Comprehensive genomic analysis and expression profiling of cysteine-rich polycomb-like transcription factor gene family in tea tree

Cysteine-rich polycomb-like(CPP)is a small gene family in plants,which plays key role in plant development and stress response.Although CPP transcription factors have been characterized in several other plant species,a genome-wide characterization of the CPP gene family has been absent in Camellia sinensis.In this study,we totally identified 7,8,and 8 non-redundant CsCPP genes in three published genomes,including Camellia sinensis var.assamica cv.Yunkang-10(CSA-YK10),Camellia sinensis var.sinensis cv.Biyun(CSS-BY)and Camellia sinensis var.sinensis cv.Shuchazao(CSS-SCZ).CPP proteins from tea tree and other plant species were classified into three groups,which were further divided into four subgroups based on phylogenetic relationships.Most CPP genes in the same subgroup had similar gene structures and conserved motifs.The cis-acting elements analysis indicated that CPP genes might be involved in plant growth,development and stress responses.Analysis of gene expression using qRT-PCR experiments validated that CPP genes exhibited different expression patterns across the examined tissues.All the genes were expressed differentially in a range of tissues,indicating that CPPs were involved in a range of developmental and physiological processes.This study has obtained new insights into the evolution and function of the CPP gene family in the growth and development of tea plants,and also provide candidate genes for further functional characterization in tea tree.

Identification of potential immune-related prognostic biomarkers of lung cancer using gene co-expression network analysis

Objective The objective of this study was to identify new carcinogenetic hub genes and develop the integration of differentially expressed genes to predict the prognosis of lung cancer.Methods GSE139032 microarray data packages were downloaded from the Gene Expression Omnibus for planning,testing,and review of data.We identified KRT6C,LAMC2,LAMB3,KRT6A,and MYEOV from a key module for validation.Results We found that the five genes were related to a poor prognosis,and the expression levels of these genes were associated with tumor stage.Furthermore,Kaplan-Meier plotter showed that the five hub genes had better prognostic values.The mean levels of methylation in lung adenocarcinoma(LUAD)were significantly lower than those in healthy lung tissues for the hub genes.However,gene set enrichment analysis(GSEA)for single hub genes showed that all of them were immune-related.Conclusion Our findings demonstrated that KRT6C,LAMC2,LAMB3,KRT6A,and MYEOV are all candidate diagnostic and prognostic biomarkers for LUAD.They may have clinical implications in LUAD patients not only for the improvement of risk stratification but also for therapeutic decisions and prognosis prediction.

Gene signatures to therapeutics:Assessing the potential of ivermectin against t(4;14)multiple myeloma

BACKGROUND Multiple myeloma(MM)is a terminal differentiated B-cell tumor disease characterized by clonal proliferation of malignant plasma cells and excessive levels of monoclonal immunoglobulins in the bone marrow.The translocation,(t)(4;14),results in high-risk MM with limited treatment alternatives.Thus,there is an urgent need for identification and validation of potential treatments for this MM subtype.Microarray data and sequencing information from public databases could offer opportunities for the discovery of new diagnostic or therapeutic targets.AIM To elucidate the molecular basis and search for potential effective drugs of t(4;14)MM subtype by employing a comprehensive approach.METHODS The transcriptional signature of t(4;14)MM was sourced from the Gene Expression Omnibus.Two datasets,GSE16558 and GSE116294,which included 17 and 15 t(4;14)MM bone marrow samples,and five and four normal bone marrow samples,respectively.After the differentially expressed genes were identified,the Cytohubba tool was used to screen for hub genes.Then,the hub genes were analyzed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis.Using the STRING database and Cytoscape,protein–protein interaction networks and core targets were identified.Potential small-molecule drugs were identified and validated using the Connectivity Map database and molecular docking analysis,respectively.RESULTS In this study,a total of 258 differentially expressed genes with enriched functions in cancer pathways,namely cytokine receptor interactions,nuclear factor(NF)-κB signaling pathway,lipid metabolism,atherosclerosis,and Hippo signaling pathway,were identified.Ten hub genes(cd45,vcam1,ccl3,cd56,app,cd48,btk,ccr2,cybb,and cxcl12)were identified.Nine drugs,including ivermectin,deforolimus,and isoliquiritigenin,were predicted by the Connectivity Map database to have potential therapeutic effects on t(4;14)MM.In molecular docking,ivermectin showed strong binding affinity to all 10 identified targets,especially cd45 and cybb.Ivermectin inhibited t(4;14)MM cell growth via the NF-κB pathway and induced MM cell apoptosis in vitro.Furthermore,ivermectin increased reactive oxygen species accumulation and altered the mitochondrial membrane potential in t(4;14)MM cells.CONCLUSION Collectively,the findings offer valuable molecular insights for biomarker validation and potential drug development in t(4;14)MM diagnosis and treatment,with ivermectin emerging as a potential therapeutic alternative.

