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Integrated Physiological and Transcriptomic Analysis Reveals Key Transcriptional Responses to Prolonged Heat Stress in Chinese Cabbage 认领 引用
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作者 Jongwon Park Jinhyoung Lee +5 位作者 Gunhee Lee Eunji Lee Jiwoo Kim Seunghwan Wi Tae-Cheol Seo Seonghoe Jang 《Phyton-International Journal of Experimental Botany》 SCIE 2026年第6期248-270,共23页
Heat stress severely impairs plant growth and productivity,particularly in cool-season crops such as Chinese cabbage(Brassica rapa subsp.pekinensis).While short-term heat responses have been extensively studied,the me... Heat stress severely impairs plant growth and productivity,particularly in cool-season crops such as Chinese cabbage(Brassica rapa subsp.pekinensis).While short-term heat responses have been extensively studied,the mechanisms underlying prolonged heat stress adaptation remain insufficiently understood.In this study,we conducted an integrative analysis of Chinese cabbage exposed to sustained high temperatures.Our approach combined physiological characterization,antioxidant profiling,and transcriptome-wide gene expression analysis to dissect long-term heat stress responses.Prolonged heat stress caused marked growth inhibition,including leaf chlorosis and a 39%reduction in leaf length by day 9.Biochemical analyses revealed a progressive accumulation of ROS,indicated by elevated MDA content,while increased SOD and APX activities reflected active antioxidant responses.Transcriptome analysis identified over 10,000 DEGs at both 2 and 5 days,reflecting dynamic transcriptional reprogramming.GO and KEGG enrichment highlighted a temporal shift from RNA modification to protein synthesis pathways.Six transcription factors,including BrHSF B-1,BrNAC13,and BrbZIP43,were strongly induced,suggesting roles as early and persistent stress responders.Together,our findings offer a comprehensive,time-resolved view of B.rapa responses to prolonged heat stress and offer potential molecular targets for enhancing thermotolerance in Brassica breeding programs. 展开更多
关键词 Chinese cabbage heat stress reactive oxygen species transcription factor transcriptome analysis
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Selection and transcriptomic analysis of coagulase-negative Staphylococcus with high proteolytic activity isolated from Chinese Dong fermented pork(Nanx Wudl) 认领 引用
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作者 Suyue Xiong Ruifang Mi +5 位作者 Xi Chen Hang Gao Xiao Tan Ruixi Liu Jiapeng Li Shouwei Wang 《Food Science and Human Wellness》 SCIE CAS CSCD 2025年第10期4200-4212,共13页
Although coagulase-negative Staphylococcus(CNS),along with technological activities,plays a key role in fermented sausage flavour and nutrient production,the molecular mechanism of these activities remains elusive.In ... Although coagulase-negative Staphylococcus(CNS),along with technological activities,plays a key role in fermented sausage flavour and nutrient production,the molecular mechanism of these activities remains elusive.In this study,18 CNS strains with high proteolytic activity were isolated from Chinese Dong fermented pork(Nanx Wudl),and their technological and transcriptomic properties were investigated.After biochemical identification and genetic analysis,their technological properties,including nitrate reductase,catalase,antioxidant,and lipolytic activities and their growth under varying temperatures,salt concentrations,and p H levels were evaluated.Their aroma-producing potential was also determined in a model medium resembling fermented sausages.Transcriptomic analysis was performed using the most promising isolates.Biochemical identification and 16S rDNA sequencing revealed that the 18 Staphylococcus strains belonged to Staphylococcus xylosus,Staphylococcus saprophyticus,Staphylococcus carnosus,Staphylococcus sciuri,and Staphylococcus equorum.In terms of technological properties,16 strains showed a nitrate-reducing ability,while 11 strains had a lipolytic activity.All strains exhibited superoxide dismutase(SOD)and catalase activities;four strains displayed an SOD activity of>50%.They also tolerated 10%NaCl and 150 mg/kg of nitrite.They showed significant differences in ketone and acid production.The transcriptomic analysis of S.xylosus strains Sx3 and Sx6,which were selected because of their excellent enzymatic activities and aroma-producing ability,revealed the remarkable effect of genes related to pyruvate catabolism and amino acid metabolism on aroma generation.Therefore,this study provided valuable insights into the metabolic mechanisms underlying the technological properties of CNS and identified promising candidates as starter cultures in fermented sausage manufacturing. 展开更多
关键词 Staphylococcus xylosus Nanx Wudl Proteolytic activity Starter culture Transcriptomic analysis
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High-throughput transcriptomic analysis of circadian rhythm under different photoperiods in carrot 认领 引用
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作者 Nan Zhang Zhi-Hang Hu +4 位作者 Li-Xiang Wang Chen Chen Jing Zhuang Hui Liu Ai-Sheng Xiong 《Vegetable Research》 2025年第1期79-89,共11页
