GST family genes in jujube actively respond to phytoplasma infection

Jujube witches’broom(JWB)caused by phytoplasma has a severely negative effect on multiple metabolisms in jujube.The GST gene family in plants participates in the regulation of a variety of biotic and abiotic stresses.This study aims to identify and reveal the changes in the jujube GST gene family in response to phytoplasma infection.Here,70 ZjGSTs were identified in the jujube genome and divided into 8 classes.Among them,the Tau-class,including 44 genes,was the largest.Phylogenetic analysis indicated that Tau-class genes were highly conserved among species,such as Arabidopsis,cotton,chickpea,and rice.Through chromosome location analysis,37.1%of genes were clustered,and 8 of 9 gene clusters were composed of Tau class members.Through RT-PCR,qRT-PCR and enzyme activity detection,the results showed that the expression of half(20/40)of the tested ZjGSTs was inhibited by phytoplasma infection in field and tissue culture conditions,and GST activity was also significantly reduced.In the resistant and susceptible varieties under phytoplasma infection,ZjGSTU49-ZjGSTU54 in the cluster IV showed opposite expression patterns,which may be due to functional divergence during evolution.Some upregulated genes(ZjGSTU45,ZjGSTU49,ZjGSTU59,and ZjGSTU70)might be involved in the process of jujube against JWB.The yeast two-hybrid results showed that all 6 Tauclass proteins tested could form homodimers or heterodimers.Overall,the comprehensive analysis of the jujube GST gene family revealed that ZjGSTs responded actively to phytoplasma infection.Furthermore,some screened genes(ZjGSTU24,ZjGSTU49-52,ZjGSTU70,and ZjDHAR10)will contribute to further functional studies of jujube-phytoplasma interactions.

Effects of Heterologously Overexpressing PIP5K-Family Genes in Arabidopsis on Inflorescence Development

Castor is one of the top 10 oil crops in the world and has extremely valuable uses.Castor inflorescences directly affect yield,so the study of inflorescence development is very important in increasing castor yield.Our previous studies have shown that the PIP5K gene family(PIP5Ks)is associated with inflorescence development.In this study,to determine the function of each PIP5K gene in castor,a female Lm-type castor line,aLmAB2,was used to determine the relative expression levels of the PIP5Ks in castor inflorescences.Six PIP5K genes were heterologously overexpressed in Arabidopsis thaliana,the relative expression of each gene and the effect on plants was determined in A.thaliana,and the relationships among the PIP5Ks in castor were inferred.The expression levels of the PIP5Ks in the female Lm-type castor line aLmAB2 were analyzed.The relative expression levels of the PIP5K9 and PIP5K11 genes were high(p<0.05)in isofemale inflorescences,and those of PIP5K1,PIP5K2,PIP5K6,and PIP5K8 were high(p<0.05)in female inflorescences but low(p<0.05)in bisexual inflorescences.The PIP5Ks were heterologously overexpressed in A.thaliana,and T3-generation plants with stable genetic resistance,i.e.,AT-PIP5K^(+)plants(AT-PIP5K1^(+),AT-PIP5K2^(+),AT-PIP5K6^(+),AT-PIP5K8^(+),AT-PIP5K9^(+),and ATPIP5K11^(+) plants),were obtained.Biological tests of the AT-PIP5K+plants showed that the growth of the main stem was significantly delayed in AT-PIP5K+plants compared with Columbia wild-type(WT)A.thaliana plants;the PIP5K1 and PIP5K2 genes promoted lateral stem growth and flower and silique development;and the PIP5K6,PIP5K8,PIP5K9 and PIP5K11 genes inhibited lateral stem growth and flower and silique development.The correlations among PIP5Ks in castor suggest that there may be a synergistic relationship among PIP5K1,PIP5K2,and PIP5K6 in castor inflorescences,and PIP5K8,PIP5K9,and PIP5K11 are complementary to the other three genes.

