compared,which suggested that Mn might be associated with resistance to Roucongbing disease.A comparative analysis of the endogenous hormone profiles between healthy and diseased fruits from the same tree revealed significant differences,with jasmonic acid(JA),gibberellin(GA),abscisic acid(ABA),and auxin(IAA)exhibiting pronounced increments in the diseased fruits.The transcriptome analysis showed that the differentially expressed genes(DEGs)were mainly enriched in the plant-pathogen interaction pathway,which included multiple genes encoding some WRKY transcription factor family members,and the pathogenesis-related protein PR1.Our results indicated a strong correlation between the DEGs of these pathways and JA signaling,implying that the upregulation of genes involved in JA biosynthesis might serve as a pivotal defensive response against Roucongbing disease in bayberry fruits.Furthermore,the expression patterns of select DEGs were validated by quantitative Real-time PCR(qRT-PCR).This study explored the response mechanism at physiological and molecular levels,providing a theoretical foundation for the prevention and control of Roucongbing disease and the breeding of resistant cultivars. 展开更多
关键词 overall nutrient content Morella rubra roucongbing disease transcriptome analysis prevent treatin production marketing physiological analysis diseased trees
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Transcriptome Analysis Provides New Insights into Bulbil Formation in Bistorta vivipara 认领 引用
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作者 Weimin Zhao Guomin Shi +6 位作者 Jialei Guo Guifang He Peilan Li Xiaoying Ren Leqi Yang Taikun Qi Tao He 《Phyton-International Journal of Experimental Botany》 SCIE 2025年第2期393-406,共14页
Bistorta vivipara is a facultative reproductive plant capable of asexual reproduction through underground rhizomes and bulbils,as well as sexual reproduction via seeds.The phenomenon of vegetative organ vivipary is a ... Bistorta vivipara is a facultative reproductive plant capable of asexual reproduction through underground rhizomes and bulbils,as well as sexual reproduction via seeds.The phenomenon of vegetative organ vivipary is a complex biological process regulated by a network of genes.However,the developmental mechanism regulating bulbil vivipary in B.vivipara remains largely unexplored.This study investigated different developmental stages of B.vivipara using RNA sequencing and transcriptome analysis.Approximately 438 million high-quality reads were generated,with over 61.65%of the data mapped to the de novo transcriptome sequence.A total of 154,813 reads were matched in at least one public database,and 49,731 genes were differentially expressed across developmental stages.Functional analysis revealed significant enrichment of these genes in phenylpropanoid biosynthesis,plant hormone signal transduction,protein processing,starch and sucrose metabolism,and plant-pathogen interaction.Ninety-four genes involved in phytohormones,plant pigments,enzymes,and transcription factors were identified as potential candidates for inducing vegetative organ vivipary.These differentially expressed genes(DEGs),detected through comparative transcriptome analysis,may serve as candidate genes for bulbil vivipary in B.vivipara,establishing a foundation for future studies on the molecular mechanisms underlying vegetative organ vivipary. 展开更多
关键词 Bistorta vivipara vegetative organ vivipary bulbil transcriptome analysis
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Transcriptome analysis of CsWOX1 mutant and overexpressing lines reveals downstream genes regulating cucumber leaf morphogenesis 认领 引用
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作者 Anran Zhang Xiangbao Li +4 位作者 Helong Zhang Yanxin Jiang Qingqing Li Junjun Shen Zheng Li 《Vegetable Research》 2025年第1期456-466,共11页
