Genome-wide identification of WD40 superfamily genes and prediction of WD40 gene of flavonoid-related genes in Ginkgo biloba

The WD40 transcription factor family is a superfamily found in eukaryotes and implicated in regulating growth and development. In this study, 167 WD40 family genes are identified in the Ginkgo biloba genome. They are divided into 5 clusters and 16 subfamilies based on the difference analysis of a phylogenetic tree and domain structures. The distribution of WD40 genes in chromosomes, gene structures, and motifs is analyzed. Promoter analysis shows that five GbWD40 gene promoters contain the MYB binding site participating in the regulation of flavonoid metabolism, suggesting that these five genes may participate in the regulation of flavonoid synthesis in G. biloba. The correlation analysis is carried out based on FPKM value of WD40 gene and flavonoid content in 8 tissues of G. biloba. Six GbWD40 genes that may participate in flavonoid metabolism are screened. The biological functions of the WD40 family genes in G. biloba are systematically analyzed, providing a foundation for further elucidating their regulatory mechanisms. A number of WD40 candidate genes involved in the biosynthesis and metabolism of G. biloba also predicted. This study presents an important basis and direction for conducting further research on the regulatory network of flavonoid synthesis and metabolism.

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Genome-wide identification and expression pattern analysis of lipoxygenase gene family in banana

Scientific Reports ◽

10.1038/s41598-021-89211-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Fan Liu ◽

Hua Li ◽

Junwei Wu ◽

Bin Wang ◽

Na Tian ◽

...

Keyword(s):

High Temperature ◽

Low Temperature ◽

Pcr Analysis ◽

Type I ◽

Segmental Duplications ◽

Expression Levels ◽

Genome Wide ◽

Encoded Proteins ◽

Gene Structures ◽

Lipoxygenase Gene Family

AbstractThe LOX genes have been identified and characterized in many plant species, but studies on the banana LOX genes are very limited. In this study, we respectively identified 18 MaLOX, 11 MbLOX, and 12 MiLOX genes from the Musa acuminata, M. balbisiana and M. itinerans genome data, investigated their gene structures and characterized the physicochemical properties of their encoded proteins. Banana LOXs showed a preference for using and ending with G/C and their encoded proteins can be classified into 9-LOX, Type I 13-LOX and Type II 13-LOX subfamilies. The expansion of the MaLOXs might result from the combined actions of genome-wide, tandem, and segmental duplications. However, tandem and segmental duplications contribute to the expansion of MbLOXs. Transcriptome data based gene expression analysis showed that MaLOX1, 4, and 7 were highly expressed in fruit and their expression levels were significantly regulated by ethylene. And 11, 12 and 7 MaLOXs were found to be low temperature-, high temperature-, and Fusarium oxysporum f. sp. Cubense tropical race 4 (FocTR4)-responsive, respectively. MaLOX8, 9 and 13 are responsive to all the three stresses, MaLOX4 and MaLOX12 are high temperature- and FocTR4-responsive; MaLOX6 and MaLOX17 are significantly induced by low temperature and FocTR4; and the expression of MaLOX7 and MaLOX16 are only affected by high temperature. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression levels of several MaLOXs are regulated by MeJA and FocTR4, indicating that they can increase the resistance of banana by regulating the JA pathway. Additionally, the weighted gene co-expression network analysis (WGCNA) of MaLOXs revealed 3 models respectively for 5 (MaLOX7-11), 3 (MaLOX6, 13, and 17), and 1 (MaLOX12) MaLOX genes. Our findings can provide valuable information for the characterization, evolution, diversity and functionality of MaLOX, MbLOX and MiLOX genes and are helpful for understanding the roles of LOXs in banana growth and development and adaptations to different stresses.

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Genome-Wide Analysis and Expression Tendency of Banana (Musa acuminata L.) Calcineurin B-Like (MaCBL) Genes under Potassium Stress

Horticulturae ◽

10.3390/horticulturae7040070 ◽

2021 ◽

Vol 7 (4) ◽

pp. 70

Author(s):

Ying Xiong ◽

Ruimei Li ◽

Xuejun Lin ◽

Yangjiao Zhou ◽

Fenlian Tang ◽

...

