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 Analysis of the Cyclin-Dependent Kinases(CDK)and Cyclin Family in Molluscs

Cell cycle regulation that plays a pivotal role during organism growth and development is primarily driven by cyclindependent kinases(CDKs)and Cyclins.Although CDK and Cyclin genes have been characterized in some animals,the studies of CDK and Cyclin families in molluscs,the ancient bilaterian groups with high morphological diversity,is still in its infancy.In this study,we identified and characterized 95 CDK genes and 114 Cyclin genes in seven representative species of molluscs,including Octopus bimaculoides,Pomacea canaliculata,Biomphalaria glabrata,Lottia gigantea,Mizuhopecten yessoensis,Crassostrea gigas and Aplysia californica.Genes in CDK and Cyclin families were grouped into eight and 15 subfamilies by phylogenetic analysis,respectively.It should be noted that duplication of CDK9 gene was detected in P.canaliculate,L.gigantea and M.yessoensis genomes,which has never been recorded in animals.It is speculated that duplication may be the main course of expansion of the CDK9 subfamily in the three molluscs,which also sheds new light on the function of CDK9.In addition,Cyclin B is the largest subfamily among the Cyclin family in the seven molluscs,with the average of three genes.Our findings are helpful in better understanding CDK and Cyclin function and evolution in molluscs.

A genome-wide analysis of the chloroplast NADH dehydrogenase - like genes in Zostera marina

The chloroplast NADH dehydrogenase-like(NDH)complex,homologous to respiratory complex I,participates in photosystem I cyclic electron flow(PSI-CEF)and chlororespiration in photosynthesis.Phylogenetic analyses indicated that Zostera marina,a widely distributed seagrass,has a complete NDH complex,which is rarely observed in marine macrophytes.We identified all 31 ndh genes necessary for the functional NDH complex,of which ndhB and pnsb3 occurred as duplication events.Secondary structural analyses of antiporter-like subunits showed that the long amphipathic helix of NdhF was lost in Z.marina,which could exhibit an alternative mode in the generation of trans-thylakoid proton gradient.The splicing pattern of ndh exhibited tissue-specific patterns and responded to light stress.RNA editing in Z.marina presented the ancestral pattern with many of the primitive editing sites and types.The partial editing in ndhF reflected the link between light stress and RNA editing.Moreover,the predominant expression in leaves of most ndh genes suggested that their major function is in photosynthesis.The quantitative real time-PCR results show that the expression of ndh was signifi cantly upregulated in response to light stress.Nevertheless,there were two diverse responsive mechanisms of the NDH complex in PSI-CEF and chlororespiration.Overall,the presence of a complete structure,upregulated gene expression level,and multiple post-transcriptional regulations could provide a molecular basis for the powerful NDH complex and enable Z.marina to maintain eff ective photosynthetic performance.

Genome-wide analysis of heat shock transcription factor families in rice and Arabidopsis

The heat shock transcription factors （HSFs） are the major heat shock factors regulating the heat stress response. They participate in regulating the expression of heat shock proteins （HSPs）, which are critical in the protection against stress damage and many other important biological processes. Study of the HSF gene family is important for understanding the mechanism by which plants respond to stress. The completed genome sequences of rice （Oryza sativa） and Arabidopsis （Arabidopsis thaliana） constitute a valuable resource for comparative genomic analysis, as they are representatives of the two major evolutionary lineages within the angiosperms： the monocotyledons and the dicotyledons. The identification of phylogenefic relationships among HSF proteins in these species is a fundamental step to unravel the functionality of new and yet uncharacterized genes belonging to this family.In this study, the full complement of HSF genes in rice and Arabidopsis has probably been identified through the genome-wide scan. Phylogenetic analyses resulted in the identification of three major clusters of orthologous genes that contain members belonging to both species, which must have been represented in their common ancestor before the taxonomic splitting of the angiosperms. Fttrther analysis of the phylogenetic tree reveals a possible dicot specific gene group. We also identified nine pairs of paralogs, as evidence for studies on the evolution history of rice HSF family and rice genome evolution. Expression data analysis indicates that HSF proteins are widely expressed in plants. These results provide a solid base for future functional genomic studies of the HSF gene family in rice and Arabidopsis.

