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Genome-Wide Identification of Tomato (Solanum lycopersicum L.) CKX Gene Family and Expression Analysis in the Callus Tissue under Zeatin Treatment
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作者 Zhengfeng Lai Dongmei Lian +6 位作者 Shaoping Zhang Yudong Ju Bizhen Lin Yunfa Yao Songhai Wu Jianji Hong Zhou Li 《Phyton-International Journal of Experimental Botany》 SCIE 2024年第6期1143-1158,共16页
The cytokinin oxidase/dehydrogenase(CKX)enzyme is essential for controlling thefluctuating levels of endogen-ous cytokinin(CK)and has a significant impact on different aspects of plant growth and development.Nonethe-les... The cytokinin oxidase/dehydrogenase(CKX)enzyme is essential for controlling thefluctuating levels of endogen-ous cytokinin(CK)and has a significant impact on different aspects of plant growth and development.Nonethe-less,there is limited knowledge about CKX genes in tomato(Solanum lycopersicum L.).Here we performed genome-wide identification and analysis of nine SlCKX family members in tomatoes using bioinformatics tools.The results revealed that nine SlCKX genes were unevenly distributed onfive chromosomes(Chr.1,Chr.4,Chr.8,Chr.10,and Chr.12).The amino acid length,isoelectric points,and molecular weight of the nine SlCKX proteins ranged from 453 to 553,5.77 to 8.59,and 51.661 to 62.494 kD,respectively.Subcellular localization analysis indi-cated that SlCKX2 proteins were located in both the vacuole and cytoplasmic matrix;SlCKX3 and SlCKX5 pro-teins were located in the vacuole;and SlCKX1,4,6,7,8,and 9 proteins were located in the cytoplasmic matrix.Furthermore,we observed differences in the gene structures and phylogenetic relationships of SlCKX proteins among different members.SlCKX1-9 were positioned on two out of the three branches of the CKX phylogenetic tree in the multispecies phylogenetic tree construction,revealing their strong conservation within phylogenetic subgroups.Unique patterns of expression of CKX genes were noticed in callus cultures exposed to varying con-centrations of exogenous ZT,suggesting their roles in specific developmental and physiological functions in the regeneration system.These results may facilitate subsequent functional analysis of SlCKX genes and provide valu-able insights for establishing an efficient regeneration system for tomatoes. 展开更多
关键词 tomato SlCKX gene family phylogenetic relationships TRANS-ZEATIN expression pattern
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Genome-Wide Identification and Expression Analysis of the GSK3 Gene Family in Sunflower under Various Abiotic Stresses
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作者 Xianwen Ji Ziying Jiang +2 位作者 Jichao Wang Lili Dong Xinyi Deng 《Phyton-International Journal of Experimental Botany》 SCIE 2024年第8期1839-1850,共12页
Genes in the glycogen synthase kinase 3(GSK3)family are essential in regulating plant response to stressful conditions.This study employed bioinformatics to uncover the GSK3 gene family from the sunflower genome datab... Genes in the glycogen synthase kinase 3(GSK3)family are essential in regulating plant response to stressful conditions.This study employed bioinformatics to uncover the GSK3 gene family from the sunflower genome database.The expressions of GSK3 genes in different tissues and stress treatments,such as salt,drought,and cold,were assessed using transcriptome sequencing and quantitative real-time PCR(qRT-PCR).The study results revealed that the 12 GSK3 genes of sunflower,belonging to four classes(Classes I–IV),contained the GSK3 kinase domain and 11–13 exons.The majority of GSK3 genes were highly expressed in the leaf axil and flower,while their expression levels were relatively lower in the leaf.As a result of salt stress,six of the GSK3 genes(HaSK11,HaSK22,HaSK23,HaSK32,HaSK33,and HaSK41)displayed a notable increase in expression,while HaSK14 and HaSK21 experienced a significant decrease.With regard to drought stress,five of the GSK3 genes(HaSK11,HaSK13,HaSK21,HaSK22,and HaSK33)experienced a remarkable rise in expression.When exposed to cold stress,seven of the GSK3 genes(HaSK11,HaSK12,HaSK13,HaSK32,HaSK33,HaSK41,and HaSK42)showed a substantial increase,whereas HaSK21 and HaSK23 had a sharp decline.This research is of great importance in understanding the abiotic resistance mechanism of sunflowers and developing new varieties with improved stress resistance. 展开更多
关键词 SUNFLOWER abiotic stress GSK expression analysis
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Comparative Transcriptomic Analysis of Two Tomato Cultivars with Different Shelf-Life Traits
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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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Identification and expression analysis of chlorogenic acid biosynthesis key gene PpHCT in peach
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作者 Ziwen Su Meng Sun +7 位作者 Zhixiang Cai Shaolei Guo Jiyao Li Bintao Zhao Zhijun Shen Ruijuan Ma Juan Yan Mingliang Yu 《Horticultural Plant Journal》 SCIE CAS CSCD 2023年第4期670-680,共11页