WUSCHEL-related homeobox 1(WOX1),categorized into the WUS clade,has been determined as the essential gene for leaf expansion as well as promoting leaf outgrowth along the mediolateral axis.The phenotypic characteristi... WUSCHEL-related homeobox 1(WOX1),categorized into the WUS clade,has been determined as the essential gene for leaf expansion as well as promoting leaf outgrowth along the mediolateral axis.The phenotypic characteristics of transgenic cucumber plants with CsWOX1 overexpression(CsWOX1-OE)and mutants(designated as mango fruit,mf)have been reported.Specifically,CsWOX1-OE cucumber plants exhibit leaves with a distinctive'butterfly-shaped'appearance,while mf mutants show a rapid reduction in the area of their leaf tips.In this study,RNA-Seq was employed to sequence the transcriptome of CsWOX1-OE to reveal its differentially expressed genes(DEGs).Combined with the transcriptome sequencing data of the mf mutant,GO classification,and KEGG pathway enrichment analyses were performed,revealing new links between the WOX1 protein and many core plant regulatory pathways.The further joint analysis identified 80 common DEGs between CsWOX1-OE and mf,with a significant proportion of these common DEGs being annotated to the circadian pathway and the auxin polarity transport pathway.Six genes(CsGI,CsFKF1,CsRVE6,CsRVE8,CsABCB,and CsPin1At)were selected for Y1H and Dual-LUC interaction validation experiments.These experiments demonstrated that CsWOX1 directly targets the promoters of CsRVE6,which regulates leaf expansion,and CsPin1At,which is involved in auxin polarity transport,thereby promoting their transcription.In conclusion,these findings provide a foundation for exploring the potential regulatory mechanisms associated with CsWOX1,expecting to contribute to the construction of a more comprehensive gene network for leaf morphogenesis. 展开更多
关键词 rapid reduction area their leaf ti overexpressing lines transgenic cucumber plants cswox overexpression cswox oe transcriptome analysis phenotypic characteristics cucumber plants mango fruitmf
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Transcriptome Analysis of Derris fordii and Derris elliptica to Identify Potential Genes Involved in Rotenoid Biosynthesis 认领 引用
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作者 Yanlin Pan Yibin Zhang +2 位作者 Xingui Wang Hongbo Qin Lunfa Guo 《Phyton-International Journal of Experimental Botany》 SCIE 2025年第1期123-136,共14页
Derris fordii and Derris elliptica belong to the Derris genus of the Fabaceae family, distinguished by their high isoflavonoid content, particularly rotenoids, which hold significance in pharmaceuticals and agricultur... Derris fordii and Derris elliptica belong to the Derris genus of the Fabaceae family, distinguished by their high isoflavonoid content, particularly rotenoids, which hold significance in pharmaceuticals and agriculture. Rotenone, as a prominent rotenoid, has a longstanding history of use in pesticides, veterinary applications, medicine, and medical research. The accumulation of rotenoids within Derris plants adheres to species-specific and tissue-specific patterns and is also influenced by environmental factors. Current research predominantly addresses extraction techniques, pharmacological applications, and pesticide formulations, whereas investigations into the biosynthesis pathway and regulatory mechanism of rotenoids remain relatively scarce. In this study, we observed notable differences in rotenone content across the roots, stems, and leaves of D. fordii, as well as within the roots of D. elliptica. Utilizing RNA sequencing (RNA-seq), we analyzed the transcriptomes and expression profiles of unigenes from these four tissues, identifying a total of 121,576 unigenes. Differentially expressed genes (DEGs) across four comparison groups demonstrated significant enrichment in the phenylpropanoid and flavonoid biosynthesis pathways. Key unigenes implicated in the rotenoid biosynthesis pathway were identified, with PAL, C4H, CHS, CHI, IFS, and HI4OMT playing critical roles in D. fordii, while IFS and HI4OMT were determined to be essential for rotenoid biosynthesis in D. elliptica. These findings enhance our understanding of the biosynthesis mechanism of rotenoids in Derris species. The unigenes identified in this study represent promising candidates for future investigations aimed at validating their roles in rotenoid biosynthesis. 展开更多
关键词 Derris fordii Derris elliptica RNA-seq rotenoid comparative transcriptomic analysis
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Toxoplasma gondii infection induces cell apoptosis via multiple pathways revealed by transcriptome analysis 认领 引用 被引量：8
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作者 Kaige DU Fei LU +5 位作者 Chengzuo XIE Haojie DING Yu SHEN Yafan GAO Shaohong LU Xunhui ZHUO 《Journal of Zhejiang University-SCIENCE B》 SCIE CAS CSCD 2022年第4期315-327,共13页