Genome-wide analysis and identification of cytokinin oxidase/dehydrogenase(CKX) gene family in foxtail millet(Setaria italica)

Cytokinin oxidase/dehydrogenase(CKX; EC.1.5.99.12) regulates cytokinin(CK) level in plants and plays an essential role in CK regulatory processes. CKX proteins are encoded by a small gene family with a varying number of members in different plants. In spite of their physiological importance, systematic analyses of SiCKX genes in foxtail millet have not yet been examined. In this paper, we report the genome wide isolation and characterization of SiCKXs using bioinformatic methods. A total of 11 members of the family were identified in the foxtail millet genome. SiCKX genes were distributed in seven chromosomes(chromosome 1, 3, 4, 5, 6, 7, and 11). The coding sequences of all the SiCKX genes were disrupted by introns, with numbers varying from one to four. These genes expanded in the genome mainly due to segmental duplication events. Multiple alignment and motif display results showed that all SiCKX proteins share FAD- and CK-binding domains. Putative cis-elements involved in Ca2+-response, abiotic stress response, light and circadian rhythm regulation, disease resistance and seed development were present in the promoters of SiCKX genes. Expression data mining suggested that SiCKX genes have diverse expression patterns. Real-time PCR analysis indicated that all 11 SiCKX genes were up-regulated in embryos under 6-BA treatment, and some were NaCl or PEG inducible. Collectively, these results provide molecular insights into CKX research in plants.

Genome-wide analysis of basic leucine zipper transcription factor families in Arabidopsis thaliana,Oryza sativa and Populus trichocarpa

The basic leucine zipper （bZIP） transcription factors form a large gene family that is important in pathogen defense, light and stress signaling, etc. The Completed whole genome sequences of model plants Arabidopsis （Arabidopsis thaliana）, rice （Oryza sativa） and poplar （Populus trichocarpa） constitute a valuable resource for genome-wide analysis and genomic comparative analysis, as they are representatives of the two major evolutionary lineages within the angiosperms： the monocotyledons and the dicotyledons. In this study, bioinformatics analysis identified 74, 89 and 88 bZIP genes respectively in Arabidopsis, rice and poplar. Moreover, a comprehensive overview of this gene family is presented, including the gene structure, phylogeny, chromosome distribution, conserved motifs. As a result, the plant bZIPs were organized into 10 subfamilies on basis of phylogenetic relationship. Gene duplication events during the family evolution history were also investigated. And it was further concluded that chromosomal/segmental duplication might have played a key role in gene expansion of bZIP gene family.

Genome-wide analysis of the barley non-specific lipid transfer protein gene family

Non-specific lipid transfer proteins(nsLTPs) are small, basic proteins that are characterized by an eight-cysteine motif. The biological functions of these proteins have been reported to involve plant reproduction and biotic or abiotic stress response. With the completion of the barley genome sequence, a genome-wide analysis of nsLTPs in barley(Hordeum vulgare L.)(HvLTPs) will be helpful for understanding the function of nsLTPs in plants. We performed a genome-wide analysis of the nsLTP gene family in barley and identified 70 nsLTP genes,which can be divided into five types(1, 2, C, D, and G). Each type of nsLTPs shares similar exon and intron gene structures. Expression analysis showed that barley nsLTPs have diverse expression patterns, revealing their various roles. Our results shed light on the phylogenetic relationships and potential functions of barley nsLTPs and will be useful for future studies of barley development and molecular breeding.

Genome-wide analysis of NDR1/HIN1-like genes in pepper(Capsicum annuum L.)and functional characterization of CaNHL4 under biotic and abiotic stresses

Plant NDR1/HIN1-like(NHL)genes play an important role in triggering plant defenses in response to biotic stresses.In this study,we performed a genome-wide identification of the NHL genes in pepper(Capsicum annuum L.)and characterized the functional roles of these CaNHL genes in response to abiotic stresses and infection by different pathogens.Phylogenetic analysis revealed that CaNHLs can be classified into five distinct subgroups,with each group containing generic and specific motifs.Regulatory element analysis showed that the majority of the promoter regions of the identified CaNHLs contain jasmonic acid(JA)-responsive and salicylic acid(SA)-responsive elements,and transcriptomic analysis revealed that CaNHL genes are expressed in all the examined tissues of pepper.The CaNHL1,CaNHL4,CaNHL6,CaNHL10,CaNHL11,and CaNHL12 genes were significantly upregulated under abiotic stress as well as in response to different pathogens,such as TMV,Phytophthora capsici and Pseudomonas syringae.In addition,we found that CaNHL4 localizes to the plasma membrane.CaNHL4-silenced pepper plants display significantly increased susceptibility to TMV,Phytophthora capsici and Pseudomonas syringae,exhibiting reduced expression of JA-related and SA-related genes and reduced ROS production.However,transient overexpression of CaNHL4 in pepper increases the expression of JArelated and SA-related genes,enhances the accumulation of ROS,and inhibits the infection of these three pathogens.Collectively,for the first time,we identified the NHL genes in pepper and demonstrated that CaNHL4 is involved in the production of ROS and that it also regulates the expression of JA-related and SA-related genes in response to different pathogens,suggesting that members of the CaNHL family play an essential role in the disease resistance of pepper.