Comprehensive analysis of clinical and biological value of ING family genes in liver cancer

BACKGROUND Liver cancer(LIHC)is a malignant tumor that occurs in the liver and has a high mortality in cancer.The ING family genes were identified as tumor suppressor genes.Dysregulated expression of these genes can lead to cell cycle arrest,senescence and/or apoptosis.ING family genes are promising targets for anticancer therapy.However,their role in LIHC is still not well understood.AIM To have a better understanding of the important roles of ING family members in LIHC.METHODS A series of bioinformatics approaches(including gene expression analysis,genetic alteration analysis,survival analysis,immune infiltration analysis,prediction of upstream microRNAs(miRNAs)and long noncoding RNAs(lncRNAs)of ING1,and ING1-related gene functional enrichment analysis)was applied to study the expression profile,clinical relationship,prognostic significance and immune infiltration of ING in LIHC.The relationship between ING family genes expression and tumor associated immune checkpoints was investigated in LIHC.The molecular mechanism of ING1 mediated hepatocarcinogenesis was preliminarily discussed.RESULTS mRNA/protein expression of different ING family genes in LIHC was analyzed in different databases,showing that ING family genes were highly expressed in LIHC.In 47 samples from 366 LIHC patients,the ING family genes were altered at a rate of 13%.By comprehensively analyzing the expression,clinical pathological parameters and prognostic value of ING family genes,ING1/5 was identified.ING1/5 was related to poor prognosis of LIHC,suggesting that they may play key roles in LIHC tumorigenesis and progression.One of the target miRNAs of ING1 was identified as hsa-miR-214-3p.Two upstream lncRNAs of hsa-miR-214-3p,U91328.1,and HCG17,were identified.At the same time,we found that the expression of ING family genes was correlated with immune cell infiltration and immune checkpoint genes.CONCLUSION This study lays a foundation for further research on the potential mechanism and clinical value of ING family genes in the treatment and prognosis of LIHC.

Deciphering the role of FSCN family genes in cancer:a pan-cancer bioinformatics study

Background:The Fascin(FSCN)family,comprising actin-bundling proteins,plays vital roles in cytoskeletal reorganization and cell migration.FSCN1,FSCN2,and FSCN3 are implicated in cancer progression through cell motility,invasion,and metastasis.However,their specific contributions across different cancer types remain unclear.Methods:We conducted a pan-cancer bioinformatics analysis of FSCN genes using data from The Cancer Genome Atlas.This included differential expression patterns,copy number variations(CNVs),mutations,methylation status,and correlations with tumor mutational burden,microsatellite instability,and immune checkpoint molecule expression.Differential expression was analyzed using DESeq2,while CNV and mutation analyses utilized GISTIC2.0 and MuTect2.Methylation data were assessed using the Illumina Human Methylation 450K BeadChip.Results:FSCN1 and FSCN2 showed significant differential expression in multiple cancers,often correlating with poor prognosis.FSCN3 exhibited less variability but a protective role in certain contexts.CNV analysis indicated frequent gene gains in FSCN genes,correlating with increased expression.FSCN3 had a higher mutation rate,suggesting genetic instability.Methylation analysis showed hypomethylation of FSCN1 and FSCN2 in tumors compared to normal tissues,whereas FSCN3 had minor changes.Significant associations were found between FSCN gene expression and tumor mutational burden,microsatellite instability,and immune checkpoint molecules,suggesting their involvement in tumor immunogenicity and the immune microenvironment.Conclusions:This pan-cancer analysis highlights the multifaceted roles of FSCN genes in cancer biology,emphasizing their potential as biomarkers and therapeutic targets.FSCN1 and FSCN2 are associated with poor prognosis and aggressive phenotypes,while FSCN3 shows protective roles in specific contexts.These findings offer new avenues for cancer diagnosis and treatment,particularly in personalized medicine.Future studies should validate these findings and explore the underlying mechanisms to fully harness the clinical potential of FSCN family proteins in oncology.

Genome-wide identification,characterization and functional prediction of the SRS gene family in sesame(Sesamum indicum L.)

