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.

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.

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.

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.

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 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 characterization of the SAUR gene family in sweet cherry and functional analysis of PavSAUR55 in the process of abscission

Small auxin up RNA(SAUR) is a large gene family that is widely distributed among land plants. In this study, a comprehensive analysis of the SAUR family was performed in sweet cherry, and the potential biological functions of PavSAUR55 were identified using the method of genetic transformation. The sweet cherry genome encodes 86 SAUR members, the majority of which are intron-less. These genes appear to be divided into seven subfamilies through evolution. Gene duplication events indicate that fragment duplication and tandem duplication events occurred in the sweet cherry. Most of the members mainly underwent purification selection pressure during evolution. During fruit development, the expression levels of Pav SAUR16/45/56/63 were up-regulated, and conversely, those of Pav SAUR12/61were down-regulated. Due to the significantly differential expressions of PavSAUR13/16/55/61 during the fruitlet abscission process, they might be the candidate genes involved in the regulation of physiological fruit abscission in sweet cherry. Overexpression of PavSAUR55 in Arabidopsis produced earlier reproductive growth, root elongation, and delayed petal abscission. In addition, this gene did not cause any change in the germination time of seeds and was able to increase the number of lateral roots under abscisic acid(ABA) treatment. The identified SAURs of sweet cherry play a crucial role in fruitlet abscission and will facilitate future insights into the mechanism underlying the heavy fruitlet abscission that can occur in this fruit crop.

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 the KANADI Gene Family and Its Expression Patterns under Different Nitrogen Concentrations Treatments in Populus trichocarpa

KANADI(KAN)is a plant-specific gene that controlled the polarity development of lateral organs.It mainly acted on the abaxial characteristics of plants to make the lateral organs asymmetrical.However,it had been less identified in woody plants.In this study,the members of the KAN gene family in Populus trichocarpa were identified and analyzed using the bioinformatics method.The results showed that a total of 8 KAN family members were screened out,and each member contained the unique GARP domain and conserved region of the family proteins.Phylogenetic analysis and their gene structures revealed that all KAN genes from P.trichocarpa,Arabidopsis thaliana,and Nicotiana benthamiana could be divided into four subgroups,while the eight genes in P.trichocarpa were classified into three subgroups,respectively.The analysis of tissue-specific expression indicated that PtKAN1 was highly expressed in young leaves,PtKAN6 was highly expressed in young leaves and mature leaves,PtKAN2,PtKAN5,and PtKAN7 were highly expressed in nodes and internodes,PtKAN8 was highly expressed in roots,and PtKAN3 and PtKAN4 showed low expression levels in all tissues.Among them,PtKAN2 and PtKAN6,and PtKAN4 and PtKAN5 might have functional redundancy.Under high nitrogen concentrations,PtKAN2 and PtKAN8 were highly expressed in mature stems and leaves,respectively,while PtKAN4,PtKAN5,and PtKAN7 were highly expressed in roots.This study laid a theoretical foundation for further study of the KAN genemediated nitrogen effect on root development.

Genome-Wide Identification, Evolution and Expression Analyses of GA2ox Gene Family in Brassica napus L.

Gibberellin 2-oxidases(GA2ox)are important enzymes that maintain the balance of bioactive GAs in plants.GA2ox genes have been identified and characterized in many plants,but these genes were not investigated in Brassica napus.Here,we identified 31 GA2ox genes in B.napus and 15 of these BnaGA2ox genes were distributed in the A and C subgenomes.Subcellular localization predictions suggested that all BnaGA2ox proteins were localized in the cytoplasm,and gene structure analysis showed that the BnaGA2ox genes contained 2–4 exons.Phylogenetic analysis indicated that BnGA2ox family proteins in monocotyledons and dicotyledons can be divided into four groups,including two C_(19)-GA2ox and two C_(20)-GA2ox clades.Group 4 is a C_(20)-GA2ox Class discovered recently.Most BnaGA2ox genes had a syntenic relationship with AtGA2ox genes.BnaGA2ox genes in the C subgenome had experienced stronger selection pressure than genes in the A subgenome.BnaGA2ox genes were highly expressed in specific tissues such as those involved in growth and development,and most of them were mainly involved in abiotic responses,regulation of phytohormones and growth and development.Our study provided a valuable evolutionary analysis of GA2ox genes in monocotyledons and dicotyledons,as well as an insight into the biological functions of GA2ox family genes in B.napus.