Genome-wide analysis of expression quantitative trait loci(eQTLs)reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato

Dissecting the genetic regulation of gene expression is critical for understanding phenotypic variation and species evolution.However,our understanding of the transcriptional variability in sweet potato remains limited.Here,we analyzed two publicly available datasets to explore the landscape of transcriptomic variations and its genetic basis in the storage roots of sweet potato.The comprehensive analysis identified a total of 724,438 high-confidence single nucleotide polymorphisms(SNPs)and 26,026 expressed genes.Expression quantitative trait locus(eQTL)analysis revealed 4408 eQTLs regulating the expression of 3646 genes,including 2261 local eQTLs and 2147 distant eQTLs.Two distant eQTL hotspots were found with target genes significantly enriched in specific functional classifications.By combining the information from regulatory network analyses,eQTLs and association mapping,we found that IbMYB1-2 acts as a master regulator and is the major gene responsible for the activation of anthocyanin biosynthesis in the storage roots of sweet potato.Our study provides the first insight into the genetic architecture of genome-wide expression variation in sweet potato and can be used to investigate the potential effects of genetic variants on key agronomic traits in sweet potato.

Genome-wide analysis of runs of homozygosity identifies new susceptibility regions of lung cancer in Han Chinese

Runs of homozygosity （ROHs） are a class of important but poorly studied genomic variations and may be in- volved in individual susceptibility to diseases. To better understand ROH and its relationship with lung cancer, we performed a genome-wide ROH analysis of a subset of a previous genome-wide case-control study （1,473 cases and 1,962 controls） in a Han Chinese population. ROHs were classified into two classes, based on lengths, intermedi- ate and long ROils, to evaluate their association with lung cancer risk using existing genome-wide single nucleofide polymorphism （SNP） data. We found that the overall level of intermediate ROHs was significantly associated with a decreased risk of lung cancer （odds ratio = 0.63; 95% confidence interval： 0.51-0.77; P = 4.78 × 10-6 ）, while the long ROHs seemed to be a risk factor of lung cancer. We also identified one ROH region at 14q23A that was con- sistently associated with lung cancer risk in the study. These results indicated that ROHs may be a new class of variation which may be associated with lung cancer risk, and genetic variants at 14q23.1 may be involved in the development of lung cancer.

Genome-wide analysis of expansins and their role in fruit spine development in cucumber(Cucumis sativus L.)

Cucumber is one of the most widely consumed vegetables worldwide,and the fruit spine is an important fruit quality trait.Expansins play critical roles in fruit development;however,the regulation of expansins in cucumber fruit spine development has not been reported.In this study,33 expansin genes were identified in the cucumber genome V3;additionally,expansin genes in Citrullus lanatus,Cucumis melo,Cucurbita maxima,Lagenaria siceraria,and Benincasa hispida were also identified.Phylogenetic analysis of expansin proteins in Cucurbitaceae and Arabidopsis showed that they evolved separately in each plant species.Phylogenetic analysis showed that C.maxima was derived earlier than the other five Cucurbitaceae species.The expression of CsEXPA2,CsEXPA14,and CsEXLA3 varied in cucumber lines with different fruit spine densities.A yeast two-hybrid assay showed that a putative auxin transporter encoded by numerous spine gene(ns)interacts with CsEXLA2,which may be involved in the development of the numerous spines in cucumber.These results provide novel insights into the expansins related to plant development and fruit spine development in cucumber.

Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for chinese cabbage biomass

Heterosis is a complex phenomenon in which hybrids show better phenotypic characteristics than their parents do.Chinese cabbage(Brassica rapa L.spp.pekinensis)is a popular leafy crop species,hybrids of which are widely used in commercial production;however,the molecular basis of heterosis for biomass of Chinese cabbage is poorly understood.We characterized heterosis in a Chinese cabbage hybrid cultivar and its parental lines from the seedling stage to the heading stage;marked heterosis of leaf weight and biomass yield were observed.Small RNA sequencing revealed 63 and 50 differentially expressed microRNAs(DEMs)at the seedling and early-heading stages,respectively.The expression levels ofthe majority of miRNA clusters in the hybrid were lower than the mid-parent values(MPVs).Using degradome sequencing,we identi fied 1,819 miRNA target genes.Gene ontology(GO)analyses demonstrated that the target genes ofthe MPV-DEMs and low parental expression level dominance(ELD)miRNAs were signi ficantly enriched in leaf morphogenesis,leaf development,and leaf shaping.Transcriptome analysis revealed that the expression levels of photosynthesis and chlorophyll synthesis-related MPV-DEGs(differentially expressed genes)were signi ficantly different in the F_(1) hybrid compared to the parental lines,resulting in increased photosynthesis capacity and chlorophyll content in the former.Furthermore,expression of genes known to regulate leaf development was also observed at the seedling stage.Arabidopsis plants overexpressing BrGRF4.2 and bra-miR396 presented increased and decreased leaf sizes,respectively.These results provide new insight into the regulation of target genes and miRNA expression patterns in leaf size and heterosis for biomass of B.rapa.

Genome-wide Analysis of Ovate Family Proteins in Arabidopsis

Arabidopsis thaliana ovate family proteins （AtOFPs） is a newly found plant-specific protein family interacting with TALE （3-aa loop extension homeodomain proteins） homeodomain proteins in Arabidopsis. Here, based on bioinformatic analysis, we found that Arabidopsis genome actually encoded 17 OVATE domain-containing proteins. One of them, AtOFP19, has not been previously identified. Based on their amino acid sequence similarity, AtOFPs proteins can be divided into two groups. Most of the AtOFPs were located in nuclear, four of them were presented in chloroplast and the remaining two members appeared in cytoplasmic. A genome- wide microarray based gene expression analysis involving 47 stages of vegetative and reproductive development revealed that AtOFPs have diverse expression pattems. Investigation of proteins interaction showed that nine AtOFPs only interacted with TALE homeodomain proteins, which are fundamental regulators of plant meristem function and leaf development. Our work could provide important leads toward functional genomics studies of ovate family proteins, which may be involved in a previously unrecognized control mechanism in plant development

Genome-wide association analysis identified molecular markers and candidate genes for flower traits in Chinese orchid (Cymbidium sinense)

The orchid,the champagne of f lowers,brings luxury,elegance,and novelty to nature.Cymbidium sinense is a symbol of gigantic floral variability on account ofwavering shapes and sizes of f loral organs,althoughmarker-trait association(MTA)has not been studied for its f loral traits.We evaluated markers associated with 14 f loral traits of C.sinense through a genome-wide association study(GWAS)of 195 accessions.A total of 65318522 single-nucleotide polymorphisms(SNPs)and 3906176 insertion/deletion(InDel)events were identified through genotyping-by-sequencing.Among these,4694 potential SNPs and 477 InDelswere identified as MTAs at−log10 P>5.The genes related to these SNPs and InDels were largely associated with f loral regulators,hormonal pathways,cell division,and metabolism,playing essential roles in tailoring f loral morphology.Moreover,20 candidate SNPs/InDels linked to 11 genes were verified,8 of which were situated on exons,onewas located in the 5-UTR and twowere positioned in introns.Here,themultitepal trait-related gene RABBIT EARS(RBE)was found to be the most crucial gene.We analyzed the role of CsRBE in the regulation of flower-related genes via efficient transient overexpression in C.sinense protoplasts,and found that the floral homeotic genes CsAP3 and CsPI,as well as organ boundary regulators,including CsCUC and CsTCP genes,were regulated by CsRBE.Thus,we obtained key gene loci for important ornamental traits of orchids using genome-wide association analysis of populations with natural variation.The findings of this study can do a great deal to expedite orchid breeding programs for shape variability.