Toxoplasma gondii is a worldwide parasite that can infect almost all kinds of mammals and cause fatal toxoplasmosis in immunocompromised patients.Apoptosis is one of the principal strategies of host cells to clear pat... Toxoplasma gondii is a worldwide parasite that can infect almost all kinds of mammals and cause fatal toxoplasmosis in immunocompromised patients.Apoptosis is one of the principal strategies of host cells to clear pathogens and maintain organismal homeostasis,but the mechanism of cell apoptosis induced by T.gondii remains obscure.To explore the apoptosis influenced by T.gondii,Vero cells infected or uninfected with the parasite were subjected to apoptosis detection and subsequent dual RNA sequencing(RNA-seq).Using high-throughput Illumina sequencing and bioinformatics analysis,we found that pro-apoptosis genes such as DNA damage-inducible transcript 3(DDIT3),growth arrest and DNA damage-inducibleα(GADD45 A),caspase-3(CASP3),and high-temperature requirement protease A2(Htr A2)were upregulated,and anti-apoptosis genes such as poly(adenosine diphosphate(ADP)-ribose)polymerase family member 3(PARP3),B-cell lymphoma 2(Bcl-2),and baculoviral inhibitor of apoptosis protein(IAP)repeat containing 5(BIRC5)were downregulated.Besides,tumor necrosis factor(TNF)receptor-associated factor 1(TRAF1),TRAF2,TNF receptor superfamily member 10 b(TNFRSF10 b),disabled homolog2(DAB2)-interacting protein(DAB2 IP),and inositol 1,4,5-trisphosphate receptor type 3(ITPR3)were enriched in the upstream of TNF,TNF-related apoptosis-inducing ligand(TRAIL),and endoplasmic reticulum(ER)stress pathways,and TRAIL-receptor2(TRAIL-R2)was regarded as an important membrane receptor influenced by T.gondii that had not been previously considered.In conclusion,the T.gondii RH strain could promote and mediate apoptosis through multiple pathways mentioned above in Vero cells.Our findings improve the understanding of the T.gondii infection process through providing new insights into the related cellular apoptosis mechanisms. 展开更多
关键词 Toxoplasma gondii Transcriptome analysis Apoptosis Infection
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Transcriptome analysis reveals the regulatory mechanism by which MdWOX11 suppresses adventitious shoot formation in apple 认领 引用 被引量：5
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作者 Jiangping Mao Doudou Ma +6 位作者 Chundong Niu Xiaolong Ma Ke Li Muhammad Mobeen Tahir Shiyue Chen Xiuxiu Liu Dong Zhang 《Horticulture Research》 SCIE CSCD 2022年第1期1979-1991,共13页
Adventitious shoot(AS)regeneration accelerates plant reproduction and genetic transformation.WOX11 is involved in many biological processes,but its regulation of AS regeneration has not been reported.Here,we showed th... Adventitious shoot(AS)regeneration accelerates plant reproduction and genetic transformation.WOX11 is involved in many biological processes,but its regulation of AS regeneration has not been reported.Here,we showed that the genotype and CK/IAA ratio of apple leaves were the key factors that affected their capacity for AS formation.Moreover,the expression level of MdWOX11 was negatively correlated with the capacity for AS formation.Phenotypic analysis of MdWOX11 transgenic plants showed that overexpression of MdWOX11 inhibited AS formation.Endogenous hormone analysis demonstrated that the contents of auxin(IAA),cytokinin(CK),and abscisic acid(ABA)were higher in MdWOX11-RNAi plants than in MdWOX11-OE transgenic plants.We used RNA sequencing to examine the transcriptional responses of genes in MdWOX11-RNAi and MdWOX11-OE transgenic apple plants at different AS stages.We identified 8066 differentially expressed genes and focused our analysis on those involved in the IAA,CK,ABA,and gibberellin(GA)hormone signaling pathways.The expression of genes related to the CK signaling pathway and shoot development was higher in GL-3 than in MdWOX11-OE transgenic plants during the callus and AS emergence stages.However,the expression of MdCKX5 was higher in MdWOX11-OE transgenic plants than in GL3 and MdWOX11-RNAi transgenic plants.Yeast one-hybrid(Y1H)assays,dual-luciferase reporter assays,and ChIP-qPCR showed thatMdWOX11 binds to the promoter of MdCKX5,and a dual-luciferase reporter assay showed that MdWOX11 enhanced the promoter activity of MdCKX5.We concluded that MdCKX5 acts downstream of MdWOX11 to control AS formation,and we built a regulatory model of the suppression of AS formation by MdWOX11 in apple. 展开更多
关键词 transgenic plants regulatory mechanism adventitious shoot formation biological processesbut apple leaves genetic transformationwox transcriptome analysis mdwox
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Metabolome profiling and transcriptome analysis unveiling the crucial role of magnesium transport system for magnesium homeostasis in tea plants 认领 引用 被引量：4