Carrot(Daucus carota L.)is an important root vegetable crop belonging to the Apiaceae family.The biological clock,or circadian rhythm,is typically a 24 h endogenous cycle that plays a crucial role in how higher plants... Carrot(Daucus carota L.)is an important root vegetable crop belonging to the Apiaceae family.The biological clock,or circadian rhythm,is typically a 24 h endogenous cycle that plays a crucial role in how higher plants perceive environmental changes through its function as an internal timing molecular network.Photoperiod regulates growth and development processes,and also affects the chlorophyll synthesis of carrot plants.This study employed highthroughput transcriptome analysis technology to investigate changes in gene expression within chlorophyll metabolism-related genes of carrots under different treatments in a single photoperiod(24 h).Three distinct environments were used:photoperiodic lighting(16 h of light:8 h of dark,16L/8D),photoperiodic lighting(12 h of light:12 h of dark,12L/12D),and photoperiodic lighting(8 h of light:16 h of dark,8L/16D)conditions.Time-series sampling was conducted at 3 h intervals(24 h),during which chlorophyll values were measured.Subsequently,transcriptome sequencing was performed at four time points,and bioinformatics analysis was used to identify and annotate differentially expressed genes involved in chlorophyll metabolism.The present results demonstrate that long-day conditions(16L/8D)significantly promote the accumulation of chlorophyll a,chlorophyll b,and total chlorophyll in carrot leaves,with peak values reaching 1.160 and 0.486 mg·g-1at 15 h,respectively.Transcriptome analysis revealed numerous differentially expressed genes(DEGs)associated with the circadian rhythm and chlorophyll metabolism across the different photoperiods.Key chlorophyll biosynthetic genes,such as Hem and POR,were upregulated under long-day conditions,whereas genes like CAO and CHL showed differential expression patterns indicative of photoperiodic regulation.The present findings provide a potential molecular basis for understanding how photoperiods regulate chlorophyll metabolism in carrots,revealing the intrinsic mechanisms of circadian rhythm regulation in carrots. 展开更多
关键词 circadian rhythm root vegetable highthroughput transcriptome analysis technology photoperiod high throughput transcriptomic analysis biological clockor circadian rhythmis internal timing molecular networkphotoperiod
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High-throughput transcriptomic analysis of circadian rhythm of flavonoid metabolism under different photoperiods in celery 认领 引用
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作者 Chen Chen Ting Huang +11 位作者 Li-Xiang Wang Jin-Song Xiong Meng-Yao Li Guo-Fei Tan Pei-Zhuo Liu Ya-Peng Li Zhi-Hang Hu Hui Liu Heng-Min Lv Xiong You Jian-Ping Tao Ai-Sheng Xiong 《Vegetable Research》 2025年第1期216-226,共11页
Photoperiod is important for plants to predict the changing trend of the environment and adjust their physiological,metabolic rhythm.In this study,we investigated the transcriptional responses of celery(Apium graveole... Photoperiod is important for plants to predict the changing trend of the environment and adjust their physiological,metabolic rhythm.In this study,we investigated the transcriptional responses of celery(Apium graveolens L.),an important leaf vegetable whose physiological cycles were photoperioddependent,under two different light regimes for 24 h:truncated photoperiod(light/dark:6 h/6 h,recorded as T)and full periodic illumination(light/dark:24 h/0 h,recorded as F).Samples were collected continuously for high-throughput transcriptome sequencing and differentially expressed genes(DEGs)were annotated and analyzed.Compared with the treatment beginning,4,466~7,398 DEGs were identified in each sample,with the largest number between T0h vs T12h.For comparison between T24h and F24h,the number of DEGs was the lowest(3,056).GO annotation showed that DEGs were mainly enriched in biological processes and cell composition.KEGG enrichment pathway analysis showed that the DEGs were mainly concentrated in the secondary metabolism-related pathways(lysine,phenylalanine,and flavonoids).Compared to truncated photoperiod,full periodic illumination for 24 h enhanced the expression of flavonoid biosynthetic genes(particularly AgCHS,AgFNS,and AgF3'H)and increased flavonoid accumulation.Our results demonstrated that the transcriptional rhythms of celery were dynamically regulated by both light-dark cycles and circadian clock mechanisms,with flavonoid pathway genes exhibiting particular sensitivity to photoperiodic changes.These findings provide important insights into the molecular mechanisms underlying plant photoperiod responses and may serve as a valuable foundation for future research on the circadian regulation of plant metabolism and development. 展开更多
关键词 leaf vegetable full periodic illumination light dark circadian rhythm flavonoid metabolism transcriptional responses physiological cycles photoperiod high throughput transcriptomic analysis
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Integrated physiological and transcriptomic analysis reveals key drought tolerance mechanisms in Festuca rubra 认领 引用
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作者 Xianxian Liu Xinyue Xiong +4 位作者 Yuzhan Tang Yuqing Jing Yuqian Chen Hailong Zhang Qianqian Guo 《Grass Research》 2025年第1期21-31,共11页