Keyword(s):

Elongation Factor ◽

Subcellular Location ◽

Potassium Deficiency ◽

Pcr Analysis ◽

Calcineurin B ◽

Group I ◽

Genome Wide ◽

Ef Hand ◽

Deficient Medium ◽

Gene Structures

Calcineurin B-like (CBL) proteins are reported to play significant roles in plant development and ion-transport regulation. Potassium shortages are a serious problem in banana cultivation. However, to date, the members of the banana CBL gene family, and their function in regulating potassium stress, remain unclear. In this study, 11 CBL genes were identified from the banana genome and grouped into four groups (Group I–IV) based on their phylogenetic relationships. The genomic features of these MaCBL genes were analyzed, focusing on their gene structures, standpat motifs, chromosomal distributions, and evolutionary history. Expression pattern analysis revealed that the MaCBLs were function-specific. Further qRT-PCR analysis indicated that the presence of MaCBL2 was indeed a response to potassium deficiency stress. The MaCBL2 gene was cloned, and sequence alignment indicated that it contained four elongation factor hand (EF-hand) domains, the conserved N-terminal myristoylation domain “MGCXXS/K(T)” and the “FPSF” motif. Subcellular location analysis showed that MaCBL2 was located in the plasma membrane, nucleus and cytoplasm. The overexpression of MaCBL2 could restore the growth of the yeast mutant R5421 on a K+-deficient medium. The overexpression of MaCBL2 could promote the root length of transgenic seedlings on K+-deficient medium. These findings indicate that MaCBL2 was, in our study, the key gene of the CBL family in responding to potassium deficiency in bananas. Our discoveries have established a considerable basis for the further study and application of MaCBL genes.

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Genome-Wide Identification and Analysis of CC-NBS-LRR Family in Response to Downy Mildew and Black Rot in Chinese Cabbage

International Journal of Molecular Sciences ◽

10.3390/ijms22084266 ◽

2021 ◽

Vol 22 (8) ◽

pp. 4266

Author(s):

Yan Liu ◽

Dalong Li ◽

Na Yang ◽

Xiaolong Zhu ◽

Kexin Han ◽

...

Keyword(s):

Downy Mildew ◽

Chinese Cabbage ◽

Plant Disease Resistance ◽

Expression Profiles ◽

Black Rot ◽

Genome Wide ◽

Pathogenesis Related ◽

Effector Triggered Immunity ◽

Gene Structures ◽

Bacteria And Fungi

The nucleotide-binding site–leucine-rich repeat (NBS–LRR) gene family is the largest group of plant disease resistance (R) genes widespread in response to viruses, bacteria, and fungi usually involved in effector triggered immunity (ETI). Forty members of the Chinese cabbage CC type NBS–LRR family were investigated in this study. Gene and protein characteristics, such as distributed locations on chromosomes and gene structures, were explored through comprehensive analysis. CC–NBS–LRR proteins were classified according to their conserved domains, and the phylogenetic relationships of CC–NBS–LRR proteins in Brassica rapa, Arabidopsis thaliana, and Oryza sativa were compared. Moreover, the roles of BrCC–NBS–LRR genes involved in pathogenesis-related defense were studied and analyzed. First, the expression profiles of BrCC–NBS–LRR genes were detected by inoculating with downy mildew and black rot pathogens. Second, sensitive and resistant Chinese cabbage inbred lines were screened by downy mildew and black rot. Finally, the differential expression levels of BrCC–NBS–LRR genes were monitored at 0, 1, 3, 6, 12 and 24 h for short and 0, 3, 5, 7, 10 and 14 days for long inoculation time. Our study provides information on BrCC–NBS–LRR genes for the investigation of the functions and mechanisms of CC-NBS-LRR genes in Chinese cabbage.

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Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat

BMC Genomics ◽

10.1186/s12864-021-07849-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Guang Yang ◽

Wenqiu Pan ◽

Ruoyu Zhang ◽

Yan Pan ◽

Qifan Guo ◽

...