Shikimic acid/quinic acid hydroxy cinnamyl transferase(HCT)is one of the key enzymes in the phenylpropanoid pathway.However,the role of the HCT gene in chlorogenic acid(CGA)biosynthesis in peach fruit remains unclear.... Shikimic acid/quinic acid hydroxy cinnamyl transferase(HCT)is one of the key enzymes in the phenylpropanoid pathway.However,the role of the HCT gene in chlorogenic acid(CGA)biosynthesis in peach fruit remains unclear.For this,we identified the accumulation pattern of CGA in four peach cultivars,cloned and characterized 11 PpHCT gene members,and further analyzed the expression patterns of these PpHCT genes during fruit development.The contents of CGAs in the four peach cultivars all exhibited a trend of increasing and then decreasing during the fruit growth and development.Moreover,the contents of CGAs in the peel and flesh were tissue-specific.Gene structure analysis indicated that the PpHCT genes were highly conserved,containing two exons and one intron.The protein structure analysis demonstrated that the PpHCT proteins contained two conserved motifs(HXXXD,DFGWG)and a transferase domain(PF02458),which belonged to the BAHD acyltransferase family.The cis-acting element analysis suggested that the promoters of PpHCT genes contained many light-related,hormone-related,stress-related,tissue-specific,and circadian-related elements,and they could participate in a variety of biological processes.Phylogenetic analysis showed that the HCT proteins of peach were closely related to the HCT proteins of plum and had a close evolutionary relationship.The qRT-PCR analysis indicated that the expression levels of PpHCT1 and PpHCT2 showed an opposite trend to the accumulation of CGA,whereas the expression levels of PpHCT4,PpHCT5,PpHCT7,PpHCT8,and PpHCT11 demonstrated the same trend as CGA accumulation.It was worth noting that only PpHCT4 and PpHCT5 were highly expressed in the two high-CGA cultivars but showed low levels of expression in the two low-CGA cultivars.Therefore,it was hypothesized that these two genes might be key genes to the synthesis of CGA in peach fruit.Those findings provide a theoretical basis for further study on the biological functions of the HCT gene and help to reveal the molecular mechanism of CGA. 展开更多
关键词 Prunus persica(L.) Chlorogenic acid PpHCT Bioinformatics analysis Gene expression
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Analysis of differentially expressed genes related to cerebral ischaemia in young rats based on the Gene Expression Omnibus database
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作者 Yu Xia Han Liu Rui Zhu 《World Journal of Clinical Cases》 SCIE 2023年第7期1467-1476,共10页
BACKGROUND The incidence rate of cerebral infarction in young people is increasing day by day,the age of onset tends to be younger,and its internal pathogenesis and mechanism are very complicated,which leads to greate... BACKGROUND The incidence rate of cerebral infarction in young people is increasing day by day,the age of onset tends to be younger,and its internal pathogenesis and mechanism are very complicated,which leads to greater difficulties in treatment.Therefore,it is essential to analyze the key pathway that affects the onset of cerebral infarction in young people from the perspective of genetics.AIM To compare the differentially expressed genes in the brain tissue of young and aged rats with middle cerebral artery occlusion and to analyse their effect on the key signalling pathway involved in the development of cerebral ischaemia in young rats.METHODS The Gene Expression Omnibus 2R online analysis tool was used to analyse the differentially expressed genes in the GSE166162 dataset regarding the development of cerebral ischaemia in young and aged groups of rats.DAVID 6.8 software was further used to filter the differentially expressed genes.These genes were subjected to Gene Ontology(GO)function analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis to determine the key gene pathway that affects the occurrence of cerebral ischaemia in young rats.RESULTS Thirty-five differentially expressed genes(such as Igf2,Col1a2,and Sfrp1)were obtained;73 GO enrichment analysis pathways are mainly involved in biological processes such as drug response,amino acid stimulation response,blood vessel development,various signalling pathways,and enzyme regulation.They are involved in molecular functions such as drug binding,protein binding,dopamine binding,metal ion binding,and dopamine neurotransmitter receptor activity.KEGG pathway enrichment analysis showed a significantly enriched pathway:The cyclic adenosine monophosphate(c-AMP)signalling pathway.CONCLUSION The c-AMP signalling pathway might be the key pathway in the intervention of cerebral infarction in young people. 展开更多
关键词 Gene expression Omnibus database Cerebral infarction in young people RATS Differential gene enrichment analysis PATHWAY