Drought stress significantly impairs plants'growth and productivity.Festuca rubra,a perennial turfgrass,is valued for its strong drought tolerance.However,the integrated physiological and molecular mechanisms unde... Drought stress significantly impairs plants'growth and productivity.Festuca rubra,a perennial turfgrass,is valued for its strong drought tolerance.However,the integrated physiological and molecular mechanisms underlying this trait remain poorly understand.In this study,following 21 d of drought stress,systematic physiological and transcriptomic analyses were conducted on F.rubra.Compared with the well-watered controls,the plants under drought stressexhibited a significant decrease in key photosynthetic parameters,accompanied by a notable upregulation in antioxidant enzyme activities.Concurrently,these plants also showed an augmented accumulation of osmoregulatory substances,including proline and soluble sugars.Under drought stress,25,063differentially expressed genes(DEGs)were identified by transcriptome analysis,including AP2/ERF,NAC,and bHLH transcription factors.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment revealed the repression of photosynthesis concurrent with the activation of planthormone and mitogen-activated protein kinase(MAPK)signaling pathways.Furthermore,key genes involved in proline biosynthesis and peroxisomefunction were markedly upregulated,indicating enhanced osmotic adjustment and oxidative stress defense.These results clarify the coordinated droughtresponse mechanisms in F.rubra and provide valuable genetic resources for improving drought tolerance in turfgrass and related crops. 展开更多
关键词 drought stress physiological analysis osmoregulatory substances antioxidant enzyme Festuca rubra drought tolerance transcriptomic analysis physiological transcriptomic analyses
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Transcriptomic analysis to understand the alternative splicing event on regulating secondary metabolism during flowering stages of Lonicera japonica 认领 引用 被引量：1
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作者 Jie Chen Xu Tian +6 位作者 Xinying Weng Haofu Ni Hu Yang Farhat Yasmeen Lin Zhang Nenghua Zhang Bingxian Yang 《Medicinal Plant Biology》 2025年第1期312-320,共9页
Lonicera japonica Thunb.is an important traditional Chinese medicinal resource.The synthetic pathways,as well as the functional genes involved in the biosynthesis of phenolic acids and flavonoids,have been intensively... Lonicera japonica Thunb.is an important traditional Chinese medicinal resource.The synthetic pathways,as well as the functional genes involved in the biosynthesis of phenolic acids and flavonoids,have been intensively studied;however,the mechanism of post-transcriptional regulation during the flowering stages remains largely unexplained.In this study,the L.japonica transcriptome and genome were used to identify the alternative splicing(AS)events that occur during L.japonica flowering and the relevant genes.A total of 31,739,30,752,31,147,and 32,071 AS events were identified based on a comparison of flowering stages with the first flowering stage,and 20,916,20,501,20,632,and 21,020 genes were involved in the AS events.Exon skipping(ES)has been identified as the most frequent type of alternative splicing event,whereas mutually exclusive exons(MXE)are typically among the least frequently occurring types.Functional analysis of genes underlying the two types of AS events showed these genes were mainly related to protein metabolism,RNA metabolism,cell cycle,transport,signaling,and secondary metabolism.Further pathway mapping analysis demonstrated the occurrence of AS event in chalcone isomerase(CHI),2'-hydroxyisoflavone reductase(IFR),tyrosine decarboxylase(TYDC),and strictosidine synthase(STR)genes,which are responsible for the production of liquiritigenin,vestitone,tyramine,and strychnine,respectively.PCR and sequencing confirmed these AS events,further validating our findings.Our study elucidates the correlation between alterations in secondary metabolism and alternative splicing events during L.japonica flowering,which enhances our understanding of the complex regulation of its secondary metabolism and provides a basis for subsequent in-depth exploration of the regulatory mechanisms of active ingredient synthesis in L.japonica. 展开更多
关键词 phenolic acids secondary metabolism transcriptomic analysis synthetic pathwaysas lonicera japonica alternative splicing flowering stages
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Comparative hormonal and transcriptomic analysis of heat stress responses in cassava and potato 认领 引用
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作者 Jia Luo Jin Xiao +3 位作者 Haozheng Li Shujuan Wang Wenquan Wang Xin Guo 《Tropical Plants》 CSCD 2025年第1期47-59,共13页
Improving crop heat tolerance is essential under the increasingly frequent extreme temperature conditions worldwide.Cassava(Manihot esculenta Crantz)is a tropical crop with strong resistance to high temperature and hi... Improving crop heat tolerance is essential under the increasingly frequent extreme temperature conditions worldwide.Cassava(Manihot esculenta Crantz)is a tropical crop with strong resistance to high temperature and high light,whereas potato(Solanum tuberosum L.)is a temperate crop highly sensitive to heat stress.To elucidate the differences in heat stress responses between cassava and potato,this study combined transcriptome sequencing with hormonal profiling.The results revealed that cassava exhibited significant changes in hormone signaling with relatively lower amplitude,whereas potato showed large fluctuations in both hormone levels and signaling pathways.Transcriptome analysis identified numerous differentially expressed genes(DEGs)in cassava cultivars KU50 and SC205 and in potato cultivars FAVORITA and Qingshu No.9.Weighted gene co-expression network analysis(WGCNA)identified 13 regulatory modules in cassava and 11 in potato.In cassava,heat-responsive transcription factors and heat shock proteins(HSPs)were generally downregulated,while genes involved in photosynthetic electron transport and lignin biosynthesis were upregulated;the opposite trend was observed in potato.RT-qPCR validation confirmed the transcriptome data.These findings provide valuable gene resources for breeding heat-tolerant crop varieties and offer insights into the molecular mechanisms underlying heat tolerance in tropical vs temperate crops. 展开更多