Sesame(Sesamum indicum L.)is an ancient oilseed crop of the Pedaliaceae family with high oil content and potential health benefits.SHI RELATED SEQUENCE(SRS)proteins are the transcription factors(TFs)specific to plants that contain RING-like zinc finger domain and are associated with the regulation of several physiological and biochemical processes.They also play vital roles in plant growth and development such as root formation,leaf development,floral development,hormone biosynthesis,signal transduction,and biotic and abiotic stress responses.Nevertheless,the SRS gene family was not reported in sesame yet.In this study,identification,molecular characterization,phylogenetic relationship,cis-acting regulatory elements,protein-protein interaction,syntenic relationship,duplication events and expression pattern of SRS genes were analyzed in S.indicum.We identified total six SiSRS genes on seven different linkage groups in the S.indicum genome by comparing with the other species,including the model plant Arabidopsis thaliana.The SiSRS genes showed variation in their structure like2–5 exons and 1–4 introns.Like other species,SiSRS proteins also contained‘RING-like zinc finger'and‘LRP1'domains.Then,the SiSRS genes were clustered into subclasses via phylogenetic analysis with proteins of S.indicum,A.thaliana,and some other plant species.The cis-acting regulatory elements analysis revealed that the promoter region of SiSRS4(SIN_1011561)showed the highest 13 and 16 elements for light-and phytohormone-responses whereas,SiSRS1(SIN_1015187)showed the highest 15 elements for stress-response.The ABREs,or ABA-responsive elements,were found in a maximum of 8 copies in the SiSRS3(SIN 1009100).Moreover,the available RNA-seq based expression of SiSRS genes revealed variation in expression patterns between stress-treated and non-treated samples,especially in drought and salinity conditions in.S.indicum.Two SiSRS genes like SiSRS1(SIN_1015187)and SiSRS5(SIN_1021065),also exhibited variable expression patterns between control vs PEG-treated sesame root samples and three SiSRS genes,including SiSRS1(SIN_1015187),SiSRS2(SIN_1003328)and SiSRS5(SIN_1021065)were responsive to salinity treatments.The present outcomes will encourage more research into the gene expression and functionality analysis of SiSRS genes in S.indicum and other related species.

Genome wide investigation of Hsf gene family in Phoebe bournei:identification,evolution,and expression after abiotic stresses

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.

Genome-Wide Identification of Tomato (Solanum lycopersicum L.) CKX Gene Family and Expression Analysis in the Callus Tissue under Zeatin Treatment

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.

Identification and Molecular Characterization of the Alkaloid Biosynthesis Gene Family in Dendrobium catenatum

As one of the main active components of Dendrobium catenatum, alkaloids have high medicinal value. The physicochemicalproperties, conserved domains and motifs, phylogenetic analysis, and cis-acting elements of the genefamily members in the alkaloid biosynthesis pathway of D. catenatum were analyzed by bioinformatics, and theexpression of the genes in different years and tissues was analyzed by qRT-PCR. There are 16 gene families,including 25 genes, in the D. catenatum alkaloid biosynthesis pathway. The analysis of conserved domains andmotifs showed that the types, quantities, and orders of domains and motifs were similar among members ofthe same family, but there were significant differences among families. Phylogenetic analysis indicated that thegene family members showed some evolutionary conservation. Cis-acting element analysis revealed that therewere a large number of light-responsive elements and MYB (v-myb avian myeloblastosis viral oncogene homolog)-related elements in these genes. qRT-PCR showed that expressions of gene family members involved in alkaloidsynthesis were different in different years and tissues of D. catenatum. This study provides a theoretical basisfor further exploration of the regulatory mechanisms of these genes in the alkaloid biosynthesis of D. catenatum.

Identification and Analysis of the WRKY Transcription Factor Gene Family in Verbena bonariensis

The WRKY transcription factor gene family is one of the unique gene families in plants.It plays an important role in response to abiotic stresses such as cold and drought,hormone signal transduction,regulation of biosynthesis,leaf senescence seed germination,etc.However,little information is available about WRKY transcription factors in Verbena bonariensis.In this study,70 VbWRKY genes were identified from the whole genome.The phylogenetic analysis of the WRKY gene family in V.bonariensis and Arabidopsis shows that the WRKY genes in V.bonariensis can be divided into three groups:I,II,and III,which contain 13,47,and 10 members,respectively.Group II can be further divided into five subclasses:IIa(5),IIb(10),IIc(18),IId(6),and IIe(8).Conservative motif analysis showed that 64 proteins encoded by the VbWRKY gene had conserved motifs 1,2 and 3,and the same subclass motif elements were approximately the same.The collinearity analysis showed that there were 44 homologous gene pairs among the VbWRKYs,and these homologous gene pairs may have the same function.Promoter sequence analysis showed that the VbWRKY gene has multiple cis-acting elements,including not only cis-acting elements related to low-temperature and light responses,but also cis-acting elements related to hormone regulation,Among them,most VbWRKY genes contain response elements about low-temperature,and 30 VbWRKY genes contain low-temperature response elements(LTR),and 61 VbWRKY genes contain abscisic acid response elements(ABRE),indicating that VbWRKY plays a crucial role in plant growth and abiotic stress.According to the expression of VbWRKY in the cold stress and different tissues transcriptome,70 VbWRKY genes played their respective roles in various tissues and stages to regulate plant growth,Also,some of them participated in the process of cold stress tolerance,52 VbWRKYs showed significant differences in expression under cold stress,and 37 VbWRKY genes were up-regulated under cold stress.9 VbWRKY genes were selected for quantitative real-time PCR(qRT-PCR)analysis under low-temperature stress,and the results showed that all 9 genes were upregulated under low-temperature stress.Ultimately,the present study provides a comprehensive analysis of the predicted V.bonariensis WRKY genes family,which provided a theoretical basis for the study of low-temperature resistance and growth and development of V.bonariensis.