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Identification of key genes underlying clinical features of hepatocellular carcinoma based on weighted gene co‑expression network analysis and bioinformatics analysis
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作者 ZHANG Kan LONG Fu‑li +3 位作者 LI Yuan SHU Fa‑ming YAO Fan WEI Ai‑Ling 《Journal of Hainan Medical University》 2023年第2期49-55,共7页
Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagno... Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagnosis and treatment. Methods: GSE84598 chip data were downloaded from the GEO database, and module genes closely related to the clinical features of HCC were extracted by comprehensive weighted gene co‑expression network analysis. Hub genes were identified through protein interaction network analysis by the maximum clique centrality (MCC) algorithm;Finally, the expression of hub genes was validated by TCGA database and the Kaplan Meier plotter online database was used to evaluate the prognostic relationship between hub genes and HCC patients. Results: By comparing the gene expression data between HCC tissue samples and normal liver tissue samples, a total of 6 262 differentially expressed genes were obtained, of which 2 207 were upregulated and 4 055 were downregulated. Weighted gene co‑expression network analysis was applied to identify 120 genes of key modules. By intersecting with the differentially expressed genes, 115 candidate hub genes were obtained. The results of enrichment analysis showed that the candidate hub genes were closely related to cell mitosis, p53 signaling pathway and so on. Further application of the MCC algorithm to the protein interaction network of 115 candidate hub genes identified five hub genes, namely NUF2, RRM2, UBE2C, CDC20 and MAD2L1. Validation of hub genes by TCGA database revealed that all five hub genes were significantly upregulated in HCC tissues compared to normal liver tissues;Moreover, survival analysis revealed that high expression of hub genes was closely associated with poor prognosis in HCC patients. Conclusions: This study identifies five hub genes by combining multiple databases, which may provide directions for the clinical diagnosis and treatment of HCC. 展开更多
关键词 Weighted gene co‑expression network analysis Bioinformatics Hepatocellular carcinoma Maximal clique centrality algorithm
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Bioinformatics and Expression Pattern Analysis of Tomato ns LTP 2-like cDNA full-length Gene Clone
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作者 Zhang Jia He Shan-shan +3 位作者 Zhao Ting-ting Jiang Jing-bin Li Jing-fu Xu Xiang-yang 《Journal of Northeast Agricultural University(English Edition)》 CAS 2019年第1期28-36,共9页
TDF1(transcription-drived fragment) was homologous to the predicted S. lycopersicum nonspecific lipid-transfer protein,nsLTP 2-like(91%), and it was significantly upregulated in response to C. fulvum(cladosporium fulv... TDF1(transcription-drived fragment) was homologous to the predicted S. lycopersicum nonspecific lipid-transfer protein,nsLTP 2-like(91%), and it was significantly upregulated in response to C. fulvum(cladosporium fulvum) infection in tomato plants.In this experiment, the full-length cDNA of nsLTP 2-like was cloned using RACE technology based on the sequence of TDF1(GenBank: JZ717725). A full-length, 625 bp(GenBank: KU366289), cDNA sequence, which with 98% similarity to nsLTP 2-like gene(GenBank: XM015233692) was obtained. This cDNA contains an ORF(open reading frame) with full-length of 345 bp, coding of 114 amino acids, including 12.3% Ala and Gly. Protein molecular weight was 11.51 ku, the isoelectric point(pI) was 8.99, and average overall hydrophilicity was 0.412, with one phosphorylation sites, belonging to volatile acidic nuclear protein. Secondary structure prediction showed that α-Helix accounts for 30.7%, extension chain for 12.28%, β-corner for 9.65%, and random coil for 47.37%. Through comparative analysis of the homology among species, it was found that the amino acid sequence of tomato nsLTP 2-like protein had a high similarity with other plants, and with a specific conserved sequence which might related features in nsLTP 2-like protein. It also be analyzed the gene expression pattern of tomato in different parts and under different stress conditions.The results showed that nsLTP 2-like gene was up-regulated in varying degrees, under the condition of cold stress, exogenous hormone spraying and cladosporium fulvum infection. Therefore, it was speculated that the gene played a role in response to abiotic and biotic stress in tomato. 展开更多
关键词 tomato NSLTP 2-like CDNA CLONE BIOINFORMATICS analysis expression pattern
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Cloning and expression analysis of a long type peptidoglycan recognition protein(PGRP-L) from Xenopus tropicalis 被引量:2
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作者 齐志涛 张启焕 +4 位作者 王资生 王爱民 黄贝 昌鸣先 聂品 《Zoological Research》 CAS CSCD 北大核心 2011年第4期371-378,共8页