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作者 Jing Li Ting Wen +7 位作者 Ruiming Zhang Xinlong Hu Fei Guo Hua Zhao Pu Wang Yu Wang Dejiang Ni Mingle Wang 《Horticulture Research》 SCIE CSCD 2024年第7期335-352,共18页
Magnesium(Mg 2+)is a crucial nutrient for the growth and development of Camellia sinensis and is closely related to the quality of tea.However,the underlying mechanisms responding to low-Mg 2+stress in tea plant... Magnesium(Mg 2+)is a crucial nutrient for the growth and development of Camellia sinensis and is closely related to the quality of tea.However,the underlying mechanisms responding to low-Mg 2+stress in tea plants remain largely unknown.In this study,photosynthetic parameters,metabolomics,and transcriptomics were utilized to explore the potential effects of low Mg2+on the growth and metabolism of C.sinensis.Low-Mg 2+treatment increased the ratio of shoot dry weight to root dry weight but decreased the photosynthesis of C.sinensis.Forty and thirty metabolites were impacted by Mg 2+shortage in C.sinensis shoots and roots,respectively.Integrated transcriptome and metabolome analyses revealed the possible reasons for the decreased contents of chlorophyll and catechins and the increased theanine content in C.sinensis roots.Weighted gene co-expression network analysis indicated that the Mg 2+transport system was essential in the regulation of Mg 2+homeostasis in C.sinensis,in which CsMGT5 was identified to be the key regulator according to CsMGT5-overexpressing and complementary assays in Arabidopsis thaliana.Moreover,silencing of CsMGT5 in vivo reduced the content of chlorophyll in C.sinensis shoots.In addition,CsMGT5 might collaborate with ammonium transporters to keep the amino acid content steady,suggesting its potential application for tea quality improvement.All these findings demonstrate the key roles of CsMGTs for Mg 2+homeostasis in C.sinensis,providing a theoretical basis for Mg2+efficient utilization in plants. 展开更多
关键词 metabolome profiling metabolomics transcriptome analysis magnesium transport system camellia sinensis photosynthetic parameters transcriptomics magnesium homeostasis
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Physiological and transcriptome analysis elucidates the metabolic mechanism of versatile Porphyridium purpureum under nitrogen deprivation for exopolysaccharides accumulation 认领 引用 被引量：3
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作者 Liang Ji Shaohua Li +3 位作者 Cheng Chen Haojie Jin Haizhen Wu Jianhua Fan 《Bioresources and Bioprocessing》 SCIE EI 2021年第1期886-901,共16页
Porphyridium purpureum is a mesophilic,unicellular red alga rich in phycoerythrin,sulfate polysaccharides,and polyunsaturated fatty acids.Nitrogen deficiency inhibited the growth of P.purpureum and resulted in yellowi... Porphyridium purpureum is a mesophilic,unicellular red alga rich in phycoerythrin,sulfate polysaccharides,and polyunsaturated fatty acids.Nitrogen deficiency inhibited the growth of P.purpureum and resulted in yellowing of the cells and thickening of the extracellular viscousness sheath.Under nitrogen stress,the contents of total lipids and exopolysaccharides in P.purpureum were increased by 65.2% and 188.0%,respectively.We demonstrate that the immediate response of P.purpureum to nitrogen deficiency is mediated by carbon flow to polysaccharide synthesis,while the synthesis of lipids is enhanced as a permanent energy storage substance at the later stage.Based on transcriptome annotation information,we elucidate the synthesis pathway of polysaccharides from P.purpureum from the perspective of glycosyl-donor interconversion,and demonstrate that the n-6 pathway is the main synthesis pathway of polyunsaturated fatty acids.This study not only provides a production strategy for polysaccharides and fatty acids by single-celled marine red algae P.purpureum,but also provides targets for further genetic modification. 展开更多
关键词 Porphyridium purpureum Nitrogen deprivation Transcriptome analysis Exopolysaccharides Polyunsaturated fatty acids Phycoerythrin
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Comparative transcriptome analysis on the alteration of gene expression in ayu (Plecoglossus altivelis)larvae associated with salinity change 认领 引用 被引量：3
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作者 Xin-Jiang LU Hao ZHANG +2 位作者 Guan-Jun YANG Ming-Yun LI Jiong CHEN 《Zoological Research》 SCIE CSCD 2016年第3期126-135,共10页