Transcriptome profiling and RXR gene family identification reveals the molecular mechanism of rapid aging after spawning of cuttlefish Sepiella japonica

Sepiella japonica is a worldwide marine cuttlefish species of high economic value.S.japonica routinely modifying behaviors in reproductive life,such as rapid aging until death after spawning,has been recognized in artificial breeding.However,reproductive behavior at the level of genes is rarely reported,thus,the research on the genetic basis of behavior,reproduction,and artificial breeding was limited.We applied RNA-seq in different stages of reproduction to investigate the reason of rapid aging after spawning,pre-maturity,pre-spawning after maturity,and post-spawning.The retinoid X receptor(RXR)gene family in S.japonica was identified,and 1343–1452 differentially expressed genes(DEGs)in all 3 stages of reproductive life were identified from pairwise m RNA comparisons.Furthermore,through the GO term and KEGG analysis,S.japonica could handle neuronal development and network formation before maturity and have a functional degradation of neural communication,signal transduction,vision,and gene expression after spawning.Eight Sj RXRαs have been identified and they played different roles in growth development or reproduction.Therefore,the regulation of several channels and receptors is the intrinsic molecular mechanism of rapid aging after spawning in S.japonica.This study revealed the survival strategy and provided fundamental data on the level of genes for understanding the reproductive behavior and the reproduction of S.japonica.

Functional Studies of Castor(Ricinus communis L.)PLC Family Genes in Arabidopsis Inflorescence Development

Castor(Ricinus communis L.)is one of the top 10 oil crops in the world,and inflorescence is a trait that directly affects its yield.Phospholipase C(PLCs)is involved in many plant activities and metabolic processes.To study the functions of PLC family genes in the regulation of the inflorescence development of the female line of Lm-type castor aLmAB2,we determined the expression levels of six PLC family genes of three types of inflorescences of aLmAB2(isofemale line,female line,bisexual line)at different developmental stages.The results showed that the 6 genes of the castor PLC family had relative expression levels at different developmental stages of the three types of inflorescences.The subcellular location of all six protein products was the cell membrane.The six genes were heterologously overexpressed in Arabidopsis thaliana to obtain the T3 generation-resistant Arabidopsis thaliana plants.The results showed that the overexpression of six genes significantly promoted the maturation of Arabidopsis thaliana,the growth of lateral moss,and the development of flowers and pods,but the development of basal leaves and stem leaves of Arabidopsis thaliana was significantly inhibited.According to homology analysis,it is speculated that PLC2,PLC2M,PLC2N,PLC4,PLC4X2,and PLC6 genes have the same regulatory function.

Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes

The biological function of the novel zinc-finger SWIM domain-containing protein family(ZSWIM)during embryonic development remains elusive.Here,we conducted a genome-wide analysis to explore the evolutionary processes of the ZSWIM gene family members in mice,Xenopus tropicalis,zebrafish,and humans.We identified nine putative ZSWIM genes in the human and mouse genome,eight in the Xenopus genome,and five in the zebrafish genome.Based on multiple sequence alignment,three members,ZSWIM5,ZSWIM6,and ZSWIM8,demonstrated the highest homology across all four species.Using available RNA sequencing(RNAseq)data,ZSWIM genes were found to be widely expressed across different tissues,with distinct tissuespecific properties.To identify the functions of the ZSWIM protein family during embryogenesis,we examined temporal and spatial expression patterns of zswim family genes in Xenopus embryos.Quantitative real-time polymerase chain reaction(qRT-PCR)revealed that each member had a distinct expression profile.Whole-mount in situ hybridization showed that both zswim1 and zswim3 were maternally expressed genes;zswim5 and zswim6were expressed throughout embryogenesis and displayed dynamic expression in the brain,eyes,somite,and bronchial arch at the late tailbud stages;zswim7 was detected in the eye area;zswim8 showed a dynamic expression pattern during the tailbud stages,with expression detected in the brain,eyes,and somite;zswim9 was faintly expressed throughout embryonic development.This study provides a foundation for future research to delineate the functions of ZSWIM gene members.