Peptidoglycan recognition proteins(PGRPs) are a family of pattern recognition receptors(PRRs) of the immune system,which bind and hydrolyze bacterial peptidoglycan.Here,a long type PGRP(PGRP-L) was first cloned ... Peptidoglycan recognition proteins(PGRPs) are a family of pattern recognition receptors(PRRs) of the immune system,which bind and hydrolyze bacterial peptidoglycan.Here,a long type PGRP(PGRP-L) was first cloned in the lower vertebrate species Xenopus tropicalis(Xt).The XtPGRP-L possessed a conserved genomic structure with five exons and four introns.The alignment and phylogenetic analysis indicated that XtPGRP-L might be a type of amidase-like PGRP.The 3-D model showed that XtPGRP-L possessed a conserved structure compared with the Drosophila PGRP-Lb.During embryonic development,XtPGRP-L was not expressed until the 72 h tadpole stage.In adult tissues,it was strongly expressed in the liver,lung,intestine,and stomach.Furthermore,after LPS stimulation,the expression of XtPGRP-L was up-regulated significantly in the liver,intestine and spleen,indicating that XtPGRP-L may play an important role in the innate immunity of Xenopus tropicalis. 展开更多
关键词 Peptidoglycan recognition protein Gene clone expression analysis Xenopus tropicalis
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Genome wide investigation of Hsf gene family in Phoebe bournei:identification,evolution,and expression after abiotic stresses 被引量:1
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作者 Wenhai Liao Xinghao Tang +6 位作者 Jingshu Li Qiumian Zheng Ting Wang Shengze Cheng Shiping Chen Shijiang Cao Guangqiu Cao 《Journal of Forestry Research》 SCIE EI CAS CSCD 2024年第5期201-215,共15页
Heat shock transcription factors(Hsfs)have important roles during plant growth and development and responses to abiotic stresses.The identification and func-tion of Hsf genes have been thoroughly studied in various he... Heat shock transcription factors(Hsfs)have important roles during plant growth and development and responses to abiotic stresses.The identification and func-tion of Hsf genes have been thoroughly studied in various herbaceous plant species,but not woody species,especially Phoebe bournei,an endangered,unique species in China.In this study,17 members of the Hsf gene family were identi-fied from P.bournei using bioinformatic methods.Phyloge-netic analysis indicated that PbHsf genes were grouped into three subfamilies:A,B,and C.Conserved motifs,three-dimensional structure,and physicochemical properties of the PbHsf proteins were also analyzed.The structure of the PbHsf genes varied in the number of exons and introns.Pre-diction of cis-acting elements in the promoter region indi-cated that PbHsf genes are likely involved in responses to plant hormones and stresses.A collinearity analysis dem-onstrated that expansions of the PbHsf gene family mainly take place via segmental duplication.The expression levels of PbHsf genes varied across different plant tissues.On the basis of the expression profiles of five representative PbHsf genes during heat,cold,salt,and drought stress,PbHsf pro-teins seem to have multiple functions depending on the type of abiotic stress.This systematic,genome-wide investigation of PbHsf genes in P.bournei and their expression patterns provides valuable insights and information for further func-tional dissection of Hsf proteins in this endangered,unique species. 展开更多
关键词 Phoebe bournei Hsf gene family Evolutionary analysis expression mechanism Abiotic stresses
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Molecular Cloning, Sequence Analysis and Prokaryotic Expression of Ovine Activin Receptor Type IIB(ActRIIB) Gene 被引量:1
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作者 张雪梅 安静 +1 位作者 张宁 刘明军 《Agricultural Science & Technology》 CAS 2014年第10期1644-1648,共5页
Objective] This study aimed to clone ovine activin receptor type llB (Ac-tRIIB) gene, construct the prokaryotic expression vector and express the target gene in vitro, thus providing basis for further function verif... Objective] This study aimed to clone ovine activin receptor type llB (Ac-tRIIB) gene, construct the prokaryotic expression vector and express the target gene in vitro, thus providing basis for further function verification. [Method] The template cDNA which was reversely transcribed from total RNA of sheep liver tissue, was subjected to polymerase chain reaction (PCR) using specific primers of ActRIIB. The ful-length cDNA of ovine ActRIIB was obtained by pMD18-T cloning and sequencing for bioinformatics analysis. Ovine ActRIIB encoding sequence was subcloned into prokaryotic expression vector pET41a with restriction sites BamHl/Notl, and then transformed into BL21 (DE3). The induced products by lPTG were analyzed with SDS-PAGE and Western Blot. [Result] The amplified ful-length cDNA of ovine Ac-tRllB gene was 1 564 bp in length (Genbank accession number: JX422071.1) with an open reading frame of 1 539 bp, encoding 512 amino acides. Ovine ActRllB shared the highest homology (99.6%) with bovine ActRllB. ActRllB had highly ho-mologous C-terminal domains and belonged to the TGFβ family. After prokaryotic expression, an approximately 92 kD His-tagged ActRllB recombinant protein was obtained, which was consistent with the excepted result. [Conclusion] Cloning and successful expression of ovine ActRIIB laid solid foundation for further investigation of its biological function. 展开更多
