Characterization and abiotic stress-responsive expression analysis of SGT1 genes in Brassica oleracea

SGT1 genes are involved in enhancing plant responses to various biotic and abiotic stresses. Brassica oleracea is known to contain two types of SGT1 genes, namely suppressor of G2 allele of SKP1 and suppressor of GCR2. In this study, through systematic analysis, four putative SGT1 genes were identified and characterized in B. oleracea. In phylogenetic analysis, the genes clearly formed separate groups, namely BolSGT1a, BolSGT1b (both suppressor of G2 allele of SKP1 types), and BolSGT1 (suppressor of GCR2). Functional domain analysis and organ-specific expression patterns suggested possible roles for BolSGT1 genes during stress conditions. BolSGT1 genes showed significant changes in expression in response to heat, cold, drought, salt, or ABA treatment. Interaction network analysis supported the expression analysis, and showed that the BolSGT1a and BolSGT1b genes are strongly associated with co-regulators during stress conditions. However, the BolSGT1 gene did not show any strong association. Hence, BolSGT1 might be a stress resistance-related gene that functions without a co-regulator. Our results show that BolSGT1 genes are potential target genes to improve B. oleracea resistance to abiotic stresses such as heat, cold, and salt.

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Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max

Plants ◽

10.3390/plants10071465 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1465

Author(s):

Ramon de Koning ◽

Raphaël Kiekens ◽

Mary Esther Muyoka Toili ◽

Geert Angenon

Keyword(s):

Common Bean ◽

Seed Development ◽

Expression Analysis ◽

De Novo ◽

Expression Patterns ◽

Gene Families ◽

Rna Seq ◽

Raffinose Family Oligosaccharides ◽

Specific Expression ◽

Raffinose Synthase

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

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Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽

10.1139/gen-2017-0163 ◽

2018 ◽

Vol 61 (2) ◽

pp. 121-130 ◽

Cited By ~ 4

Author(s):

Chenghao Zhang ◽

Wenqi Dong ◽

Zong-an Huang ◽

MyeongCheoul Cho ◽

Qingcang Yu ◽

...

Keyword(s):

Capsicum Annuum ◽

Abiotic Stresses ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Families ◽

Environmental Stresses ◽

Transcriptional Level ◽

Specific Expression ◽

Capsicum Annuum L ◽

Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

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Genome-Wide Analysis of Basic Helix–Loop–Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.)

Genes ◽

10.3390/genes10110914 ◽

2019 ◽

Vol 10 (11) ◽

pp. 914

Author(s):

Shan ◽

Zhang ◽

Yu ◽

Wang ◽

Li ◽

...

Keyword(s):

Brassica Oleracea ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Chilling Stress ◽

Expression Patterns ◽

Comprehensive Analysis ◽

Bhlh Transcription Factor ◽

Specific Expression ◽

Basic Helix Loop Helix ◽

Helix Loop Helix

Basic helix–loop–helix (bHLH) transcription factor (TF) family is commonly found in eukaryotes, which is one of the largest families of regulator proteins. It plays an important role in plant growth and development, as well as various biotic and abiotic stresses. However, a comprehensive analysis of the bHLH family has not been reported in Brassica oleracea. In this study, we systematically describe the BobHLHs in the phylogenetic relationships, expression patterns in different organs/tissues, and in response to chilling stress, and gene and protein characteristics. A total of 234 BobHLH genes were identified in the B. oleracea genome and were further clustered into twenty-three subfamilies based on the phylogenetic analyses. A large number of BobHLH genes were unevenly located on nine chromosomes of B. oleracea. Analysis of RNA-Seq expression profiles revealed that 21 BobHLH genes exhibited organ/tissue-specific expression. Additionally, the expression of six BobHLHs (BobHLH003, -048, -059, -093, -109, and -148) were significantly down-regulated in chilling-sensitive cabbage (CS-D9) and chilling-tolerant cabbage (CT-923). At 24h chilling stress, BobHLH054 was significantly down-regulated and up-regulated in chilling-treated CS-D9 and CT-923. Conserved motif characterization and exon/intron structural patterns showed that BobHLH genes had similar structures in the same subfamily. This study provides a comprehensive analysis of BobHLH genes and reveals several candidate genes involved in chilling tolerance of B. oleracea, which may be helpful to clarify the roles of bHLH family members and understand the regulatory mechanisms of BobHLH genes in response to the chilling stress of cabbage.