关键词 cassava transcriptome sequencing hormonal profilingthe differences heat stress responses transcriptomic analysis hormonal profiling heat stress improving crop heat tolerance
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Unveiling the role of the TIR1/AFB gene family in Capsicum annuum:genome-wide identification,characterization,and transcriptomic analysis under Ralstonia solanacearum infection 认领 引用
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作者 Wenchao Du Zhiyu Yu +8 位作者 Xiaoyan Miao Zhongcai Teng Chao Zhang Bingqian Zhang Meng Xia Jingbin Hua Umer Karamat Peiqing Liu Zhenhua Jia 《Vegetable Research》 2025年第1期159-166,共8页
TIR1/AFB proteins play key roles in plants responding to Solanum crop disease.In this study,five putative TIR1/AFB proteins were identified in pepper(Capsicum annuum).Chromosomal mapping revealed that CaTIR1/AFB genes... TIR1/AFB proteins play key roles in plants responding to Solanum crop disease.In this study,five putative TIR1/AFB proteins were identified in pepper(Capsicum annuum).Chromosomal mapping revealed that CaTIR1/AFB genes are located on chromosomes DH02,DH03,DH04,and DH06.Phylogenetic tree analysis based on TIR1/AFB protein sequences from Arabidopsis,tomato,and eggplant revealed that the CaTIR1/AFB genes in pepper belong to three of the four identified subgroups.One collinear gene pair(CaTIR1C and CaTIR1B)was identified in pepper,suggesting the TIR1/AFB gene family in pepper experienced segmental duplications in evolution.Seventy-eight cis-elements related to the hormone,defense,drought,and light response were identified.RNA-sequencing data and expression profiling showed that TIR1/AFB genes were expressed differently under R.solanacearum treatment;downregulated expression of all CaTIR1/AFBs was observed in the resistant variety,while CaTIR1C was upregulated in the susceptible variety.Subcellular localization analysis showed that CaTIR1C is a nuclear-localized protein.Further virus-induced gene silencing(VIGS)assays revealed that knocking down CaTIR1C enhanced pepper resistance to R.solanacearum,indicating that CaTIR1C is a negative regulator in response to R.solanacearum.These findings contribute to the molecular breeding of bacterial wilt-resistant pepper and hold the potential to improve disease control efficiency by further exploring the function of CaTIR1C. 展开更多
关键词 genome wide identification tree analysis phylogenetic tree analysis Capsicum annuum Ralstonia solanacearum infection collinear gene pair transcriptomic analysis tir afb proteins
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Comparative transcriptomic analysis revealed specific modules and hub heat-responsive genes in perennial ryegrass 认领 引用
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作者 Wenxi Zha Lingshuang Zeng +2 位作者 Ziyi Zhang Jing Zhang Bin Xu 《Grass Research》 2025年第1期105-115,共11页
Perennial ryegrass(Lolium perenne)is one of the most important cool-season grasses used for forage and turf purposes.Heat stress is the primary abioticfactor threatening its pastureurf persistence.In this study,heat-r... Perennial ryegrass(Lolium perenne)is one of the most important cool-season grasses used for forage and turf purposes.Heat stress is the primary abioticfactor threatening its pastureurf persistence.In this study,heat-responsive genes common between or specific to two ryegrass varieties with contrastingheat tolerance traits were analyzed at the transcriptomic level.The result identified 5,399 common heat-responsive differentially expressed genes(DEGs)between the two ryegrass varieties enriched in KEGG pathways such as ribosomes,spliceosomes,ribosome biogenesis,photosynthetic antenna proteins,etc.Weighted gene co-expression network analysis(WGCNA)revealed specific DEGs in the heat-tolerant ryegrass variety that were mainly enriched inglyoxylate and dicarboxylate metabolism,glycolysis,protein processing in the endoplasmic reticulum,spliceosome,and ascorbate-glutathione cycle,etc.Furthermore,heat-tolerant variety-specific hub DEGs and transcription factors were also identified using Core Gene Co-expression Network analysis.Knowledge gained from this study provides a basis for the genetic improvement of heat-tolerant ryegrass and other cool-season perennial grass species. 展开更多
关键词 transcriptomic analysis heat responsive genes weighted gene co expression network analysis perennial ryegrass transcription factors kegg pathway heat stress hub genes
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Comparative transcriptomic analysis on compatible/incompatible grafts in Citrus 认领 引用 被引量：10
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作者 Wen He Rui Xie +8 位作者 Yan Wang Qing Chen Hao Wang Shaofeng Yang Ya Luo Yong Zhang Haoru Tang Frederick G.Gmitter Jr Xiaorong Wang 《Horticulture Research》 SCIE CSCD 2022年第1期985-993,共9页