Integrating genome-wide association and transcriptome analysis to provide molecular insights into heterophylly and eco-adaptability in woody plants

Heterophylly is regard as an important adaptive mechanism in response to different environments within plants.However,the genetic mechanisms responsible for heterophylly in woody plants are still poorly understood.Herein,the divergence of heterophyllous leaves was investigated at morphogenesis and using microdissection and physiological indexes in paper mulberry,and the genetic basis of heterophylly was further revealed combined with genome-wide association study(GWAS),transcriptome analysis and weighted gene coexpression network analysis(WGCNA).Our results revealed that the flavonoid content and antioxidant activity increased gradually from the entire leaf to the palmatisect leaf,while the hormone content and net photosynthetic rate decreased.Through GWAS and transcriptome analysis,a total of 98 candidate genes and 2338 differentially expressed genes associated with heterophylly were identified.Importantly,we uncovered critical variations in the candidate genes Bp07g0981(WOX)and Bp07g0920(HHO),along with significant differences in haplotypes and expression levels among heterophyllous leaves.Our results also suggested that the genes involved in hormone signaling pathways,antioxidant activity,and f lavonoid metabolism might be closely related to the heterophylly of paper mulberry,which could account for the physiological data.Indeed,CR-wox mutant lines showed significant changes in leaf phenotypes,and differential expression profile analysis also highlighted the expression of genes related to phytohormones and transcription factors.Together,the genetic variations and candidate genes detected in this study provide novel insights into the genetic mechanism of heterophylly,and would improve the understanding of eco-adaptability in heterophyllous woody plants.

An integrated genome-wide analysis identifies HUR/ELAVL1 as a positive regulator of osteogenesis through enhancing theβ-catenin signaling activity

Osteoporosis is a prevalent multifactorial bone disease with a strong genetic contribution.The heritability of traits that contribute to osteoporosis(bone mass,bone mineral density(BMD),bone size,bone loss and fractures)ranges from 50 to 85%,suggesting that a comprehensive understanding of the genetic basis may help identify new therapeutic targets.1 However,the genetic characteristics remain obscure,and the existing drug targets are associated with various challenges.Numerous studies have demonstrated that high-throughput sequencing data analysis is fruitful for identifying novel targets of human diseases.2 We therefore integrated GWAS and transcriptome analyses through Multi-marker Analysis of GenoMic Annotation(MAGMA)and weighted gene co-expression network analysis3(WGCNA)to identify new network modules and potential therapeutic genes for osteoporosis.As an illustration,the flow chart presenting the process of the present study was shown in Figure S1.

Genome-Wide Analysis and Expression Patterns of the YUCCA Genes in Maize

Auxin plays important roles in various aspects of plant growth and development （Zhao, 2010）. In Arabidopsis, a number of YUCCA （YUC） genes, which are involved in auxin biosyn- thesis, have been identified （Zhao et al., 2001; Woodward et al., 2005; Cheng et al., 2006, 2007; Kim et al., 2007; Chen et al., 2014）. YUC genes encode flavin monooxygenases （FMOs） that convert indole-3-pyruvate （IPA） to indole-3-acetic acid （IAA） （Zhao, 2012）. The Arabidopsis YUC family is comprised of 11 members （Zhao et al., 2001;

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.

Lagrangian coherent structure analysis on transport of Acetes chinensis along coast of Lianyungang,China

Spatial heterogeneity or“patchiness”of plankton distributions in the ocean has always been an attractive and challenging scientific issue to oceanographers.We focused on the accumulation and dynamic mechanism of the Acetes chinensis in the Lianyungang nearshore licensed fishing area.The Lagrangian frame approaches including the Lagrangian coherent structures theory,Lagrangian residual current,and Lagrangian particle-tracking model were applied to find the transport pathways and aggregation characteristics of Acetes chinensis.There exist some material transport pathways for Acetes chinensis passing through the licensed fishing area,and Acetes chinensis is easy to accumulate in the licensed fishing area.The main mechanism forming this distribution pattern is the local circulation induced by the nonlinear interaction of topography and tidal flow.Both the Lagrangian coherent structure analysis and the particle trajectory tracking indicate that Acetes chinensis in the licensed fishing area come from the nearshore estuary.This work contributed to the adjustment of licensed fishing area and the efficient utilization of fishery resources.

Genome-wide association mapping and genomic prediction of stalk rot in two mid-altitude tropical maize populations

Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G×E)interaction increased genomic prediction accuracy.