关键词 SHEEP ActRIIB gene Sequence analysis Prokaryotic expression
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Cloning and Expression Analysis of PtFATB Gene Encoding the Acyl-acyl Carrier Protein Thioesterase in Populus tomentosa Carr 被引量:1
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作者 周洲 张德强 卢孟柱 《Journal of Genetics and Genomics》 SCIE CAS CSCD 北大核心 2007年第3期267-274,共8页
Acyl-ACP thioesterases (FATs) terminates the fatty acid synthesis and allow the transport of fatty acids out of the plastids, which are the important determinants of cellular metabolism. FATB is a member of FAT enzy... Acyl-ACP thioesterases (FATs) terminates the fatty acid synthesis and allow the transport of fatty acids out of the plastids, which are the important determinants of cellular metabolism. FATB is a member of FAT enzymes that has been described previously in most of the plants. In silico cloning is a new method that utilizes the bioinformatics on the complete genome and available EST database. In this study, a full-length cDNA clone of PtFATB gene was isolated from Populus tomentosa using this approach. It is 1,450 bp in length and the open reading frame encodes a peptide of 421 amino acids. The predicted amino acid sequence shows significant homology with those from other plant species, which contain typical domains owned by FATB proteins. The transcripts of PtFATB were abundant in leaves, and less in roots detected by using semiquantitative RT-PCR. When the shoots were subjected to the stress treatments (cold, dry, NaC1) and ABA (Abscisic acid), the expression of PtFATB was only slightly reduced under the treatment of low temperature. This suggests that the expression of PtFATB is in a constitutive fashion. This study provides the basis not only for the identification and characterization of this gene but also for the improvement of cold tolerance by controlling the expression of the PtFATB gene in trees in near future. 展开更多
关键词 Populus tomentosa Carr. Acyl-acyl carrier protein thioesterase (PtFATB) in silico and molecular cloning RT-PCR expression analysis
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Cloning,Identification and Differential Expression Analysis of Full-length cDNA of Carp Interleukin-1β
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作者 何江帅 卢强 +3 位作者 李伟 赵晓 冯祥汝 陈义龙 《Agricultural Science & Technology》 CAS 2011年第3期405-408,412,共5页
[Objective] The research aimed to carry out the cloning,identification and differential expression analysis of carp interleukin-1β (IL-1β) cDNA. [Method] By using DD-RTPCR method,the differential expression cDNA f... [Objective] The research aimed to carry out the cloning,identification and differential expression analysis of carp interleukin-1β (IL-1β) cDNA. [Method] By using DD-RTPCR method,the differential expression cDNA fragments were gained. The cDNA library of carp peripheral blood leucocytes which was stimulated by the mitogen was screened,and the full length cDNA of carp IL-1β was cloned. Moreover,the sequence analysis and differential expression analysis were carried out. [Result] The positive clone which had a whole ORF that encoded 276 amino acids was obtained. The cluster analysis showed that the amino acid sequence of carp IL-1β and Japanese carp closely gathered as a branch,and the homoeology of amino acid sequence reached 95%. The clustering order was the carassius,zebra fish,pig,cattle,horse,human and mouse in turn. The differential expression analysis showed that the expression of IL-1β in the leucocytes significantly increased in the prior period (4 h) after the mitogen stimulated. But as the time went by (12 and 24 h),it didn't increase in the same period. The total trend of expression amount presented the peak type. [Conclusion] The research laid the foundation for further studying the expression manner,function characteristic,regulation mechanism of IL-1β in vivo and its action mechanisms in the inflammatory reaction,emergency reaction and immune response. 展开更多
关键词 CARP INTERLEUKIN-1Β cDNA cloning IDENTIFICATION Differential expression analysis
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Transcriptome analysis reveals the genetic basis of crest cushion formation in duck
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作者 Lan Huang Qixin Guo +4 位作者 Yong Jiang Zhixiu Wang Guohong Chen Guobin Chang Hao Bai 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2024年第12期4172-4185,共14页