Grafting is a useful cultivation technology to resist abiotic and biotic stresses and is an integral part of citrus production.However,some widely utilized rootstocks may still exhibit graft incompatibility in the orc... Grafting is a useful cultivation technology to resist abiotic and biotic stresses and is an integral part of citrus production.However,some widely utilized rootstocks may still exhibit graft incompatibility in the orchard.‘Hongmian miyou’(Citrus maxima(Burm.)Merrill)is mutated from‘Guanxi miyou’,but these two scions showed different compatibility with available Poncirus trifoliata rootstock.Foliage etiolation is an observed symptom of graft incompatibility,but its mechanism remains poorly understood.This study is the first to investigate the morphological,physiological,and anatomical differences between compatible and incompatible grafts,and perform transcriptome profiling at crucial stages of the foliage etiolation process.Based on comprehensive analyses,hormonal balance was disordered,and two rate-limiting genes,NCED3(9-cis-epoxycarotenoid dioxygenase 3)and NCED5,being responsible for ABA(abscisic acid)accumulation,were highlighted.Further correlation analysis indicated that IAA(indole-3-acetic acid)and ABA were themost likely inducers of the expression of stress-related genes.In addition,excessive starch accumulation was observed in the lamina and midribs of leaves of incompatible grafts.These results provide a new insight into the role of hormonal balance and ABA biosynthesis genes in regulating and contributing to graft incompatibility,and will further define and deploy candidate genes to explore the mechanisms underlying citrus rootstock–scion interactions. 展开更多
关键词 hormonal balance abscisic acid graft incompatibility citrus transcriptomic analysis cultivation technology poncirus trifoliata rootstockfoliage etiolation graft incompatibilitybut
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Transcriptomic analysis provides insight into the regulation mechanism of silver ions(Ag+)and jasmonic acid methyl ester(MeJA)on secondary metabolism in the hairy roots of Salvia miltiorrhiza Bunge(Lamiaceae) 认领 引用 被引量：6
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作者 Ying Cheng Xinyu Hong +5 位作者 Lan Zhang Wan Yang Youran Zeng Zhuoni Hou Zongqi Yang Dongfeng Yang 《Medicinal Plant Biology》 2023年第1期199-208,共10页
Salvia miltiorrhiza Bunge(Lamiaceae)is a traditional medicinal plant.Its main active components are tanshinones and salvianolic acid B(SAB).Abiotic elicitors such as silver ions(Ag+)and jasmonic acid methyl ester(MeJA... Salvia miltiorrhiza Bunge(Lamiaceae)is a traditional medicinal plant.Its main active components are tanshinones and salvianolic acid B(SAB).Abiotic elicitors such as silver ions(Ag+)and jasmonic acid methyl ester(MeJA)are reported to promote the accumulation of secondary metabolites in the hairy roots of S.miltiorrhiza.However,the mechanisms underlying the working of the elicitors remains unclear.For this reason,transcriptome quantitative analysis was conducted to describe the overall expression of elicitors-treated hairy roots,and key protein-encoding genes were identified in the MVA pathway which had a positive effect on tanshinone accumulation.Upstream genes in the biosynthetic pathway of SAB were more responsive to MeJA.Transcription factors(SmWRKY73,SmbHLH25),genes in the GA signaling pathway(SmGA2ox,SmGA3ox)and ABA signaling pathway(SmNCED,SmCYP707A)may be involved in regulating tanshinone and SAB biosynthesis.Upregulated transcription factors were highly correlated in response to Ag+treatment and MeJA treatment,and Ag+treatment had a better induction effect on transcription factors than MeJA treatment.Gene cluster mining and co-expression network construction further revealed the contribution of gene clusters to tanshinone biosynthesis,and Sm2OGD was likely involved in tanshinone biosynthesis.In conclusion,the current study screened the key genes for transcription factors and hormone signaling pathways that may promote the accumulation of tanshinones and SAB.The results improved the regulatory network of Ag+and MeJA-mediated secondary metabolite biosynthesis in S.miltiorrhiza hairy roots,and improved our insight into the regulatory mechanisms involved in the biosynthesis of tanshinones and SAB. 展开更多
关键词 silver ions jasmonic acid methyl ester secondary metabolites salvianolic acid silver ions ag transcriptomic analysis quantitative analysis salvia miltiorrhiza
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Transcriptomic analysis of Andrias davidianus meat and experimental validation for exploring its bioactive components as functional foods 认领 引用 被引量：5
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作者 Changge Guan Zhenglin Tan +6 位作者 Shucheng Li Yi Wang Naoyuki Yamamoto Chong Zhang Songjun Wang Junjie Chen Xinhui Xing 《Food Science and Human Wellness》 SCIE CAS CSCD 2024年第1期166-172,共7页
Andrias davidianus(Chinese giant salamander,CGS)is the largest and oldest extant amphibian species in the world and is a source of prospective functional food in China.However,the progress of functional peptides minin... Andrias davidianus(Chinese giant salamander,CGS)is the largest and oldest extant amphibian species in the world and is a source of prospective functional food in China.However,the progress of functional peptides mining was slow due to lack of reference genome and protein sequence data.In this study,we illustrated full-length transcriptome sequencing to interpret the proteome of CGS meat and obtain 10703 coding DNA sequences.By functional annotation and amino acid composition analysis,we have discovered various genes related to signal transduction,and 16 genes related to longevity.We have also found vast variety of functional peptides through protein coding sequence(CDS)analysis by comparing the data obtained with the functional peptide database.Val-Pro-Ile predicted by the CDS analysis was released from the CGS meat through enzymatic hydrolysis,suggesting that our approach is reliable.This study suggested that transcriptomic analysis can be used as a reference to guide polypeptide mining in CGS meat,thereby providing a powerful mining strategy for the bioresources with unknown genomic and proteomic sequences. 展开更多