In silico genome-wide identification,phylogeny and expression analysis of the R2R3-MYB gene family in Medicago truncatula

The R2R3-MYB genes make up one of the largest transcription factor families in plants, and play regulatory roles in various biological processes such as development, metabolism and defense response. Although genome-wide analyses of this gene family have been conducted in several species, R2R3-MYB genes have not been systematically analyzed in Medicago truncatula, a sequenced model legume plant. Here, we performed a comprehensive, genome-wide computational analysis of the structural characteristics, phylogeny, functions and expression patterns of M. truncatula R2R3-MYB genes. DNA binding domains are highly conserved among the 155 putative MtR2R3-MYB proteins that we identified. Chromosomal location analysis revealed that these genes were distributed across all eight chromosomes. Results showed that the expansion of the MtR2R3-MYB family was mainly attributable to segmental duplication and tandem duplication. A comprehensive classification was performed based on phylogenetic analysis of the R2R3-MYB gene families in M. truncatula, Arabidopsis thaliana and other plant species. Evolutionary relationships within clades were supported by clade-specific conserved motifs outside the MYB domain. Species-specific clades have been gained or lost during evolution, resulting in functional divergence. Also, tissue-specific expression patterns were investigated. The functions of stress response-related clades were further verified by the changes in transcript levels of representative R2R3-MYB genes upon treatment with abiotic and biotic stresses. This study is the first report on identification and characterization of R2R3-MYB gene family based on the genome of M. truncatula, and will facilitate functional analysis of this gene family in the future.

Comprehensive identification and analyses of the Hsf gene family in the whole-genome of three Apiaceae species

Apiaceae is a major family from Apiales and includes many important vegetable and medicinal crops.Heat shock transcription factors(Hsf)play important roles in heat tolerance during plant development.Here,we conducted systematic analyses of the Hsf gene family in three Apiaceae species,including 17 Apium graveolens(celery),32 Coriandrum sativum(coriander),and 14 Daucus carota(carrot).A total of 73 Hsf genes were identified in three representative species,including Arabidopsis thaliana,Vitis vinifera,and Lactuca sativa.Whole-genome duplication played important roles in the Hsf gene family’s expansion within Apiaceae.Interestingly,we found that coriander had more Hsf genes than celery and carrot due to greater expansion and fewer losses.Twenty-seven branches of the phylogenetic tree underwent considerable positive selection in these Apiaceae species.We also explored the expression patterns of Hsf genes in three plant organs.Collectively,this study will serve as a rich gene resource for exploring the molecular mechanisms of heat tolerance.Additionally,this is the first study to report on the Hsf gene family in Apiaceae;thus,our research will provide guidance for future comparative and functional genomic studies on the Hsf gene family and others in Apiaceae.

Genome-wide analysis of the calcium-dependent protein kinase gene family in Gossypium raimondii

Plant calcium-dependent protein kinases （CDPKs） play important roles in diverse physiological processes by regulating the downstream components of calcium signaling. To date, only a few species of the plant CDPK gene family have been functionally identified. In addition, there has been no systematic analysis of the CDPK family in cotton. Here, 41 putative cotton CDPK （GrCDPK） genes were identified via bioinformatics analysis of the entire genome of Gossypium raimondii and were classified into four groups based on evolutionary relatedness. Gene structure analysis indicated that most of these GrCDPK genes share a similar intron-exon structure （7 or 8 exons）, strongly supporting their close evolutionary relationships. Chromosomal distributions and phylogenetics analysis showed that 13 pairs of GrCDPK genes arose via segmental duplication events. Furthermore, using microarray data of upland cotton （G. hirsutum L.）, comparative profiles analysis of these GhCDPKs indicated that some of the encoding genes might be involved in the responses to multiple abiotic stresses and play important regulatory roles during cotton fiber development. This study is the first genome-wide analysis of the CDPK family in cotton, and it will provide valuable information for the further functional characterization of cotton CDPK genes.

Genome-wide identification and characterization of the bHLH gene family in an ornamental woody plant Prunus mume

The basic helix-loop-helix(bHLH)transcription factor family is the second-largest family in plants,where it plays essential roles in development,and the responses to multiple abiotic and biotic stressors.However,little information is available about this gene family in Prunus mume,which is widely cultivated in East Asia as an ornamental fruit tree.Here,100 PmbHLH genes were identified,and their evolution and functions were explored in P.mume for the first time.The PmbHLH genes were classified into 21 subfamilies.The chromosomal distribution,physicochemical properties,bHLH domain,conserved motif,and intron/exon compositions were also analyzed.Furthermore,the evolutionary pattern,divergence time of the PmbHLH family,and genetic relationships among P.mume,Arabidopsis thaliana,and Prunus persica and Fragaria vesca of Rosaceae were explored.The functional prediction analysis of these PmbHLHs indicated that their functions varied,and included participating in the formation of organs and tissues,responding to stress,and the biosynthesis and metabolism of hormones and other secondary metabolites.Interestingly,expression analyses of PmbHLHs also revealed diverse expression patterns.Most of the PmbHLH genes were highly expressed in roots and stems,and a few were highly expressed in leaves,buds,and fruits,indicating tissue expression specificity.Eight PmbHLH genes,which were upregulated during low-temperature stress,may have critical roles in the response to cold stress.Ten PmbHLHs were differentially expressed between weeping and upright branches in a P.mume F_(1) population.These results shed light on the structure and evolution of the PmbHLH gene family,and lay a foundation for further functional studies of the bHLH genes.