Genome-wide identification and expression analysis of Gossypium RING-H2 finger E3 ligase genes revealed their roles in fiber development,and phytohormone and abiotic stress responses

Background： RING H2 finger E3 ligase （RH2FE3） genes encode cysteine rich proteins that mediate E3 ubiquitin ligase activity and degrade target substrates. The roles of these genes in plant responses to phytohormones and abiotic stresses are well documented in various species, but their roles in cotton fiber development are poorly understood. To date, genome wide identification and expression analyses of Gossypium hirsutum RH2FE3 genes have not been reported. Methods： We performed computational identification, structural and phylogenetic analyses, chromosomal distribution analysis and estimated KJKs values of G hirsutum RH2FE3 genes. Orthologous and paralogous gene pairs were identified by all versus all BLASTP searches. We predicted cis regulatory elements and analyzed microarray data sets to generate heatmaps at different development stages. Tissue specific expression in cotton fiber, and hormonal and abiotic stress responses were determined by quantitative real time polymerase chain reaction （qRT PCR） analysis. Results： We investigated 140 G hirsutum, 80 G. orboreum, and evolutionary mechanisms and compared them with orthologs 89 G. roimondii putative RH2FB genes and their in Arobidopsis and rice. A domain based analysis of the G hirsutum RH2FE3 genes predicted conserved signature motifs and gene structures. Chromosomal localization showed the genes were distributed across all G hirsutum chromosomes, and 60 duplication events （4 tandem and 56 segmental duplications） and 98 orthologs were detected, cis elements were detected in the promoter regions of G hirsutum RH2FE3 genes. Microarray data and qRT PCR analyses showed that G hirsutum RH2FE3 genes were strongly correlated with cotton fiber development. Additionally, almost all the （brassinolide, gibberellic acid （GA）, indole 3-acetic acid drought, and salt）. dentified genes were up regulated in response to phytohormones （IAA）, and salicylic acid （SA）） and abiotic stresses （cold, heat, Conclusions： The genome wide identification, comprehensive analysis, and characterization of conserved domains and gene structures, as well as phylogenetic analysis, cis element prediction, and expression profile analysis of G hirsutum RH2FE3 genes and their roles in cotton fiber development and responses to plant hormones and abiotic stresses are reported here for the first time. Our findings will contribute to the genome wide analysis of putative RH2FE3 genes in other species and lay a foundation for future physiological and functional research on G hirsutum RH2FE3 genes.

Identification of functional genes regulating gastric cancer progression using integrated bioinformatics analysis