Keyword(s):

Coenzyme A ◽

Expression Patterns ◽

Lignin Biosynthesis ◽

Head Blight ◽

Genome Wide ◽

Genome Search ◽

Gene Structures ◽

Main Components ◽

Main Regulator ◽

Group Sharing

Abstract Background Lignin is one of the main components of the cell wall and is directly associated with plant development and defence mechanisms in plants, especially in response to Fusarium graminearum (Fg) infection. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is the main regulator determining the efficiency of lignin synthesis and composition. Although it has been characterized in many plants, to date, the importance of the CCoAOMT family in wheat is not well understood. Results Here, a total of 21 wheat CCoAOMT genes (TaCCoAOMT) were identified through an in silico genome search method and they were classified into four groups based on phylogenetic analysis, with the members of the same group sharing similar gene structures and conserved motif compositions. Furthermore, the expression patterns and co-expression network in which TaCCoAOMT is involved were comprehensively investigated using 48 RNA-seq samples from Fg infected and mock samples of 4 wheat genotypes. Combined with qRT-PCR validation of 11 Fg-responsive TaCCoAOMT genes, potential candidates involved in the FHB response and their regulation modules were preliminarily suggested. Additionally, we investigated the genetic diversity and main haplotypes of these CCoAOMT genes in bread wheat and its relative populations based on resequencing data. Conclusions This study identified and characterized the CCoAOMT family in wheat, which not only provided potential targets for further functional analysis, but also contributed to uncovering the mechanism of lignin biosynthesis and its role in FHB tolerance in wheat and beyond.

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Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Animals ◽

10.3390/ani10030493 ◽

2020 ◽

Vol 10 (3) ◽

pp. 493

Author(s):

Salvatore Mastrangelo ◽

Filippo Cendron ◽

Gianluca Sottile ◽

Giovanni Niero ◽

Baldassare Portolano ◽

...

Keyword(s):

Genome Wide Association Study ◽

Snp Array ◽

Fixation Index ◽

Phenotypic Traits ◽

Plumage Color ◽

Phenotypic Marker ◽

Genome Wide ◽

A Genome ◽

The Difference ◽

Genomic Regions

Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (FST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and FST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken.

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Genome-wide miRNA analysis and integrated network for flavonoid biosynthesis in Osmanthus fragrans

BMC Genomics ◽

10.1186/s12864-021-07439-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yong Shi ◽

Heng Xia ◽

Xiaoting Cheng ◽

Libin Zhang

Keyword(s):

Secondary Metabolites ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Flavonoid Biosynthesis ◽

Integrated Network ◽

Osmanthus Fragrans ◽

Flavonoid Synthesis ◽

Genome Wide

AbstractBackgroundOsmanthus fragransis an important economical plant containing multiple secondary metabolites including flavonoids and anthocyanins. During the past years, the roles of miRNAs in regulating the biosynthesis of secondary metabolites in plants have been widely investigated. However, few studies on miRNA expression profiles and the potential roles in regulating flavonoid biosynthesis have been reported inO. fragrans.ResultsIn this study, we used high-throughput sequencing technology to analyze the expression profiles of miRNAs in leaf and flower tissues ofO. fragrans. As a result, 106 conserved miRNAs distributed in 47 families and 88 novel miRNAs were identified. Further analysis showed there were 133 miRNAs differentially expressed in leaves and flowers. Additionally, the potential target genes of miRNAs as well as the related metabolic pathways were predicted. In the end, flavonoid content was measured in flower and leaf tissues and potential role of miR858 in regulating flavonoid synthesis was illustrated inO. fragrans.ConclusionsThis study not only provided the genome-wide miRNA profiles in the flower and leaf tissue ofO. fragrans, but also investigated the potential regulatory role of miR858a in flavonoid synthesis inO. fragrans. The results specifically indicated the connection of miRNAs to the regulation of secondary metabolite biosynthesis in non-model economical plant.

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Abstract 40: Disturbed Flow Alters Genomewide DNA Methylation Patterns, Regulating Endothelial Gene Expression and Atherosclerosis

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvb.34.suppl_1.40 ◽

2014 ◽

Vol 34 (suppl_1) ◽

Author(s):

Jessilyn Dunn ◽

Haiwei Qiu ◽

Soyeon Kim ◽

Daudi Jjingo ◽

Ryan Hoffman ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Dna Methyltransferase ◽