Genome-wide identification of TPS genes in sesame and analysis of their expression in response to abiotic stresses

Trehalose and its precursor,trehalose-6-phosphate,play critical roles in plant metabolism and response to abiotic stresses.Trehalose-6-phosphate synthase(TPS)is a key enzyme in the trehalose synthesis pathway.Hence this study identified TPS genes in sesame(SiTPSs)and examined their expression patterns under various abiotic stresses.Totally,ten SiTPSs were identified and comprehensively characterized.SiTPSs were found to be unevenly distributed on five out of 13 sesame chromosomes and were predicted to be localized in chloroplasts and vacuoles of cells.Phylogenetic analysis classified SiTPS proteins into two groups(I and II),which was supported by gene structure and conserved motif analyses.Analysis of cis-acting elements in promoter regions of SiTPSs revealed that they might primarily involve developmental and environmental responses.SiTPSs exhibited different expression patterns in different tissues and under different abiotic stresses.Most group II SiTPS genes(SiTPS4-SiTPS10)were strongly induced by drought,salt,waterlogging,and osmotic stress.Particularly,SiTPS10 was the most significantly up-regulated under various abiotic stresses,indicating it is a candidate gene for improving sesame tolerance to multiple abiotic stresses.Our results provide insight into the TPS gene family in sesame and fundamental resources for genomics studies towards dissecting SiTPS genes’functions.

Genome-wide identification of the MATE gene family and functional characterization of PbrMATE9 related to anthocyanin in pear

Plant multidrug and toxic compound extrusion(MATE) genes play an important role in the process of detoxification, plant morphogenesis, and anthocyanin accumulation. However, whether the MATE gene family functions in pear peel coloration is still unknown. To evaluate and identify the MATE gene family members which are involving in anthocyanin accumulation and coloration in pear. In this study, 85 MATE genes were identified in the reference pear genome of ‘Dangshansuli’ through genome-wide identification. Based on gene structure and phylogenetic tree analysis, the MATE family was divided into five subfamilies. RNA sequencing and quantitative real-time polymerase chain reaction(qRTPCR) indicated that the expression patterns of PbrMATEs were tissue-specific. 28.24%(24) of PbrMATE genes were expressed in the fruits, and44.71%(38) of PbrMATE genes were expressed in the leaves. Additionally, we found that the expression levels of PbrMATE9, PbrMATE26,PbrMATE50, and PbrMATE69 in debagged fruits with red peel were significantly higher than those in bagged fruits without red peel, according to our bagging/debagging treatment of ‘Mantianhong’. The expression pattern of PbrMATE9 was consistent with the variation trend in anthocyanin content, suggesting that it might play an important role in anthocyanin accumulation in response to light exposure. Subcellular localization showed that PbrMATE9 was a membrane protein. More strikingly, the transient overexpression of PbrMATE9 promoted anthocyanin accumulation in the peel of pear, and the expression of structural genes(PbrCHI, PbrANS, PbrDFR, and PbrUFGT) in the anthocyanin biosynthesis pathway also increased significantly. Through co-expression network analysis, the transcription factors were identified, such as WRKY, COL,GATA, and BBX, which might be involved in the regulation of PbrMATE9. The study has enriched the genetic resources and improved the understanding of the regulation network of anthocyanin accumulation in pear.

Molecular Clone, Expression, and Prediction of Construction and Function to Key Genes of Interleukin Family of Porcine

This research was to clone, express, and analyze the structure and function of major molecules of porcine interleukin family. Genes of porcine interleukin family were cloned by RT-PCR from stimulated porcine PBMC by LPS and PHA, and then expressed in E. coli, and the structure and function of these molecules were predicted by ExPASY. The results showed that genes of IL-4, IL-6, and IL-18 were successfully cloned and expressed. Furthermore, the expression products of recombinant IL-4 and IL-6 both have multiple biological activities. By analyzing these genes with the NCBI/GenBank data, the homologies of the nucleotide acid sequence are 99.25, 99.21, and 100%, respectively, and have great species differences when compared with other animal species. The results of the prediction showed that all these molecules contain several phosphorylation, glycosylation, protein kinase, and signal transduction bonding sites in secondary structure, and all are compact globularity protein in space configuration. These characteristics of structure are the basis for their multiple biological functions. The genes, structure and function of key molecular of porcine interleukin family were successfully cloned, expressed, and analyzed in this paper.