BACKGROUND Gastric cancer(GC)is one of the most common cancers and has a poor prognosis.Treatment of GC has remained unchanged over the past few years.AIM To investigate the potential therapeutic targets and related regulatory biomarkers of GC.METHODS We obtained the public GC transcriptome sequencing dataset from the Gene Expression Omnibus database.The datasets contained 348 GC tissues and 141 healthy tissues.In total,251 differentially expressed genes(DEGs)were identified,including 187 down-regulated genes and 64 up-regulated genes.The DEGs’enriched functions and pathways include Progesterone-mediated oocyte maturation,cell cycle,and oocyte meiosis,Hepatitis B,and the Hippo signaling pathway.Survival analysis showed that BUB1,MAD2L1,CCNA2,CCNB1,and BIRC5 may be associated with regulation of the cell cycle phase mitotic spindle checkpoint pathway.We selected 26 regulated genes with the aid of the protein-protein interaction network analyzed by Molecular Complex Detection.RESULTS We focused on three critical genes,which were highly expressed in GC,but negatively related to patient survival.Furthermore,we found that knockdown of Yu K et al.Biochemical analysis in GC WJCC https://www.wjgnet.com 5024 July 26,2023 Volume 11 Issue 21 BIRC5,TRIP13 or UBE2C significantly inhibited cell proliferation and induced cell apoptosis.In addition,knockdown of BIRC5,TRIP13 or UBE2C increased cellular sensitivity to cisplatin.CONCLUSION Our study identified significantly upregulated genes in GC with a poor prognosis using integrated bioinformatics methods.

Peripheral blood RNA biomarkers can predict lesion severity in degenerative cervical myelopathy

Degenerative cervical myelopathy is a common cause of spinal cord injury,with longer symptom duration and higher myelopathy severity indicating a worse prognosis.While numerous studies have investigated serological biomarkers for acute spinal cord injury,few studies have explored such biomarkers for diagnosing degenerative cervical myelopathy.This study involved 30 patients with degenerative cervical myelopathy(51.3±7.3 years old,12 women and 18 men),seven healthy controls(25.7±1.7 years old,one woman and six men),and nine patients with cervical spondylotic radiculopathy(51.9±8.6 years old,three women and six men).Analysis of blood samples from the three groups showed clear differences in transcriptomic characteristics.Enrichment analysis identified 128 differentially expressed genes that were enriched in patients with neurological disabilities.Using least absolute shrinkage and selection operator analysis,we constructed a five-gene model(TBCD,TPM2,PNKD,EIF4G2,and AP5Z1)to diagnose degenerative cervical myelopathy with an accuracy of 93.5%.One-gene models(TCAP and SDHA)identified mild and severe degenerative cervical myelopathy with accuracies of 83.3%and 76.7%,respectively.Signatures of two immune cell types(memory B cells and memory-activated CD4^(+)T cells)predicted levels of lesions in degenerative cervical myelopathy with 80%accuracy.Our results suggest that peripheral blood RNA biomarkers could be used to predict lesion severity in degenerative cervical myelopathy.

Genome-Wide Identification,Expression Profiling and Protein-Protein Interaction Properties of the BEL-Like Homeodomain Gene Family in Apple

BEL1-like homeodomain(BLH)family proteins are homeodomain transcription factors,which are found ubiquitously in plants and play important roles in regulating meristem and flower development.Although BLH proteins have been reported in some plant species,there is very little information available for plants in the Malus genus(e.g.,apple tree:Malus domestica).In the present study,we identified 19 apple MdBLH genes.Phylogenetic analysis revealed that the MdBLH genes could be divided into five groups.Analysis of gene structure showed that MdBLH gene has four exons,and the third exon was 61 bp in length.Chromosomal location analysis suggested that the MdBLH genes are not distributed uniformly on 12 chromosomes.Eleven MdBLH genes were cloned by RT-PCR,and their expression patterns were also determined.Among them,the expression levels of MdBLH4.1 and MdBLH9.1 could be induced by sodium chloride stress,while the expression levels of MdATH1.1,MdBLH8.1,MdBLH8.3,and MdBLH11.1 were down-regulated by such stress.Transcriptional levels of MdATH1.1 and MdBLH7.2 were down-regulated by mannitol stress.The result of yeast two-hybrid experiment showed that MdBEL1.1 interacted with apple ovate family proteins 6(MdOFP6),and MdBLH3.1 interacted with the MdOFP4,MdOFP6,MdOFP13,and MdOFP16 proteins.Our results provide a strong theoretical basis and a valuable reference for analyzing of the biological functions of MdBLH proteins as transcription factors in apple growth,development,and stress and also for the construction of regulatory networks.