Methylation Status ◽

Western Diet ◽

Dependent Manner ◽

Gene Promoters ◽

Genome Wide ◽

Methylation Patterns ◽

Endothelial Gene Expression

Atherosclerosis preferentially occurs in arterial regions of disturbed blood flow (d-flow), which alters gene expression, endothelial function, and atherosclerosis. Here, we show that d-flow regulates genome-wide DNA methylation patterns in a DNA methyltransferase (DNMT)-dependent manner. We found that d-flow induced expression of DNMT1, but not DNMT3a or DNMT3b, in mouse arterial endothelium in vivo and in cultured endothelial cells by oscillatory shear (OS) compared to unidirectional laminar shear in vitro. The DNMT inhibitor 5-Aza-2’deoxycytidine (5Aza) or DNMT1 siRNA significantly reduced OS-induced endothelial inflammation. Moreover, 5Aza reduced lesion formation in two atherosclerosis models using ApoE-/- mice (western diet for 3 months and the partial carotid ligation model with western diet for 3 weeks). To identify the 5Aza mechanisms, we conducted two genome-wide studies: reduced representation bisulfite sequencing (RRBS) and transcript microarray using endothelial-enriched gDNA and RNA, respectively, obtained from the partially-ligated left common carotid artery (LCA exposed to d-flow) and the right contralateral control (RCA exposed to s-flow) of mice treated with 5Aza or vehicle. D-flow induced DNA hypermethylation in 421 gene promoters, which was significantly prevented by 5Aza in 335 genes. Systems biological analyses using the RRBS and the transcriptome data revealed 11 mechanosensitive genes whose promoters were hypermethylated by d-flow but rescued by 5Aza treatment. Of those, five genes contain hypermethylated cAMP-response-elements in their promoters, including the transcription factors HoxA5 and Klf3. Their methylation status could serve as a mechanosensitive master switch in endothelial gene expression. Our results demonstrate that d-flow controls epigenomic DNA methylation patterns in a DNMT-dependent manner, which in turn alters endothelial gene expression and induces atherosclerosis.

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A Robust Rerank Approach for Feature Selection and Its Application to Pooling-Based GWA Studies

Computational and Mathematical Methods in Medicine ◽

10.1155/2013/860673 ◽

2013 ◽

Vol 2013 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Jia-Rou Liu ◽

Po-Hsiu Kuo ◽

Hung Hung

Keyword(s):

Characteristic Curve ◽

Real Data ◽

Tuning Parameter ◽

Practical Implementation ◽

Tuning Parameters ◽

Genome Wide ◽

Feature Based ◽

The Difference ◽

Gwa Studies ◽

Selection Of

Large-p-small-ndatasets are commonly encountered in modern biomedical studies. To detect the difference between two groups, conventional methods would fail to apply due to the instability in estimating variances int-test and a high proportion of tied values in AUC (area under the receiver operating characteristic curve) estimates. The significance analysis of microarrays (SAM) may also not be satisfactory, since its performance is sensitive to the tuning parameter, and its selection is not straightforward. In this work, we propose a robust rerank approach to overcome the above-mentioned diffculties. In particular, we obtain a rank-based statistic for each feature based on the concept of “rank-over-variable.” Techniques of “random subset” and “rerank” are then iteratively applied to rank features, and the leading features will be selected for further studies. The proposed re-rank approach is especially applicable for large-p-small-ndatasets. Moreover, it is insensitive to the selection of tuning parameters, which is an appealing property for practical implementation. Simulation studies and real data analysis of pooling-based genome wide association (GWA) studies demonstrate the usefulness of our method.

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Identification of anti-norovirus genes in mouse and human cells using genome-wide CRISPR activation screening

10.1101/350090 ◽

2018 ◽

Cited By ~ 3

Author(s):

Robert C. Orchard ◽

Meagan E. Sullender ◽

Bria F. Dunlap ◽

Dale R. Balce ◽

John G. Doench ◽

...