关键词 Chinese giant salamander Transcriptomic analysis Bioactive components Functional peptides mining
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Transcriptomic analysis of zoysiagrass(Zoysia japonica)provides novel insights into the molecular basis of cold acclimation 认领 引用 被引量：1
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作者 Jessica M.Brown Carolina Escalona Weldt +6 位作者 HMcCamy P.Holloway Tan D.Tuong Aaron J.Patton Michelle DaCosta David P.Livingston Xingwang Yu Susana R.Milla-Lewis 《Grass Research》 2023年第1期215-223,共9页
Zoysia japonica(Z.japonica)is a warm-season perennial turfgrass commonly grown in the southeastern United States for its relatively low input requirements and general tolerance to drought,shade,and salinity.Improving ... Zoysia japonica(Z.japonica)is a warm-season perennial turfgrass commonly grown in the southeastern United States for its relatively low input requirements and general tolerance to drought,shade,and salinity.Improving freezing tolerance is critical for Z.japonica,as it could extend the northern boundaries that the species is able to be grown in.To deepen our understanding of the molecular basis of freezing tolerance in Z.japonica,a transcriptomic approach was utilized to identify genes involved in cold acclimation.‘Meyer',a freeze tolerant cultivar,and‘Victoria',a freeze susceptible cultivar were subjected to cold acclimation and non-cold acclimation treatments to determine the number of differentially expressed genes(DEGs).In response to cold acclimation,a total of 4,609 DEGs were up-regulated and 3,605 DEGs were down-regulated in‘Meyer',while 3,758 DEGs were up-regulated and 3,516 DEGs were down-regulated in‘Victoria'.GO and KEGG enrichment analysis showed several diverse pathways and biological processes,including photosynthesis,transmembrane transport,and plant hormone signal transduction.Integrating these information with previous studies on proteomics and QTL mapping,several candidate genes were identified to be associated with cold acclimation and freezing tolerance across different studies,such as LEA,CIPK,POD,HSF,HSP,MPK,PSII and multiple transcription factors.The candidate genes identified in this study showed great value in potentially being a target for future selection efforts for freeze-tolerant Z.japonica. 展开更多
关键词 transcriptomic approach cold acclimation zoysiagrass Zoysia japonica zoysia japonica zjaponica transcriptomic analysis freezing tolerance cold acclima
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Comparative Transcriptomic Analysis of Two Tomato Cultivars with Different Shelf-Life Traits 认领 引用 被引量：1
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作者 Abdul Karim Amin Yan He +8 位作者 Xianglong Wang Pengwei Li Muhammad Ahmad Hassan Mohammad Yousof Soltani Yiling Zhang Mohammad Alem Amin Ahmad Shah Ahmadzai Yajing Liu Songhu Wang 《Phyton-International Journal of Experimental Botany》 SCIE 2024年第8期2075-2093,共19页
Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every year.In this study,firstly from 19 t... Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every year.In this study,firstly from 19 tomato cultivars,we screened out two cultivars,Riogrand and SalarF1,having long and short shelf-life spans,respectively.Secondly,shelf-life analysis was carried out for both cultivars at room temperature.Results exhibited that Riogrand showed higher firmness and less weight loss than SalarF1.The ethylene production was higher in SalarF1,compared with Riogrand during post-harvest storages.We performed transcriptomic analysis of both cultivars in different storage stages.We discovered 2913,2188,and 11,119 differentially expressed genes(DEGs)for three post-harvest stages(0,20,and 40 Days Post-Harvest(DPH)),respectively.These genes are enriched in ethylene biosynthesis and response,as well as cell wall-related genes.Ethylene response factor(ERF)ERF2 and ERF4 were highly expressed in SalarF1 with a short shelf life in 40 DPH,and the ethylene biosynthetic genes ACO1,ACO4,ACS6,and ACS2 were significantly upregulated in SalarF1.Regarding cell wall loosening and cell wall-related genes XTH3,XTH7,XTH23,1,3;1,4-β-D-Gluc-like,pGlcT1,Cellulase,PGH1,PL5,PL-like 1,PL-like 2 exhibited the highest levels of significance,being notably upregulated in the last stage of SalarF1.The quantitative real-time polymerase chain reaction(qRT-PCR)analysis validated these gene expressions,which is in line with the transcriptome analysis.The findings suggested that the extension of tomato fruit shelf life is mostly dependent on ethylene biosynthesis,signaling pathway genes,cell wall loosening,and cell wall-associated genes. 展开更多
关键词 Shelf life transcriptome analysis tomato differentially expressed genes(DEGs) ethylene
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Integrated genomic and transcriptomic analysis reveals genes associated with plant height of foxtail millet 认领 引用 被引量：2
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作者 Mengyuan Zhu Qiang He +14 位作者 Mingjie Lyu Tiantian Shi Qian Gao Hui Zhi Huan Wang Guanqing Jia Sha Tang Xiliu Cheng Rui Wanga Andi Xu Haigang Wang Zhijun Qiao Jun Liu Xianmin Diao Ying Gao 《The Crop Journal》 SCIE CSCD 2023年第2期593-604,共12页
Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and quality.Therefore,it is ... Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and quality.Therefore,it is imperative to identify and deploy the genes controlling foxtail millet plant height.In this study,we used a semi-dwarf line 263A and an elite high-stalk breeding variety,Chuang 29 to construct an F2 population to identify dwarf genes.We performed transcriptome analysis(RNA-seq)using internode tissues sampled at three jointing stages of 263A and Chuang 29,as well as bulk segregant analysis(BSA)on their F2 population.A total of 8918 differentially expressed genes(DEGs)were obtained from RNA-seq analysis,and GO analysis showed that DEGs were enriched in functions such as‘‘gibberellin metabolic process”and‘‘oxidoreductase activity”,which have previously been shown to be associated with plant height.A total 593 mutated genes were screened by BSA-seq method.One hundred and seventy-six out of the 593 mutated genes showed differential expression levels between the two parental lines,and seven genes not only showed differential expression in two or three internode tissues but also showed high genomic variation in coding regions,which indicated they play a crucial role in plant height determination.Among them,we found a gibberellin biosynthesis related GA20 oxidase gene(Seita.5G404900),which had a single-base at the third exon,leading to the frameshift mutation at 263A.Cleaved amplified polymorphic sequence assay and association analysis proved the single-base in Seita.5G404900 co-segregated with dwarf phenotype in two independent F2 populations planted in entirely different environments.Taken together,the candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height,and the molecular marker will be useful for marker-assisted dwarf breeding. 展开更多
关键词 Foxtail millet Plant height Transcriptome analysis Bulk segregant analysis Functional markers Association analysis
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Corrigendum to“Transcriptomic and biochemical analysis of the mechanism of sodium gluconate promoting the degradation of benzo[a]pyrene by Bacillus subtilis MSC4”[Journal of Environmental Sciences,Volume 152,June 2025,Pages 39-53] 认领 引用
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《Journal of Environmental Sciences》 SCIE EI CAS CSCD 2026年第2期789-791,共3页
Rui Chena,b,Tangbing Cui a,b,∗a School of Biology and Biological Engineering,South China University of Technology,Guangzhou 510006,China b Guangdong Key Laboratory of Fermentation and Enzyme Engineering,South China Un... Rui Chena,b,Tangbing Cui a,b,∗a School of Biology and Biological Engineering,South China University of Technology,Guangzhou 510006,China b Guangdong Key Laboratory of Fermentation and Enzyme Engineering,South China University of Technology,Guangzhou 510006,China The authors regret that the published version of this article contained several errors and omissions,which are described and corrected below.1.Figs.3 and 4(figure order and legends).In the published article,Figs.3 and 4 were inadvertently published in reversed order.The figures should be swapped so that the figure content matches its caption.The correct figures and their legends are provided on the following page.2.Title correction.The compound name in the published title was incorrectly typeset as“benzo[a]pyrene”The correct spelling is“benzo[a]pyrene.”3.Text corrections in Section 2.4.Several typographical errors occurred in Section 2.4(“Up-regulation of acetoin,lactate,and kanosamine biosynthesis under sodium gluconate treatment”). 展开更多
关键词 benzo pyrene degradation correction transcriptomic analysis biochemical analysis corrigendum sodium gluconate Bacillus subtilis Msc enzyme engineeringsouth
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Integrated transcriptomic and metabolomic analysis reveals light-induced modulation of anthocyanin biosynthesis in Chinese bayberry(Myrica rubra) 认领 引用 被引量：1
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作者 Han Yang Li Sun +10 位作者 Yetong Qi Zhitao Li Kangqi Lei Feng Cheng Yuyong Wu Zhengzheng Ying Yumeng Lei Temoor Ahmed Zheping Yu Xingjiang Qi Shuwen Zhang 《Fruit Research》 2025年第1期372-381,共10页
Chinese bayberry(Myrica rubra)is a subtropical fruit rich in anthocyanins,which are significantly regulated by light during ripening.This study employed integrated transcriptomic and metabolomic analyses to investigat... Chinese bayberry(Myrica rubra)is a subtropical fruit rich in anthocyanins,which are significantly regulated by light during ripening.This study employed integrated transcriptomic and metabolomic analyses to investigate the effects of light exposure on fruit quality and anthocyanin synthesis using various light-transmitting bag treatments.A greenhouse experiment demonstrated that no-transmitting bags(HQ)treatment during early fruit development significantly reduced coloration and quality indicators,including sucrose(55.3%),glucose(59.5%),fructose(37.5%),malic acid(36.6),oxalic acid(46.5),total flavonoids(60.1%),vitamin C(93.0%),and total anthocyanins(90.8%),while increasing acidity as compared to transmitting bags(WQ)treatment.Transcriptomic analysis revealed that expression levels of flavonoid synthesis genes were significantly reduced under light conditions.The expression of LDOX(Leucoanthocyanidin dioxygenase)gene was notably higher in WQ treatment,potentially contributing to bayberry fruit coloration.Metabolomic analysis identified 44 differential metabolites related to anthocyanin synthesis,with proanthocyanidins,delphinidin-3-O-galactoside,pelargonidin glucoside,and paeonidin glucoside levels significantly higher in WQ treatment compared to HQ.Furthermore,the integration of transcriptomic and metabolomic data identified the transcription factor HY5 as a key regulator in light-mediated anthocyanin accumulation.Overall,this study provides novel insights into the molecular mechanisms underlying light-regulated pigmentation in Chinese bayberry fruits.The findings contribute to understanding fruit quality development during ripening and offer a scientific basis for enhancing fruit quality and refining cultivation techniques in Chinese bayberry and similar fruit species. 展开更多