Expression Profile Analysis of Genes Involved in Brassinosteroid Biosynthesis Pathway in Cotton Fiber Development

Cotton(Gossypium hirsutum L.) is the leading fiber crop and one of the mainstays of the economy in the world.Cotton fibers,as the main product of cotton plants,are unicellular,linear

Bioinformatics Analysis of Genes and Pathways of CD11b^(+)/Ly6C^(intermediate)Macrophages after Renal Ischemia-Reperfusion Injury

Renal ischemia-reperfusion injury(IRI)is a major cause of acute kidney injury(AKI),which could induce the poor prognosis.The purpose of this study was to characterize the molecular mechanism of the functional changes of CD11 b^(+)/Ly6 C^(intermediate)macrophages after renal IRI.The gene expression profiles of CD11 b^(+)/Ly6 C^(intermediate)macrophages of the sham surgery mice,and the mice 4 h,24 h and 9 days after renal IRI were downloaded from the Gene Expression Omnibus database.Analysis of m RNA expression profiles was conducted to identify differentially expressed genes(DEGs),biological processes and pathways by the series test of cluster.Protein-protein interaction network was constructed and analysed to discover the key genes.A total of 6738 DEGs were identified and assigned to 20 model profiles.DEGs in profile 13 were one of the predominant expression profiles,which are involved in immune cell chemotaxis and proliferation.Signet analysis showed that Atp5 a1,Atp5 o,Cox4 i,Cdc42,Rac2 and Nhp2 were the key genes involved in oxidation-reduction,apoptosis,migration,M1-M2 differentiation,and proliferation of macrophages.RPS18 may be an appreciate reference gene as it was stable in macrophages.The identified DEGs and their enriched pathways investigate factors that may participate in the functional changes of CD11 b^(+)/Ly6 C^(intermediate)macrophages after renal IRI.Moreover,the vital gene Nhp2 may involve the polarization of macrophages,which may be a new target to affect the process of AKI.

酒精性肝炎自噬关键基因的筛选及生物信息学分析

目的筛选酒精性肝炎(AH)的自噬关键基因,探讨AH潜在的生物标志物和治疗靶点。方法采用基因表达综合数据库(GEO)中的2个AH基因芯片和从MSigDB、GeneCards数据库中获得的自噬相关数据集,通过加权基因共表达网络分析(WGCNA)获取关键基因。对筛选的关键基因进行基因本体(GO)、京都基因和基因组百科全书(KEGG)功能富集分析,蛋白质相互作用(PPI)分析,免疫浸润分析,构建信使RNA(mRNA)-微小RNA(miRNA)网络,进行酒精性肝病不同分期的自噬相关关键基因的表达差异分析,并进一步通过实时荧光定量逆转录聚合酶链反应(RT-qPCR)在AH患者和小鼠肝脏组织中验证。结果本研究筛选得到了11个与AH自噬相关的基因(EEF1A2、CFTR、SOX4、TREM2、CTHRC1、HSPB8、TUBB3、PRKAA2、RNASE1、MTCL1、HGF),均为上调基因。在AH患者和小鼠肝脏组织中,SOX4、TREM2、HSPB8、PRKAA2在AH组中的相对表达量均高于对照组。结论SOX4、TREM2、HSPB8、PRKAA2可能是AH潜在的生物标志物和治疗靶点。