The Chinese crested duck is a unique duck breed having a bulbous feather shape on its duck head.However,the mechanisms involved in its formation and development are unclear.In the present study,RNA sequencing analysis... The Chinese crested duck is a unique duck breed having a bulbous feather shape on its duck head.However,the mechanisms involved in its formation and development are unclear.In the present study,RNA sequencing analysis was performed on the crested tissues of 6 Chinese crested ducks and the scalp tissues of 6 cherry valley ducks(CVs)from 2 developmental stages.This study identified 261 differentially expressed genes(DEGs),122 upregulated and 139 downregulated,in the E28 stage and 361 DEGs,154 upregulated and 207 downregulated in the D42 stage between CC and CV ducks.The subsequent results of weighted gene co-expression network analysis(WGCNA)revealed that the turquoise and cyan modules were associated with the crest trait in the D42 stage,meanwhile,the green,brown,and pink modules were associated with the crest trait in the E28 stage.Venn analysis of the DEGs and WGCNA showed that 145 and 45 genes are associated between the D42 and E28 stages,respectively.The expression of WNT16,BMP2,SLC35F2,SLC6A15,APOBEC2,ABHD6,TNNC2,MYL1,and TNNI2 were verified by real-time quantitative PCR.This study provides an approach to reveal the molecular mechanisms underlying the crested trait development. 展开更多
关键词 crested duck RNA-sequencing weighted gene co-expression network analysis differentially expressed genes
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Sequence Analysis of Transcription Factor AtWRKY35 and Construction of Prokaryotic Expression Vector
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作者 伍林涛 康公平 +4 位作者 奉斌 韩宏仕 杜才富 曾章丽 张敏琴 《Agricultural Science & Technology》 CAS 2014年第10期1649-1650,1718,共3页
As members of a super gene family, WRKY transcription factors are widely distributed in higher plants. ln this study, bioinformatic analysis of WRKY35, a member of the WRKY gene family, was carried out. Results indica... As members of a super gene family, WRKY transcription factors are widely distributed in higher plants. ln this study, bioinformatic analysis of WRKY35, a member of the WRKY gene family, was carried out. Results indicated that tran-scription factor WRKY35 harbors a WRKYGQK core domain and a Cys2His2 or Cys2His/Cys zinc finger in the 5’ end without transmembrane domain. After PCR amplification and restriction digestion, WRKY35 gene fragment was ligated to prokaryotic expression vector PET28. This study provided basis for expression anal-ysis of WRKY35 protein and subsequent functional identification of WRKY35 gene. 展开更多
关键词 WRKY transcription factor Sequence analysis Prokaryotic expression vector
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Bioinformatics Analysis of the Relationship between Dilated Cardiomyopathy and Chronic Heart Failure
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作者 Lanqing Yu Haidong Zhou +8 位作者 Bailu Deng Jiaochang Wei Mei Zhang Chongyao Xu Guiyun Wei Junxiu Zhou Jun Huang Qi Lu Shaowu Ye 《Journal of Biosciences and Medicines》 2024年第8期333-346,共14页
Objective: To screen and analyze the differentially expressed genes between dilated cardiomyopathy (DCM) and chronic heart failure (CHF) based on bioinformatics methods. Methods: The Gene Expression Omnibus (GEO) data... Objective: To screen and analyze the differentially expressed genes between dilated cardiomyopathy (DCM) and chronic heart failure (CHF) based on bioinformatics methods. Methods: The Gene Expression Omnibus (GEO) database was used for data retrieval, and the chip data GSE3585 was downloaded, which was the original data of DCM and normal control group. At the same time, the chip data GSE76701 was downloaded, which was the original data of CHF and control group. Differentially expressed mRNAs (DEmRNAs) were screened by R language limma package, the data were standardized, and the common differentially expressed genes were screened. GO function and KEGG pathway enrichment analysis were performed on the common differentially expressed genes. String11.0 online tool was used for data analysis to obtain differentially expressed genes, and the results were imported into Cytoscape 3.9.1 software. The results were imported into Cytoscape 3.9.1 software, and the common expression gene module was obtained by MOCDE algorithm. Nine Hub genes were obtained by 10 algorithms such as MCC. Results: A total of 248 differentially expressed genes were screened. GO analysis showed that differentially expressed genes were mainly concentrated in 9 different physiological and pathological processes. KEGG analysis showed that the main signaling pathways involved in differentially expressed genes were 2, and 9 key differentially expressed genes were predicted: NPPB, NPPA, MYH6, FRZB, ASPN, SFRP4, RPS4Y1, DDX3Y. Conclusion: This study preliminarily explored the molecular mechanism of DCM and CHF, and obtained the common differentially expressed genes of the two diseases. Further experimental studies are needed to verify the correlation between gene expression and clinicopathological features. Provide new ideas for clinical drug treatment research. 展开更多
关键词 Dilated Cardiomyopathy Chronic Heart Failure Bioinformatics analysis Differentially expressed Genes