Ayu （Plecoglossus altivelis） fish, which are an amphidromous species distributed in East Asia, live in brackish water （BW） during their larval stage and in fresh water （FW） during their adult stage. In this stud... Ayu （Plecoglossus altivelis） fish, which are an amphidromous species distributed in East Asia, live in brackish water （BW） during their larval stage and in fresh water （FW） during their adult stage. In this study, we found that FW-acclimated ayu larvae exhibited a slower growth ratio compared with that of BW-acclimated larvae. However, the mechanism underlying FW acclimation on growth suppression is poorly known. We employed transcriptome analysis to investigate the differential gene expression of FW acclimation by RNA sequencing. We identified 158 upregulated and 139 downregulated transcripts in FW-acclimated ayu larvae compared with that in BW-acclimated larvae. As determined by Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway mapping, functional annotation of the genes covered diverse biological functions and processes, and included neuroendo- crinology, osmotic regulation, energy metabolism, and the cytoskeleton. Transcriptional expression of several differentially expressed genes in response to FW acclimation was further confirmed by real-time quantitative PCR. In accordance with transcriptome analysis, iodothyronine deiodinase （ID）, pro-opiom- elanocortin （POMC）, betaine-homocysteine S-meth- yltransferase 1 （BHMT）, fructose-bisphosphate aldolase B （aldolase B）, tyrosine aminotransferase （TAT）, and Na＋-K＋ ATPase （NKA） were upregulated after FW acclimation. Furthermore, the mRNA expressions of b-type natriurefic peptide （BNP） and transgelin were downregulated after FW acclimation. Our data indicate that FW acclimation reduced the growth rate of ayu larvae, which might result from the expression alteration of genes related to endocrine hormones, energy metabolism, and direct osmoregulation. 展开更多
关键词 Plecoglossus altivelis Salinity change Transcriptome analysis Growth rate Real-time quantitative PCR
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Genome-wide transcriptome analysis reveals key regulatory networks and genes involved in the determination of seed hardness in vegetable soybean 认领 引用 被引量：2
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作者 Congcong Wang Jianyu Lin +6 位作者 Yuanpeng Bu Ruidong Sun Yang Lu JunYi Gai Han Xing Na Guo Jinming Zhao 《Horticulture Research》 SCIE CSCD 2024年第5期293-305,共13页
Seed hardness is an important quality trait of vegetable soybean.To determine the factors underlying seed hardness,two landraces with contrasting seed hardness,Niumaohuang(low seed hardness)and Pixiansilicao(high seed... Seed hardness is an important quality trait of vegetable soybean.To determine the factors underlying seed hardness,two landraces with contrasting seed hardness,Niumaohuang(low seed hardness)and Pixiansilicao(high seed hardness),were selected from 216 soybean accessions originating from 26 provinces in China.The contents of the main components in vegetable soybean seeds such as water,soluble sugar,starch,protein and oil were measured,and transcriptome analyses performed during five stages of seed developmental.Transcriptome analysis indicates that during the middle and late stages of seed development,a large number of genes involved in the synthesis or degradation of starch,storage protein,and fatty acids were differentially expressed,leading to differences in the accumulation of stored substances during seed maturation among Niumaohuang and Pixiansilicao.The activity of cell proliferation and the formation of cell walls in the middle and late stages of seed development may also affect the hardness of seeds to a certain extent.In addition,weighted gene co-expression network analysis(WGCNA)was undertaken to identify co-expressed gene modules and hub genes that regulate seed hardness.Overexpression of a candidate seed hardness regulatory hub gene,GmSWEET2,resulted in increased seed hardness.In this study,the important role of GmSWEET2 in regulating the hardness of vegetable soybean seeds was verified and numerous potential key regulators controlling seed hardness and the proportion of seed components were identified,laying the groundwork for improving the texture of vegetable soybean. 展开更多
关键词 vegetable soybean quality trait seed hardness vegetable soybeanto genome wide transcriptome analysis gene co expression network analysis seed development transcriptome analyses