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Genome-wide identification and expression analysis of aquaporin gene family related to abiotic stress in watermelon

Genome ◽

10.1139/gen-2019-0061 ◽

2019 ◽

Vol 62 (10) ◽

pp. 643-656 ◽

Cited By ~ 2

Author(s):

Yong Zhou ◽

Junjie Tao ◽

Golam Jalal Ahammed ◽

Jingwen Li ◽

Youxin Yang

Keyword(s):

Expression Analysis ◽

Developmental Stages ◽

Plant Responses ◽

Distribution Analysis ◽

Cis Elements ◽

Promoter Regions ◽

Specific Expression ◽

Promoter Sequences ◽

Genome Wide ◽

Aquaporin Gene

The plant aquaporins (AQPs) are highly conserved integral membrane proteins that participate in multiple developmental processes and responses to various stresses. In this study, a total of 35 AQP genes were identified in the watermelon genome. The phylogenetic analysis showed that these AQPs can be divided into five types, including 16 plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight nodulin 26-like intrinsic proteins (NIPs), two small basic intrinsic proteins (SIPs), and one uncategorized X intrinsic protein (XIP). A number of cis-elements related to plant responses to hormones and stresses were detected in the promoter sequences of ClAQP genes. Chromosome distribution analysis revealed that the genes are unevenly distributed on eight chromosomes, with chromosomes 1 and 4 possessing the most genes. Expression analysis at different developmental stages in flesh and rind indicated that most of ClAQPs have tissue-specific expression. Meanwhile, some other AQP genes showed differential expression in response to cold, salt, and ABA treatments, which is consistent with the organization of the stress-responsive cis-elements detected in the promoter regions. Our results lay a foundation for understanding the specific functions of ClAQP genes to help the genetic improvement of watermelon.

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Estrogen Receptor β: An Overview and Update

Nuclear Receptor Signaling ◽

10.1621/nrs.06003 ◽

2008 ◽

Vol 6 (1) ◽

pp. nrs.06003 ◽

Cited By ~ 166

Author(s):

Chunyan Zhao ◽

Karin Dahlman-Wright ◽

Jan-Åke Gustafsson

Keyword(s):

Estrogen Receptor ◽

Target Genes ◽

Expression Patterns ◽

Estrogen Signaling ◽

Receptor Subtypes ◽

Specific Expression ◽

Microarray Experiments ◽

Downstream Target ◽

Animal Disease Models ◽

Selective Ligands

The discovery of a second estrogen receptor (ER), designated ERβ (NR3A2), has redefined our knowledge about the mechanisms underlying cellular signaling by estrogens and has broad implications for our understanding of regulation of estrogen-responsive tissues. Highly variable and even contrasting effects of estrogens in different tissues seem to be at least partially explained by different estrogen signaling pathways, involving ERα (NR3A1) and/or ERβ. To date, two key conclusions can be drawn from the significant body of work carried out on the specific roles of the two receptor subtypes in diverse estrogen target tissues. First, ERα and ERβ have different biological functions, as indicated by their specific expression patterns and the distinct phenotypes observed in ERα and ERβ knockout (αERKO and βERKO) mice. Second, ERα and ERβ appear to have overlapping but also unique sets of downstream target genes, as judged from a set of microarray experiments. Thus, ERα and ERβ have different transcriptional activities in certain ligand, cell-type, and promoter contexts, which may help to explain some of the major differences in their tissue-specific biological actions. The phenotypes observed for βERKO mice have suggested certain therapeutic areas to be further explored. The development of ERβ-selective ligands active in animal disease models indicates new avenues for clinical exploration. ERβ agonists are being explored and validated as drugs for a growing number of indications. Hopefully, some ERβ targeted drugs will prove to be efficient in enhancing human health.