甘蓝型油菜REVEILLE家族鉴定及诱导表达分析

【目的】REVEILLE家族基因具有重要生物学功能,而在甘蓝型油菜(Brassica napus L.)中该家族基因研究较少,深入认识甘蓝型油菜中RVE家族基因功能及其与非生物胁迫的关系。【方法】利用生物信息学方法,在甘蓝型油菜、白菜(Brassica rapa)和甘蓝(B.oleracea)中分别鉴定到33、16和16个RVE基因,并对其系统进化、染色体定位、基因结构和理化性质以及启动子顺式元件进行分析。【结果】所有的RVE蛋白被分为两个亚家族。33个BnaRVE分别定位在18条A亚基因组的染色体和15条C亚基因组的染色体上。大部分成员属于较稳定的疏水蛋白;多数Ka/Ks值小于1,说明该家族受到强烈的纯化选择作用。基因结构变异较大,内含子数目在4-11之间。共线性分析结果表明,甘蓝型油菜和拟南芥、白菜、甘蓝存在大量的同源基因。大部分甘蓝型油菜RVE家族成员在子叶和叶都有表达且表达量最多。BnaRVE启动子上含有大量与激素和生物逆境相关的元件,通过定量PCR分析,4个BnaRVE在ABA与MeJA诱导和低温胁迫下的表达量显著上调。【结论】在甘蓝型油菜基因组中鉴定出33个BnaRVE家族成员。不同基因在不同发育时期和不同组织中表现出不同的表达模式。不同基因对各种胁迫存在响应,且表达模式不一。RVE家族成员对ABA、MeJA和冷胁迫具有正向响应功能。

杉木GRF和GIF基因家族鉴定、表达与互作分析

生长调节因子(GRF)和GRF相互作用因子(GIF)在植物的生长发育和逆境胁迫响应中发挥重要作用。为研究GRF和GIF基因在杉木生长发育和逆境胁迫响应中的功能,本研究基于杉木全长转录组数据,利用生物信息学手段共鉴定获得5个ClGRFs基因和2个ClGIFs基因。分析结果显示,ClGRFs氨基酸残基数目范围为386(ClGRF4)~723 aa(ClGRF3),等电点为7.07(ClGRF4)~9.26(ClGRF5);2个ClGIFs蛋白氨基酸数目分别为242和258 aa,等电点均在6左右,蛋白质分子质量分别为25.64和27.96 kDa。保守结构域和基序分析发现ClGRFs蛋白均含QLQ和WRC结构域,ClGIFs蛋白均含SSXT结构域,且高度保守。进一步分析结果显示,ClGRFs分别属于进化枝Ⅲ和进化枝Ⅵ,且均受miR396调控。表达分析结果表明,ClGRFs基因的表达具有一定的组织特异性,而ClGIFs在不同组织呈组成性表达,且ClGRFs和ClGIFs基因均能响应赤霉素(GA3)和水杨酸(SA)的处理。酵母双杂交结果表明5个ClGRFs蛋白和2个ClGIFs蛋白均存在互作关系。本研究结果为进一步研究杉木GRF和GIF基因的功能提供了理论基础。

白菜种子cDNA酵母文库的构建及BrTTG1互作蛋白的筛选及分析

【目的】通过构建白菜种子的cDNA文库,筛选WDR 40蛋白TRANSPARENT TESTA GLABRA 1(TTG1)的互作蛋白,探究TTG1参与MBW三元复合体调控种皮原花青素形成的分子机制。【方法】以棕籽白菜自交系‘B147’的种子为材料,提取总RNA并建立cDNA文库,通过gateway技术构建诱饵载体pGBKT7-TTG1并进行酵母双杂交筛库。【结果】酵母文库库容为1.2×10^(7)CFU,文库滴度是5.0×10^(7)CFU/mL,插入片段平均长度大于1000 bp,诱饵载体在酵母中无自激活活性。通过构建的诱饵载体pGBKT7-TTG1与构建的cDNA文库杂交,共获得了38个阳性互作蛋白,功能预测显示其中一个蛋白注释为MYB转录因子,注释为MYB73,序列分析结果显示该基因含有R2R3-MYB型抑制子保守基序C1和C2,推测该基因为白菜中参与种皮颜色形成的R2R3-MYB型抑制子,暗示着白菜中可能存在不同MYB转录因子参与的调控网络,影响着原花青素的形成。【结论】本研究构建了白菜种子组织的酵母双杂交cDNA文库,获得了38个TTG1阳性互作蛋白,首次挖掘到了可能影响白菜种皮颜色原花青素形成的R2R3-MYB型抑制子MYB73,为后期探究白菜种皮原花青素的调控网络奠定良好的基础。