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A Bioinformatics Analysis of FAM3A to Identify its Potential Role as a Biomarker in Liver Hepatocellular Cancer
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作者 Syed Hussain Raza 《Proceedings of Anticancer Research》 2024年第4期87-97,共11页
Liver hepatocellular cancer(LIHC)is positioned as the third cancer with the highest mortalities worldwide,and high mortalities are associated with late diagnosis and recurrence.This study advances bioinformatics analy... Liver hepatocellular cancer(LIHC)is positioned as the third cancer with the highest mortalities worldwide,and high mortalities are associated with late diagnosis and recurrence.This study advances bioinformatics analysis of FAM3A expression in LIHC to evaluate its potential as a prognostic,diagnostic and therapeutic biomarker.Bioinformatics tools such as UALCAN,GEPIA2,KM plotter,TIMER2 and cBioPortal are employed to conduct analysis.Initially,the expression analysis revealed up-regulation of FAM3A in LIHC based on various variables.Further,the study observed that FAM3A methylation regulates expression as variation in methylation level of FAM3A was assessed in LIHC.Moreover,this over-expression of FAM3A results in poor overall survival(OS)in LIHC patients.All of these proposed that FAM3A has a role in the progression and development of LIHC.While examined association of FAM3A expression and infiltration level of CD8+T cells in LIHC patients using TIMER2 revealed that FAM3A has a positive correlation with purity in LIHC that highlights the molecular landscape.Analysis of genetic alteration revealed minute role of FAM3A in LIHC still provides valuable insight.Overall,our findings reveal that FAM3A has potential as diagnostic,therapeutic and prognostic biomarkers in LIHC. 展开更多
关键词 Liver hepatocellular cancer(LIHC) FAM3A expression Bioinformatics analysis BIOMARKER
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Genome-wide identification, characterization, and expression analysis of the SWEET gene family in cucumber 被引量:12
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作者 HU Li-ping ZHANG Feng +5 位作者 SONG Shu-hui TANG Xiao-wei XU Hui LIU Guang-min WANG Ya-qin HE Hong-ju 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2017年第7期1486-1501,共16页
SWEETs (sugars will eventually be exported transporters) are a novel class of recently identified sugar transporters that play important roles in diverse physiological processes. However, only a few species of the p... SWEETs (sugars will eventually be exported transporters) are a novel class of recently identified sugar transporters that play important roles in diverse physiological processes. However, only a few species of the plant SWEETgene family have been functionally identified. Up till now, there has been no systematic analysis of the SWEETgene family in Cucurbitaceae crops. Here, a genome-wide characterization of this family was conducted in cucumber(Cucumis sativus L.). A total of 17 CsSWEETgenes were identified, which are not evenly distributed over the seven cucumber chromosomes. Cucumber SWEET protein sequences possess seven conserved domains and two putative serine phosphorylation sites. The phylo- genetic tree of the SWEET genes in cucumber, Arabidopsis thaliana, and Oryza sativa was constructed, and all the SWEET genes were divided into four clades. In addition, a number of putative cis-elements were identified in the promoter regions of these CsSWEET genes: nine types involved in phytohormone responses and eight types involved in stress responses. Moreover, the transcript levels of CsSWEETgenes were analyzed in various tissues using quantitative real-time polymerase chain reaction. A majority (70.58%) of the CsSWEET genes were confined to reproductive tissue development. Finally, 18 putative watermelon ClaSWEETgenes and 18 melon CmSWEETgenes were identified that showed a high degree of similarity with CsSWEETgenes. The results from this study provided a basic understanding of the CsSWEETgenes and may also facilitate future research to elucidate the function of SWEET genes in cucumber and other Cucurbitaceae crops. 展开更多
关键词 CUCUMBER gene expression phylogenetic analysis sugar transporter SWEET WATERMELON
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Genome-wide identification and analysis of the DREB genes and their expression profiles under abiotic stresses in Chinese jujube(Ziziphus jujuba Mill.) 被引量:8
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作者 Heying Zhou Jiping Jia +4 位作者 Decang Kong Zhendong Zhang Shuang Song Yingyue Li Xiaoming Pang 《Journal of Forestry Research》 SCIE CAS CSCD 2019年第4期1277-1287,共11页