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Transcriptome analysis of the influence of CPPU application for fruit setting on melon volatile content 认领 引用 被引量：1
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作者 CHENG Jin-tao CHEN Hai-wen +5 位作者 DING Xiao-chen SHEN Tai PENG Zhao-wen KONG Qiu-sheng HUANG Yuan BIE Zhi-long 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2021年第12期3199-3208,共10页
In fruit production,the application of the plant growth regulator 1-(2-chloro-4-pyridyl)-3-phenylurea(CPPU)dulls the fruit aroma.Gas chromatography-mass spectrometry and transcriptome analyses were performed on CPPU-t... In fruit production,the application of the plant growth regulator 1-(2-chloro-4-pyridyl)-3-phenylurea(CPPU)dulls the fruit aroma.Gas chromatography-mass spectrometry and transcriptome analyses were performed on CPPU-treated and pollinated fruits to determine how CPPU affects the production of aroma in melon fruit.The results showed that the contents of two important esters(benzyl acetate and phenethyl acetate)in the CPPU-treated fruits were significantly lower than those in the pollinated fruits.Transcriptome sequencing data revealed that most differentially expressed genes were involved in“phenylalanine metabolism”pathway,and their expression was significantly decreased in the CPPU-treated fruits.Further analysis showed that the phenylalanine content in the CPPU-treated fruits was significantly higher than that in the pollinated fruits.In summary,CPPU application interferes with phenylalanine metabolism in melon fruits and affects the production of aromatic esters. 展开更多
关键词 aroma volatiles melon CPPU fruit set transcriptome analysis gas chromatography-mass spectrometry
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Transcriptome analysis unveils a potential novel role of VvAP1 in regulating the developmental fate of primordia in grapevine 认领 引用 被引量：2
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作者 Jie Arro Yingzhen Yang +3 位作者 Guo-qing Song Peter Cousins Zongrang Liu Gan-Yuan Zhong 《Fruit Research》 2024年第1期286-295,共10页
The grapevine shoot meristem contains undifferentiated primordia known as anlagen,which can develop into either inflorescences or tendrils depending on vine age,growth status,hormone balance,and other factors.Interest... The grapevine shoot meristem contains undifferentiated primordia known as anlagen,which can develop into either inflorescences or tendrils depending on vine age,growth status,hormone balance,and other factors.Interestingly,a gain-of-function mutation in the DELLA domain of VvDELLA1 in the dwarf mutant grape,Vitis vinifera L.cv.Pixie,virtually disrupts the normal developmental course of anlagen and reroutes tendrilbounded anlagen toward inflorescence development even at the juvenile stage.To understand the underlying mechanism(s),we compared the transcriptome profiles of V.vinifera cv.Pinot Meunier(from which Pixie was derived),Pixie,and three other V.vinifera grape cultivars(Dena,Gina,and Tia)which were derived from crosses involving Pixie and carry the same DELLA mutation.Our findings revealed significant mis-regulation of hundreds of genes,profoundly reshaping both transcriptome landscapes and regulatory pathways in the mutant grapes.Interestingly,VvAP1,a central positive flower regulator in annuals,was unexpectedly co-downregulated with VvTFL1a,a flowering repressor.We also found several other key flower regulators which were either upregulated(e.g.,VvFT,VvLFY)or downregulated(e.g.,VvSOC1s)in all mutant grapes,although the overall effect was moderate.These findings,along with the previous identification of tendril-specific expression of VvAP1 and inflorescencespecific expression of VvLFY,support that VvAP1 promotes anlagens to develop tendrils,whereas VvLFY favors inflorescences formation.The balance between these factors,particularly the abundance of VvAP1 transcripts,ultimately dictates whether anlagens develop into tendrils or inflorescences. 展开更多
关键词 developmental fate tendril primordia VVDella undifferentiated primordia transcriptome analysis grapevine VVAP
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Transcriptome analysis reveals steroid hormones biosynthesis pathway involved in abdominal fat deposition in broilers 认领 引用 被引量：1
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作者 Yuting Zhu Yongli Wang +3 位作者 Yidong Wang Guiping Zhao Jie Wen Huanxian Cui 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2024年第9期3118-3128,共11页