芥菜SRO基因家族全基因组鉴定与表达分析

【目的】SRO基因家族是植物特有的一类转录因子,在植物生长发育与胁迫响应中具有重要作用,研究芥菜SRO基因家族,为解析芥菜SRO基因功能与遗传改良提供理论依据。【方法】利用生物信息学鉴定油用芥菜与菜用芥菜基因组中的SRO基因家族成员,运用TBtools、MEGA、Cytoscape、NCBI、STRING、EggNOG等软件与数据库进行理化性质、序列特征、进化关系、调控网络等分析以及RT-qPCR分析盐胁迫下的表达模式。【结果】两种类型芥菜SRO基因家族成员数量存在差异,并分属A与B两大类,其中A类SRO蛋白含有WWE、PARP及RST结构域,而B类蛋白则缺少WWE结构域,SRO基因启动子区域含有多种非生物胁迫响应与激素响应的顺式作用元件,microRNA-BjuSRO-靶基因构建复杂调控网络,参与了细胞凋亡、根系形态建成、免疫应答、异源刺激的细胞反应、对活性氧的反应等生物学过程,油用芥菜BjuOSRO基因与甘蓝SRO基因具有较近的进化关系,RT-qPCR结果显示,在盐胁迫下BjuVA1a、BjuVA1e、BjuVA2a、BjuVA3a、BjuVB1b、BjuVA2a显著上调表达。【结论】芥菜SRO基因家族具有功能多样性,BjuVA1a、BjuVA1e、BjuVA2a、BjuVA3a、BjuVB1b、BjuVA2a与盐胁迫响应密切相关,可作为培育耐盐型芥菜新品种的候选基因。

大麦DUF668家族基因鉴定及表达分析

DUF668家族基因对植物逆境胁迫响应有重要作用。为探讨大麦DUF668家族基因的结构及表达模式,采用生物信息学的方法对大麦DUF668基因结构、蛋白结构、系统进化树、共线性及表达模式进行了分析。结果显示,供试大麦中共鉴定出9个DUF668基因,分布在5条染色体上。系统发育进化树将9个DUF668基因分为三个亚组,第Ⅰ亚组包括HvDUF668-01、HvDUF668-02和HvDUF668-09,内含子数量较多,均有11个内含子;第Ⅲ亚组包括HvDUF668-04、HvDUF668-05、HvDUF668-07和HvDUF668-08,内含子数0~3个,其中HvDUF668-04与HvDUF668-05没有内含子;第Ⅱ亚组包括HvDUF668-03和HvDUF668-06,内含子数量(9和7)介于第Ⅰ亚组和第Ⅲ亚组之间。蛋白保守基序分析表明,9个蛋白均含有DUF668保守结构域的特征序列及DUF3475保守结构域的特征序列(HvDUF668-06除外);第Ⅰ亚组蛋白的Motif数量(8~10个)比第Ⅱ、Ⅲ亚组(4~6个)多,且包含第Ⅱ、Ⅲ亚组中的所有Motif。表达谱分析表明,不同DUF668基因在不同组织和发育时期的表达量存在差异,HvDUF668-09在颖果中的表达量随着颖果的发育而升高,而HvDUF668-01和HvDUF668-02则相反;HvDUF668-01和HvDUF668-02在花序中的表达量随着花序的发育而升高。qRT-PCR结果显示,受黄矮病病毒侵染大麦幼苗与未受侵染幼苗相比,HvDUF668-04、HvDUF668-05和HvDUF668-08表达量提高了100~180倍。