Keyword(s):

Antiviral Activity ◽

World Wide ◽

Human Cells ◽

Gene Promoters ◽

Murine Norovirus ◽

Individual Gene ◽

Genome Wide ◽

Host Genes ◽

Crispr Activation

AbstractNoroviruses (NoVs) are a leading cause of gastroenteritis world-wide, yet host factors that restrict NoV replication are not well understood. Here, we use a CRISPR activation (CRISPRa) genome-wide screening to identify host genes that can inhibit murine norovirus (MNoV) replication in either mouse or human cells. Our screens identified with high confidence 57 genes that can inhibit MNoV infection when overexpressed. A significant number of these genes are in interferon and immune regulation signaling networks, but surprising, the majority of the genes identified are not associated with innate or adaptive immunity nor with any antiviral activity. Confirmatory studies of eight of the genes in validate the initial screening data. Mechanistic studies on TRIM7 demonstrated a conserved role of the molecule in mouse and human cells in restricting MNoV in a step of infection after viral entry. Furthermore, we demonstrate that two isoforms of TRIM7 have differential antiviral activity. Taken together these data provide a resource for understanding norovirus biology and demonstrate a robust methodology for identifying new antiviral molecules across cell types and species.Author SummaryNorovirus is one of the leading causes of foodborne illness world-wide. Despite its prevalence, our understanding of norovirus biology is limited due to the difficulty in growing human norovirus in vitro and a lack of an animal model. Murine norovirus (MNoV) is a model norovirus system because MNoV replicates robustly in cell culture and in mice. To identify host genes that can restrict norovirus replication when overexpressed we performed genome-wide CRISPR activation (CRISPRa) screens to induce gene overexpression at the native locus through recruitment of transcriptional activators to individual gene promoters. We found 57 genes could block murine norovirus replication in either mouse or human cells. Several of these genes are associated with classical immune signaling pathways, while many of the molecules we identified have not been previously associated with antiviral activity. Our data is a resource for those studying norovirus and we provide a robust approach to identify novel antiviral genes.

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Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii

Frontiers in Genetics ◽

10.3389/fgene.2021.785934 ◽

2022 ◽

Vol 12 ◽

Author(s):

Inge Holm ◽

Luisa Nardini ◽

Adrien Pain ◽

Emmanuel Bischoff ◽

Cameron E. Anderson ◽

...

Keyword(s):

Malaria Vector ◽

Regulatory Elements ◽

Specific Cell ◽

Insect Vector ◽

Anopheles Coluzzii ◽

Gene Promoters ◽

Transcriptional Enhancers ◽

Genome Wide ◽

A Genome

Almost all regulation of gene expression in eukaryotic genomes is mediated by the action of distant non-coding transcriptional enhancers upon proximal gene promoters. Enhancer locations cannot be accurately predicted bioinformatically because of the absence of a defined sequence code, and thus functional assays are required for their direct detection. Here we used a massively parallel reporter assay, Self-Transcribing Active Regulatory Region sequencing (STARR-seq), to generate the first comprehensive genome-wide map of enhancers in Anopheles coluzzii, a major African malaria vector in the Gambiae species complex. The screen was carried out by transfecting reporter libraries created from the genomic DNA of 60 wild A. coluzzii from Burkina Faso into A. coluzzii 4a3A cells, in order to functionally query enhancer activity of the natural population within the homologous cellular context. We report a catalog of 3,288 active genomic enhancers that were significant across three biological replicates, 74% of them located in intergenic and intronic regions. The STARR-seq enhancer screen is chromatin-free and thus detects inherent activity of a comprehensive catalog of enhancers that may be restricted in vivo to specific cell types or developmental stages. Testing of a validation panel of enhancer candidates using manual luciferase assays confirmed enhancer function in 26 of 28 (93%) of the candidates over a wide dynamic range of activity from two to at least 16-fold activity above baseline. The enhancers occupy only 0.7% of the genome, and display distinct composition features. The enhancer compartment is significantly enriched for 15 transcription factor binding site signatures, and displays divergence for specific dinucleotide repeats, as compared to matched non-enhancer genomic controls. The genome-wide catalog of A. coluzzii enhancers is publicly available in a simple searchable graphic format. This enhancer catalogue will be valuable in linking genetic and phenotypic variation, in identifying regulatory elements that could be employed in vector manipulation, and in better targeting of chromosome editing to minimize extraneous regulation influences on the introduced sequences.Importance: Understanding the role of the non-coding regulatory genome in complex disease phenotypes is essential, but even in well-characterized model organisms, identification of regulatory regions within the vast non-coding genome remains a challenge. We used a large-scale assay to generate a genome wide map of transcriptional enhancers. Such a catalogue for the important malaria vector, Anopheles coluzzii, will be an important research tool as the role of non-coding regulatory variation in differential susceptibility to malaria infection is explored and as a public resource for research on this important insect vector of disease.

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