Genome-wide identification and characterization of the JAZ gene family and its expression patterns under various abiotic stresses in Sorghum bicolor

The jasmonate ZIM domain(JAZ)protein belongs to the TIFY((TIF[F/Y]XG)domain protein)family,which is composed of several plant-specific proteins that play important roles in plant growth,development,and defense responses.However,the mechanism of the sorghum JAZ family in response to abiotic stress remains unclear.In the present study,a total of 17 JAZ genes were identified in sorghum using a Hidden Markov Model search.In addition,real-time quantification polymerase chain reaction(RT-qPCR)was used to analyze the gene expression patterns under abiotic stress.Based on phylogenetic tree analysis,the sorghum JAZ proteins were mainly divided into nine subfamilies.A promoter analysis revealed that the SbJAZ family contains diverse types of promoter cis-acting elements,indicating that JAZ proteins function in multiple pathways upon stress stimulation in plants.According to RT-qPCR,SbJAZ gene expression is tissuespecific.Additionally,under cold,hot,polyethylene glycol,jasmonic acid,abscisic acid,and gibberellin treatments,the expression patterns of SbJAZ genes were distinctly different,indicating that the expression of SbJAZ genes may be coordinated with different stresses.Furthermore,the overexpression of SbJAZ1 in Escherichia coli was found to promote the growth of recombinant cells under abiotic stresses,such as PEG 6000,NaCl,and 40℃ treatments.Altogether,our findings help us to better understand the potential molecular mechanisms of the SbJAZ family in sorghum in response to abiotic stresses.

Bioinformatics analysis of structure and function in the MRP gene family and its expression in response to various drugs in Bursaphelenchus xylophilus

Genes homologous to members of the MRP gene family in Caenorhabditis elegans are important in drug resistance.To further explore the molecular mechanism of drug resistance in pine wood nematode(Bursaphelenchus xylophilus),we used bioinformatics approaches to analyze genomic data for B.xylophilus and identified Bx-MRP genes.We predicted the structure and function of the genes and encoded proteins.Using bioinformatics programs to predict and analyze various properties of the predicted proteins,including hydrophobicity,transmembrane regions,phosphorylation sites,and topologically isomeric structures,of these Bx-MRP genes,we determined that they function in transmembrane transport.From the results of RT-qPCR,the Bx-MRP family members confer significant differential resistance to different drug treatments.After treatment with different concentrations of emamectin benzoate,avermectin and matrine,the expression of each gene increased with increasing drug concentrations,indicating that the family members play a positive role in the regulation of multidrug resistance.

Genome-wide identification and expression analysis of NtbHLH gene family in tobacco(Nicotiana tabacum)and the role of NtbHLH86 in drought adaptation

The bHLH transcription factors play pivotal roles in plant growth and development,production of secondary metabolites and responses to various environmental stresses.Although the bHLH genes have been well studied in model plant species,a comprehensive investigation of the bHLH genes is required for tobacco with newly obtained high-quality genome.In the present study,a total of 309 NtbHLH genes were identified and can be divided into 23 subfamilies.The conserved amino acids which are essential for their function were predicted for the NtbHLH proteins.Moreover,the NtbHLH genes were conserved during evolution through analyzing the gene structures and conserved motifs.A total of 265 NtbHLH genes were localized in the 24 tobacco chromosomes while the remained 44 NtbHLH genes were mapped to the scaffolds due to the complexity of tobacco genome.Moreover,transcripts of NtbHLH genes were obviously tissue-specific expressed from the gene-chip data from 23 tobacco tissues,and expressions of 20 random selected NtbHLH genes were further confirmed by quantitative real-time PCR,indicating their potential functions in the plant growth and development.Importantly,overexpressed NtbHLH86 gene confers improve drought tolerance in tobacco indicating that it might be involved in the regulation of drought stress.Therefore,our findings here provide a valuable information on the characterization of NtbHLH genes and further investigation of their functions in tobacco.