绿豆7S球蛋白基因鉴定及在籽粒发育中的表达分析

为阐明绿豆7S(Vigna radiata 7S,Vr7S)球蛋白基因的基本性质及其在籽粒生长发育过程中的表达模式,本研究运用生物信息学、反转录聚合酶链式反应(reverse transcription-polymerase chain reaction,RT-PCR)对10个Vr7S球蛋白基因的理化性质、基因结构特征、蛋白三级结构、系统发育关系及基因表达谱等进行研究。结果表明,Vr7S球蛋白基因编码的蛋白长度为246~594个氨基酸,等电点位于5.02~6.40之间,分子质量为27.82~70.02 kDa;所有Vr7S球蛋白基因包含3~7个外显子、2~6个内含子、5~8个保守基序;除Vr7S B1具有1个cupin保守结构域外,其余9个基因均含有2个cupin结构域;Vr7S球蛋白三级结构有4种类型,主要包含α-螺旋、β-链等结构;在cupin保守结构域中,绿豆和其他物种共有67个保守氨基酸残基,绿豆与赤豆7S球蛋白基因间的同源关系最近,其次是菜豆、木豆及大豆等。基于不同绿豆品种、不同发育时期籽粒的转录组测序和RT-PCR表达谱分析显示,Vr7S球蛋白基因伴随着绿豆籽粒的发育成熟呈现表达量升高的趋势,这与其他豆科物种7S球蛋白基因的表达模式一致,表明其在绿豆籽粒贮藏蛋白的生成调控过程中具有积极作用。本研究为进一步解析Vr7S球蛋白基因在绿豆籽粒发育中的生物学功能奠定了基础。

Mining Heat Stress Associated Genes in Tomato Fruit (Solanum lycopersicum L.) Through RNA-seq

Tomato(Solanum lycopersicum L.)is a thermophilic vegetable crop,but sensitive to high temperature stress,especially under the greenhouse conditions.Due to global climate changes,heat stress has now become a great threat to tomato production and fruit quality.Many studies have been conducted to determine the functions of genes in tomato responsive to abiotic and biotic stresses,but transcriptomic information on heat stress responses of tomato fruit is still limited.To investigate heat stress associated genes in tomato fruit,a cDNA library was constructed using fruit harvested from tomato cv.P19-9 plants grown under 42℃for 0,1,2 and4 h and the expression profiles of heat stress responsive genes in tomato fruit were analyzed through RNA-seq.A total of 632224558 clean high quality paired-end reads were obtained and then mapped to reference genome for RNA-seq analysis.After quality control analysis,alignment analysis and transcript assembly,a total of 55457 RNA transcripts were obtained with functional annotations.Overall,6869 differentially expressed genes(DEGs)were identified with a significant response to one or more of the three heat stress treatment times.Based on GO enrichment analysis,22 genes potentially involved in tomato thermo-tolerance were selected and validated for their expressions through qPCR.The expression profile of tomato fruit genes obtained in this study could shed light on the mechanism and gene editing breeding projects for tomato thermo-tolerance.These findings could also benefit improvement of harvest and storage of tomato in greenhouse.

Wheat kinase TaSnRK2.4 forms a functional module with phosphatase TaPP2C01 and transcription factor TaABF2 to regulate drought response

SNF1-related protein kinase 2(SnRK2)family members are essential components of the plant abscisic acid(ABA)signaling pathway initiated by osmotic stress and triggering a drought stress response.This study characterized the molecular properties of TaSnRK2.4 and its function in mediating adaptation to drought in Triticum aestivum.Transcripts of TaSnRK2.4 were upregulated upon drought and ABA signaling and associated with drought-and ABA-responsive cis-elements ABRE and DRE,and MYB and MYC binding sites in the promoter as indicated by reporter GUS protein staining and activity driven by truncations of the promoter.Yeast two-hybrid,BiFC,and Co-IP assays indicated that TaSnRK2.4 protein interacts with TaPP2C01 and an ABF transcription factor(TF)TaABF2.The results suggested that TaSnRK2.4 forms a functional TaPP2C01-TaSnRK2.4-TaABF2 module with its upstream and downstream partners.Transgene analysis revealed that TaSnRK2.4 and TaABF2 positively regulate drought tolerance whereas TaPP2C01 acts negatively by modulating stomatal movement,osmotic adjustment,reactive oxygen species(ROS)homeostasis,and root morphology.Expression analysis,yeast one-hybrid,and transcriptional activation assays indicated that several osmotic stress-responsive genes,including TaSLAC1-4,TaP5CS3,TaSOD5,TaCAT1,and TaPIN4,are regulated by TaABF2.Transgene analysis verified their functions in positively regulating stomatal movement(TaSLAC1-4),proline accumulation(TaP5CS3),SOD activity(TaSOD5),CAT activity(TaCAT1),and root morphology(TaPIN4).There were high correlations between plant biomass and yield with module transcripts in a wheat variety panel cultivated under drought conditions in the field.Our findings provide insights into understanding plant drought response underlying the SnRK2 signaling pathway in common wheat.