关键词 anthocyanin biosynthesis fruit quality greenhouse experiment Chinese bayberry transcriptomic analysis chinese bayberry myrica integrated transcriptomic metabolomic analyses metabolomic analysis
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Dissecting the histological heterogeneity of ovarian carcinosarcoma and high-grade serous ovarian cancer in primary and metastatic tumors by single-cell transcriptomic analysis 认领 引用
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作者 Kaipeng Xie Shuang Liang +6 位作者 Nanxi Wang Qiaoying Zhu Jiangping Wu Zhening Pu Xiaoli Wu Dake Li Juncheng Dai 《Chinese Medical Journal》 SCIE CAS CSCD 2025年第17期2195-2197,共3页
To the Editor:Ovarian cancer(OC)is the third cause of death among women globally.[1]Approximately 90%of OC cases are derived from epithelial cells,and these tumors have distinct epidemiological,molecular,and clinical ... To the Editor:Ovarian cancer(OC)is the third cause of death among women globally.[1]Approximately 90%of OC cases are derived from epithelial cells,and these tumors have distinct epidemiological,molecular,and clinical characteristics.[2]High-grade serous ovarian cancer(HGSOC)is the most common subtype of epithelial ovarian cancer(EOC)and has been widely investigated.[3]Ovarian carcinosarcoma(OCS),also known as malignant mixed mesodermal tumor,is a rare and aggressive tumor that typically develops in the female genital tract.[4]Histologically,OCS is considered a high-grade lesion that harbors both carcinomatous and sarcomatous components.[5]Although OCS accounts for only 1–4%of EOC cases,it presents the worst prognosis among all EOC subtypes,[6,7]with a median survival time(MST)of less than 18 months.[5]Due to its rarity,ovarian OCS is challenging to study through prospective trials,resulting in a limited understanding of the disease.Despite this,no targeted treatment strategies are specifically developed for OCS. 展开更多
关键词 histological heterogeneity ovarian carcinosarcoma epithelial ovarian cancer eoc single cell transcriptomic analysis ovarian cancer malignant mixed mesodermal tumoris high grade serous ovarian cancer epithelial cellsand
Transcriptomics Analysis of Penicillium expansumΔWSC1 Infection and Defense Mechanism against It in Pear Fruits 认领 引用
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作者 ZHAO Lina HU Yize +4 位作者 SHU Yuling Solairaj DHANASEKARAN ZHANG Xiaoyun YANG Qiya ZHANG Hongyin 《食品科学》 EI CAS CSCD 北大核心 2025年第13期75-85,共11页
The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic an... The WSC proteins produced by Penicillium expansum play a crucial role in causing blue mold on pears.To analyze the role of the WSC1 gene in the pathogenic process of this fungal pathogen,we conducted transcriptomic analysis of a WSC1 knockout(ΔWSC1)strain.The knockout of WSC1 significantly altered the gene expression profile in P.expansum,particularly for genes involved in cell wall integrity,signaling,stress response,and toxin production.The differential expression of these genes might make theΔWSC1 strain more vulnerable to environmental stress,while reducing the toxin production capacity,ultimately leading to a decrease in the pathogenicity.The transcriptomic analysis revealed that the expression of genes related to stress response signals,defense mechanisms and oxidative stress management changed when pear fruits were infected with theΔWSC1 strain.These changes may trigger a cascade of responses in pear fruits.In addition,compared with those infected with the wild-type strain,pear fruits infected with theΔWSC1 strain exhibited up-regulated expression of genes related to defense and oxidative stress.This study clarifies how the WSC1 gene influences P.expansum’s ability to infect pear fruits and how pear fruits respond to the infection. 展开更多
关键词 pear fruit Penicillium expansum transcriptomic analysis infection
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Transcriptomic analysis reveals the landscape of the shared gene network between ectopic pregnancy and early pregnancy loss 认领 引用
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作者 Mengyu Jing Ying Zhou +3 位作者 Shuyue Zheng Yahui Xie Xi Chen Aixia Liu 《Genes & Diseases》 SCIE CSCD 2025年第6期47-50,共4页
The loss of a pregnancy,including ectopic pregnancy(EP)and early pregnancy loss(EPL),significantly impacts women’s quality of life.Unfortunately,definitive causes can be identified in less than half of EP and EPL cas... The loss of a pregnancy,including ectopic pregnancy(EP)and early pregnancy loss(EPL),significantly impacts women’s quality of life.Unfortunately,definitive causes can be identified in less than half of EP and EPL cases,presenting a substantial challenge for clinical treatment.Previous studies have revealed a significant relationship between the history of EPL and the increased risk of EP.1 Nevertheless,the interplay between EPL and EP remains unclear,highlighting the need to discover novel biomarkers to guide personalized treatment and clinical management. 展开更多
关键词 early pregnancy loss epl significantly ectopic pregnancy discover novel biomarkers guide transcriptomic analysis gene network early pregnancy loss biomarkers ectopic pregnancy ep
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