Excessive abdominal fat deposition reduces the feed efficiency and increase the cost of production in broilers.Therefore,it is an important task for poultry breeders to breed broilers with low abdominal fat.Abdominal ... Excessive abdominal fat deposition reduces the feed efficiency and increase the cost of production in broilers.Therefore,it is an important task for poultry breeders to breed broilers with low abdominal fat.Abdominal fat deposition is a highly complex biological process,and its molecular basis remains elusive.In this study,we performed transcriptome analysis to compare gene expression profiles at different stages of abdominal fat deposition to identify the key genes and pathways involved in abdominal fat accumulation.We found that abdominal fat weight(AFW)increased gradually from day 35(D35)to 91(D91),and then decreased at day 119(D119).Accordingly,after detecting differentially expressed genes(DEGs)by comparing gene expression profiles at D35 vs.D63 and D35 vs.D91,and identifying gene modules associated with fat deposition by weighted gene co-expression network analysis(WGCNA),we performed intersection analysis of the detected DEGs and WGCNA gene modules and identified 394 and 435 intersecting genes,respectively.The results of the Gene Ontology(GO)functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses showed that the steroid hormone biosynthesis and insulin signaling pathways were co-enriched in all intersecting genes,steroid hormones have been shown that regulated insulin signaling pathway,indicating the importance of the steroid hormone biosynthesis pathway in the development of broiler abdominal fat.We then identified 6 hub genes(ACTB,SOX9,RHOBTB2,PDLIM3,NEDD9,and DOCK4)related to abdominal fat deposition.Further analysis also revealed that there were direct interactions between 6 hub genes.SOX9 has been shown to bind to proteins required for steroid hormone receptor binding,and RHOBTB2 indirectly regulates the steroid hormones biosynthesis through cyclin factor,and ultimately affect fat deposition.Our results suggest that the genes RHOBTB2 and SOX9 play an important role in fat deposition in broilers,by regulating steroid hormone synthesis.These findings provide new targets and directions for further studies on the mechanisms of fat deposition in chicken. 展开更多
关键词 broilers abdominal fat deposition transcriptome analysis hub genes steroid hormones biosynthesis pathway
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BpMADS12 gene role in lignin biosynthesis of Betula platyphylla Suk by transcriptome analysis 认领 引用 被引量：4
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作者 Huiyu Li Yang Yang +4 位作者 Zijia Wang Xiaohong Guo Feifei Liu Jing Jiang Guifeng Liu 《Journal of Forestry Research》 SCIE CAS CSCD 2016年第5期1111-1120,共10页
MADS-box transcription factors show highly diverse regulatory functions in a wide variety of organisms. In this study, we characterized a MADS-box gene （BpMADS12） from the white birch （Betula platyphylla Suk）. Thi... MADS-box transcription factors show highly diverse regulatory functions in a wide variety of organisms. In this study, we characterized a MADS-box gene （BpMADS12） from the white birch （Betula platyphylla Suk）. This gene is a member of the suppressor of overexpression of CO 1omato MADS 3 class of MADS-box genes. We generated lines overexpressing BpMADS12 and found that these had higher levels of lignin compared to that observed in nontransgenic lines. Transcriptome anal- ysis revealed numerous changes in gene expression patterns. In total, 8794 differentially expressed genes were identified, including 5006 upregulated unigenes and 3788 downregulated unigenes in BpMADS-overexpression lines. Differentially expressed genes involved in the pathways for lignin and brassinosteroid biosynthesis were significantly enriched and may have contributed to phenotypic changes. The results from a quantitative RT-PCR analysis were consistent those obtained with the transcriptome analysis.Our transcriptome analysis, in combination with measure- ment of lignin level, indicated that BpMADS12 promotes lignin synthesis through regulation of key enzymes in response to brassinosteroid signaling. These results suggest that this MADS-box protein is crucial to all subsequent structural events and provide a good foundation for studies aiming to elucidate the developmental mechanisms underlying formation of wood. 展开更多
关键词 Betula platyphylla . BpMADS12 - Ligninbiosynthesis - Transcriptome analysis
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