Identification of microRNAs and messenger RNAs involved in human umbilical cord mesenchymal stem cell treatment of ischemic cerebral infarction using integrated bioinformatics analysis

In recent years,a large number of differentially expressed genes have been identified in human umbilical cord mesenchymal stem cell(hUMSC)transplants for the treatment of ischemic cerebral infarction.These genes are involved in various biochemical processes,but the role of microRNAs(miRNAs)in this process is still unclear.From the Gene Expression Omnibus(GEO)database,we downloaded two microarray datasets for GSE78731(messenger RNA(mRNA)profile)and GSE97532(miRNA profile).The differentially expressed genes screened were compared between the hUMSC group and the middle cerebral artery occlusion group.Gene ontology enrichment and pathway enrichment analyses were subsequently conducted using the online Database for Annotation,Visualization,and Integrated Discovery.Identified genes were applied to perform weighted gene co-suppression analyses,to establish a weighted co-expression network model.Furthermore,the protein-protein interaction network for differentially expressed genes from turquoise modules was built using Cytoscape(version 3.40)and the most highly correlated subnetwork was extracted from the protein-protein interaction network using the MCODE plugin.The predicted target genes for differentially expressed miRNAs were also identified using the online database starBase v3.0.A total of 3698 differentially expressed genes were identified.Gene ontology analysis demonstrated that differentially expressed genes that are related to hUMSC treatment of ischemic cerebral infarction are involved in endocytosis and inflammatory responses.We identified 12 differentially expressed miRNAs in middle cerebral artery occlusion rats after hUMSC treatment,and these differentially expressed miRNAs were mainly involved in signaling in inflammatory pathways,such as in the regulation of neutrophil migration.In conclusion,we have identified a number of differentially expressed genes and differentially expressed mRNAs,miRNA-mRNAs,and signaling pathways involved in the hUMSC treatment of ischemic cerebral infarction.Bioinformatics and interaction analyses can provide novel clues for further research into hUMSC treatment of ischemic cerebral infarction.

Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var.rapa

The Lateral Organ Boundaries Domain(LBD)genes encode highly conserved plant-specific LOB domain proteins which regulate growth and development in various species.However,members of the LBD gene family have yet to be identified in Brassica rapa var.rapa.In the present study,fifty-nine LBD genes were identified and distributed on 10 chromosomes.The BrrLBD proteins are predicted to encode hydrophobic polypeptides between 118 and 394 amino acids in length and with molecular weights ranging from 13.31 to 44.24 kDa;the theoretical pi for these proteins varies from 4.83 to 9.68.There were 17 paralogous gene pairs in the BrrLBD family,suggesting that the amplification of the BrrLBD gene family involved largescale gene duplication events.Members of the BrrLBD family were divided into 7 subclades(class I a to e,class II a and b).Analysis of gene structure and conserved domains revealed that most BrrLBD genes of the same subclade had similar gene structures and protein motifs.The expression profiles of 59 BrrLBD genes were determined through Quantitative Real-time fluorescent PCR(qRT-PCR).Most BrrLBD genes in the same subclade had similar gene expression profiles.However,the expression patterns of 7 genes differed from their duplicates,indicating that although the gene function of most BrrLBD genes has been conserved,some BrrLBD genes may have undergone evolutionary change.