Genome-wide identification and expression analyses of homeodomain-leucine zipper family genes reveal their involvement in stress response in apple(Malus×domestica)

The homeodomain-leucine zipper(HD-Zip)family has been shown to perform amultitude of functions during plant development and stress responses;however,the familymembers and functions have not been identified in apple(Malus×domestica).In this study,83 HD-Zips(MdHDZs)were identified in the apple genome.They were assembled into four subgroups according to the classification in Arabidopsis,where MdHDZs in the same subgroup had similar gene structures and conserved protein motifs.Putative cis-element analysis of MdHDZs promoter regions uncovered numerous elements related to the response of stress and plant hormones.In addition,twelve transcripts of the MdHDZs showed different expression patterns under salt,drought,low temperature and ABA stresses by quantitative reverse transcription-PCR(qRT-PCR)assay.To further explore the function of MdHDZs in apple,MdHDZ3 was selected to verify its function under salt,low temperature and ABA stresses;and genetic transformation was used to obtain MdHDZ3 transgenic apple calli.The results demonstrated that MdHDZ3 increased sensitivity to salt,low temperature and abscisic acid in apple calli,suggesting that MdHDZ3 plays an important role in response to stresses.Subcellular localization and three-dimensional structural analysis revealed that MdHDZ3 was a nuclear-localized protein.Taken together,these findings provide potential information for further identification of HD-Zip proteins in apple.

Identifying and validating MMP family members(MMP2,MMP9,MMP12,and MMP16)as therapeutic targets and biomarkers in kidney renal clear cell carcinoma(KIRC)

Kidney Renal Clear Cell Carcinoma(KIRC)is a malignant tumor that carries a substantial risk of morbidity and mortality.The MMP family assumes a crucial role in tumor invasion and metastasis.This study aimed to uncover the mechanistic relevance of the MMP gene family as a therapeutic target and diagnostic biomarker in Kidney Renal Clear Cell Carcinoma(KIRC)through a comprehensive approach encompassing both computational and molecular analyses.STRING,Cytoscape,UALCAN,GEPIA,OncoDB,HPA,cBioPortal,GSEA,TIMER,ENCORI,DrugBank,targeted bisulfite sequencing(bisulfite-seq),conventional PCR,Sanger sequencing,and RT-qPCR based analyses were used in the present study to analyze MMP gene family members to accurately determine a few hub genes that can be utilized as both therapeutic targets and diagnostic biomarkers for KIRC.By performing STRING and Cytohubba analyses of the 24 MMP gene family members,MMP2(matrix metallopeptidase 2),MMP9(matrix metallopeptidase 9),MMP12(matrix metallopeptidase 12),and MMP16(matrix metallopeptidase 16)genes were denoted as hub genes having highest degree scores.After analyzing MMP2,MMP9,MMP12,and MMP16 via various TCGA databases and RT-qPCR technique across clinical samples and KIRC cell lines,interestingly,all these hub genes were found significantly overexpressed at mRNA and protein levels in KIRC samples relative to controls.The notable effect of the up-regulated MMP2,MMP9,MMP12,and MMP16 was also documented on the overall survival(OS)of the KIRC patients.Moreover,targeted bisulfite-sequencing(bisulfite-seq)analysis revealed that promoter hypomethylation pattern was associated with up-regulation of hub genes(MMP2,MMP9,MMP12,and MMP16).In addition to this,hub genes were involved in various diverse oncogenic pathways.The MMP gene family members(MMP2,MMP9,MMP12,and MMP16)may serve as therapeutic targets and prognostic biomarkers in KIRC.