CBF/DREB proteins play a critical role in abiotic stress-mediated gene expression and represent attractive regulons for plant breeding programs.However,no study has been conducted for CBF/DREB protein-related genes in... CBF/DREB proteins play a critical role in abiotic stress-mediated gene expression and represent attractive regulons for plant breeding programs.However,no study has been conducted for CBF/DREB protein-related genes in jujube(Ziziphus jujuba Mill.).In this study,twenty-five ZjDREB genes were identified and annotated from the jujube(Z.jujuba‘Dongzao’)genome.Detailed analysis,including gene classification,annotation,phylogenetic evaluation,conserved motif determination and expression profiling were performed on all genes.Phylogenetic analysis showed that ZjDREB proteins were divided into five subgroups(A1–A5),but lacking a subgroup A6 corresponding to AtDREBs.The ZjDREB genes were distributed in nine of twelve chromosomes in the genome.Additionally,the expression patterns of the DREB genes under different abiotic stresses were investigated using q RT-PCR.Nineteen ZjDREB genes were down-regulated under low temperature,in contrast six ZjDREB genes(01,03,05,11,23 and 24)were up-regulated.Under drought,salinity and high temperature conditions,expression of ZjDREB03,09,10,14,15,17 and 20 genes were induced and showed similar expression patterns,suggesting that various stress conditions share common elements in the signaling pathway.The results suggest that the family of DREB genes play an important role in abiotic stresses in jujube,and provide a foundation for further functional studies of this important class of transcriptional regulators. 展开更多
关键词 Abiotic stress CHINESE JUJUBE DREB expression patterns Phylogenetic analysis
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Structure and expression analysis of the sucrose synthase gene family in apple 被引量:13
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作者 TONG Xiao-lei WANG Zheng-yang +4 位作者 MA Bai-quan ZHANG Chun-xia ZHU Ling-cheng MA Feng-wang LI Ming-jun 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2018年第4期847-856,共10页
Sucrose synthases(SUS) are a family of enzymes that play pivotal roles in carbon partitioning, sink strength and plant development. A total of 11 SUS genes have been identified in the genome of Malus domestica(Md SUSs... Sucrose synthases(SUS) are a family of enzymes that play pivotal roles in carbon partitioning, sink strength and plant development. A total of 11 SUS genes have been identified in the genome of Malus domestica(Md SUSs), and phylogenetic analysis revealed that the Md SUS genes were divided into three groups, named as SUS I, SUS II and SUS III, respectively. The SUS I and SUS III groups included four homologs each, whereas the SUS II group contained three homologs. SUS genes in the same group showed similar structural characteristics, such as exon number, size and length distribution. After assessing four different tissues, Md SUS1 s and Md SUS2.1 showed the highest expression in fruit, whereas Md SUS2.2/2.3 and Md SUS3 s exhibit the highest expression in shoot tips. Most Md SUSs showed decreased expression during fruit development, similar to SUS enzyme activity, but both Md SUS2.1 and Md SUS1.4 displayed opposite expression profiles. These results suggest that different Md SUS genes might play distinct roles in the sink-source sugar cycle and sugar utilization in apple sink tissues. 展开更多
关键词 APPLE sucrose synthase phylogenetic analysis gene expression enzyme activity
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Identification and expression analysis of group Ⅲ WRKY transcription factors in cotton 被引量:5
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作者 DOU Ling-ling GUO Ya-ning +5 位作者 Ondati Evans PANG Chao-you WEI Heng-ling SONG Mei-zhen FAN Shu-li YU Shu-xun 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2016年第11期2469-2480,共12页
The WRKY proteins constitute a large family of transcription factors in plants containing highly conserved WRKYGQK sequences and zinc-finger-like motifs. To comprehensively study WRKY III genes in cotton, we analyzed ... The WRKY proteins constitute a large family of transcription factors in plants containing highly conserved WRKYGQK sequences and zinc-finger-like motifs. To comprehensively study WRKY III genes in cotton, we analyzed the genome sequences of Gossypium hirsutum, G. raimondii and G. arboreum. According to the three genome sequences, 18 group III Gh WRKY genes were identified in G. hirsutum, 12 both in G. raimondii and G. arboreum. Phylogenetic and motif analysis showed that proteins with high similarities could be clustered together and had the same motif components. The ratios of non-synonymous(Ka) to synonymous(Ks) of the Gh WRKY to Gr WRKY or Ga WRKY were lower than 1, which indicated that group III WRKY genes in Gossypium species are under purifying selection. Expression analysis revealed that group III Gh WRKY genes expressed during fiber development and leaf senescence, and most of them could be induced by salicylic acid(SA), jasmonic acid(JA), ethylene, abscisic acid(ABA), mannitol, and Na Cl both in roots and cotyledons. Our study gives a briefly introduction on cotton group III WRKY genes and implicates their potential function in cotton fiber development, leaf senescence and abiotic stresses. 展开更多
关键词 GOSSYPIUM WRKY phylogenetic analysis expression analysis development abiotic stress
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