Prognostic and biological role of the N-Myc downstream-regulated gene family in hepatocellular carcinoma

BACKGROUND The N-Myc downstream-regulated gene(NDRG)family is comprised of four members(NDRG1-4)involved in various important biological processes.However,there is no systematic evaluation of the prognostic of the NDRG family in hepatocellular carcinoma(HCC).AIM To analyze comprehensively the biological role of the NDRG family in HCC.METHODS The NDRG family expression was explored using The Cancer Genome Atlas.DNA methylation interactive visualization database was used for methylation analysis of the NDRG family.The NDRG family genomic alteration was assessed using the cBioPortal.Single-sample Gene Set Enrichment Analysis was used to determine the degree of immune cell infiltration in tumors.RESULTS NDRG1 and NDRG3 were up-regulated in HCC,while NDRG2 was down-regulated.Consistent with expression patterns,high expression of NDRG1 and NDRG3 was associated with poor survival outcomes(P<0.05).High expression of NDRG2 was associated with favorable survival(P<0.005).An NDRG-based signature that statistically stratified the prognosis of the patients was constructed.The percentage of genetic alterations in the NDRG family varied from 0.3%to 11.0%,and the NDRG1 mutation rate was the highest.NDRG 1-3 expression was associated with various types of infiltrated immune cells.Gene ontology analysis revealed that organic acid catabolism was the most important biological process related to the NDRG family.Gene Set Enrichment Analysis showed that metabolic,proliferation,and immune-related gene sets were enriched during NDRG1 and NDRG3 high expression and NDRG2 low expression.CONCLUSION Overexpression of NDRG1 and NDRG3 and down-expression of NDRG2 are correlated with poor overall HCC prognosis.Our results may provide new insights into the indispensable role of NDRG1,2,and 3 in the development of HCC and guide a promising new strategy for treating HCC.

Identification and expression of the CEP gene family in apple (Malus×domestica)

Plant peptide hormones play important roles in plant growth and development. Among these hormones, the C-TERMINALLYENCODED PEPTIDE（CEP） belongs to a newly found peptide family that regulates root development in Arabidopsis as well as in other species. However, nothing is known about the CEP genes in apple（Malus×domestica, MdCEP）. In this study, a total of 27 apple CEP genes were identified through a genome-wide analysis and were phylogenetically divided into three classes（Ⅰ, Ⅱ and Ⅲ）. The predicted MdCEP genes were distributed across 10 of 17 chromosomes with different densities. Next, the gene structures and motif compositions of the MdCEP genes were analyzed. Subsequently, the expression analysis suggested that the MdCEP genes were highly activated in roots and that MdCEP23 may play an important role in regulating the growth and development of roots. Moreover, all of the MdCEP genes were responsive to multiple abiotic stresses, indicating that MdCEP genes may be involved with various aspects of physiological processes in apple. Nearly one-third of MdCEP genes had a significant response to low nitrogen treatment. Most of the MdCEP genes were up-regulated under stress, including mannitol, polyethylene glycol（PEG） and abscisic acid（ABA）, suggesting that MdCEP genes may be involved in the drought stress response. This study provides insight into the putative functions of the MdCEP genes using a genome-wide analysis of the CEP gene family.

Genome-wide Identification and Analysis of MVD Gene Family in Euphorbiaceae Plants

The mevalonate diphosphate deearboxylase （MVD） is an essential enzyme in mevalonate （MVA） pathway that catalyzes the irreversible Mg2＋ -ATP de- pendent decarboxylation of 6-carben compound mevalonate-5-diphosphate （MVAPP） into 5-carbon isopentenyl diphosphate （ IPP）, the building block of sterol and isoprenoid biosynthesis. In this study, based on the published geanme sequences and ESTs, a genome-wide search was carried out for the first time to identify MVD gene family in four genome-sequenced Euphorbiaceae plants, i.e. castor bean （ Ricinus communis）, physic nut （ Jatropha curcas）, cassava （Manihot esculenta） and rubber tree （Hevea brasiliensis）, and to analyze the gene structure and phylogenetic characteristics. According to the experimental results, 1, 1,2 and 2 MVD genes, which all contain 9 introns, were identh＇ied from castor bean, physic nut, cassava and rubber tree, respectively. Homology analysis indicates that MVD genes are widely distributed in eukaryotes, some archaea and eubacteria, which suggests an early origin of this gerte family. Although MVD genes were identified in most green plants, no homologous genes were found in unicellular green algae. In most genome-sequenced plants including castor bean and physic nut, a single copy of MVD gene was found; however, in cassava and rubber tree, two copies were identified just like that in moss, maize, Arabidopsis and poplar. ＂In castor bean, digital expression profiling suggests that in five examined tissues, i.e. leaf, flower, II/III stage endosperm, V/VI stage endosperm and seed, RcPMK was expressed strongly in flower and II/III stage endosperm, moderately in V/VI stage endosperm and leaf, and weakly in seed.