Characterization of Caspase Gene Family Members in Spotted Sea Bass(Lateolabrax maculatus)and Their Expression Profiles in Response to Vibrio harveyi Infection

The caspase gene family is a crucial gene cluster that regulates apoptosis which contribute to programmed cell death,cell proliferation and differentiation,and several immune responses.In our study,a complete set of 12 caspase genes were identified in spotted sea bass Lateolabrax maculatus.These genes were divided into three subfamilies:2 inflammatory caspases(casp-1 and casp-14-like),5 apoptosis initiators(casp-2,casp-8a,casp-8b,casp-9,and casp-10),and 5 apoptosis executioners(casp-3a,casp-3b,casp-3-like,casp-6,and casp-7).Their phylogenetic relationships,synteny and gene structures were systematically analyzed.Furthermore,the relative expression profiles of the caspase family members in the liver,intestine,head kidney,and spleen were measured by q PCR after infection with Vibrio harveyi.The results showed that the overall mRNA levels of the caspase genes were dramatically increased after V.harveyi infection,and the expression patterns varied among genes and tissues.More caspase genes underwent pronounced expression changes in the head kidney and spleen than in the liver or intestine,mainly after 48 h of the challenge.Specifically,casp-3a,casp-3b,casp-3-like,casp-6,casp-7,casp-8a,casp-8b,casp-10,and casp-14-like in the head kidney,and casp-3-like,casp-6,casp-7,and casp-14-like in the spleen,were the most responsive caspase genes which may contribute significantly to immune regulation in spotted sea bass.Additionally,the apoptosis level in head kidney and spleen after infection were examined using the Caspase assay.Our study provides a systemic overview of the caspase gene family in spotted sea bass after V.harveyi infection and lays a foundation for further deciphering the biological roles of these caspase genes.

Genome-Wide Identification and Expression Analysis of the Phytocyanin Gene Family in Nicotiana tabacum

Phytocyanin(PC)is a class of plant-specific blue copper proteins involved in electron transport,plant growth,development,and stress resistance.However,PC proteins have not been systematically evaluated in tobacco plants.We determined the whole-genome sequences of the PC family in the tobacco cultivar‘K326.’The transcriptome data were used to analyze the expression of the NtPC family at different development stages and tissue-specific genes.Real-time fluorescence quantitative analysis was used to analyze the expression of the NtPC gene family under low temperature and methyl jasmonate stress.The tobacco NtPC family contained 110 members and was divided into four subfamilies:early nodulin-like protein(NtENODL),uclacyanin-like protein,stellacyanin1-like protein,and plantacyanin-like protein.According to phylogenetic and structural analyses,the NtPC family could be divided into eight structural types.Fifty-three NtPCs were randomly distributed on 22 of 24 tobacco chromosomes.Collinearity analysis revealed 33 pairs of genes belonging to the NtPC family.Gene ontology analysis showed that the PC genes are components of the plasma membrane and may participate in plasma membrane-related functions.The NtPC family contained numerous elements related to hormonal and abiotic stress responses and was specifically expressed in the tobacco prosperous,maturation,and budding periods.Tissue-specific expression analysis showed that some genes were tissue specific.The expression of NtENODL58 and other genes was significantly induced by low-temperature and methyl jasmonate stress.Thus,the NtPC gene family plays an important role in plant stress response.

Genome-wide analysis of nuclear factor Y genes and functional investigation of watermelon ClNF-YB9 during seed development

The nuclear factor Y(NF-Y) gene family is a class of transcription factors that are widely distributed in eukaryotes and are involved in various biological processes. However, the NF-Y gene family members in watermelon, a valued and nutritious fruit, remain largely unknown and their functions have not been characterized. In the present study, 22 ClNF-Y genes in watermelon, 29 CsNF-Y genes in cucumber, and 24CmNF-Y genes in melon were identified based on the whole-genome investigation and their protein properties, gene location, gene structure, motif composition, conserved domain, and evolutionary relationship were investigated. ClNF-YB9 from watermelon and its homologs in cucumber and melon were expressed specifically in seeds. Its expression remained low in the early stages of watermelon seed development,increased at 20 days after pollination(DAP), and peaked at 45–50 DAP. Moreover, the knockout mutant Clnf-yb9 exhibited abnormal leafy cotyledon phenotype, implying its critical role during seed formation.Finally, protein interaction assays showed that ClNF-YB9 interacts with all ClNF-YCs and the ClNF-YB9-YC4 heterodimer was able to recruit a ClNF-YA7 subunit to assemble a complete NF-Y complex, which may function in seed development. This study revealed the structure and evolutionary relationships of the NF-Y gene family in Cucurbitaceae and the novel function of ClNF-YB9 in regulating seed development in watermelon.