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Quantitative Amplification of Cleaved Ends (qACE) to assay miRNA-directed target cleavage

F1000Research ◽

10.12688/f1000research.5266.1 ◽

2014 ◽

Vol 3 ◽

pp. 240 ◽

Cited By ~ 2

Author(s):

Suresh Damodaran ◽

Sajag Adhikari ◽

Marie Turner ◽

Senthil Subramanian

Keyword(s):

Target Genes ◽

Expression Patterns ◽

Mirna Regulation ◽

Temporal Expression ◽

Specific Expression ◽

Rna Molecules ◽

Specific Target Gene ◽

Pcr Method ◽

Spatio Temporal ◽

Fusion Primer

microRNA (miRNA) regulation is crucial to achieve precise spatio-temporal expression patterns of their target genes. This makes it crucial to determine the levels of cleavage of a particular target mRNA in different tissues and under different conditions. We developed a quantitative PCR method “quantitative Amplification of Cleaved Ends (qACE)” to assay levels of specific cleavage products in order to determine the extent of miRNA regulation for a specific target gene. qACE uses cDNA generated from adapter-ligated RNA molecules and relies on a carefully designed fusion primer that spans the adapter-cleaved RNA junction in qPCR to specifically amplify and quantify cleaved products. The levels of full-length transcripts can also be assayed in the same cDNA preparation using primers that span across the miRNA cleavage site. We used qACE to demonstrate that soybean roots over-expressing miR164 had increased levels of target cleavage and that miRNA deficient Arabidopsis thaliana hen1-1 mutants had reduced levels of target cleavage. We used qACE to discover that differential cleavage by miR164 in nodule vs. adjacent root tissue contributed to nodule-specific expression of NAC1 transcription factors in soybean. These experiments show that qACE can be used to discover and demonstrate differential cleavage by miRNAs to achieve specific spatio-temporal expression of target genes in plants.

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Transcriptomes Analysis Reveals the Regulatory Roles of Noncoding RNA in Tanshinones Synthesis Pathway of Salvia Miltiorrhiza

10.21203/rs.3.rs-736448/v1 ◽

2021 ◽

Author(s):

Caicai Lin ◽

Changhao Zhou ◽

Zhongqian Liu ◽

Xingfeng Li ◽

Zhenqiao Song

Keyword(s):

Noncoding Rna ◽

Target Genes ◽

Salvia Miltiorrhiza ◽

Expression Patterns ◽

Noncoding Rnas ◽

Synthesis Process ◽

Circular Rnas ◽

Regulation Mechanism ◽

Pentatricopeptide Repeat ◽

Specific Expression

Abstract Background: Long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) have been shown to play fundamental roles in plant development. However, the information of these noncoding RNAs (ncRNAs) in Salvia miltiorrhiza remains largely unexplored. In this study, the expression pattern of ncRNAs in six tissues from the same strain of S. miltiorrhiza was analyzed to study the biological function of ncRNAs on active ingredients synthesis.Methods: Analysis of tanshinone content differences of two root simples was carried out on high-performance liquid chromatography (HPLC). RNA sequencing, GO and KEGG enrichment analysis were applied to analyzing the targets of diferentially expressed ncRNAs in different organs.Results: A total of 6,929 lncRNAs, 6,239 circRNAs, and 360 miRNAs were identified. Forty-eight lncRNAs, 70 miRNAs, and 26 circRNAs expressed differentially between red and white root tissues with significantly different tanshinone content. GO and KEGG pathway analysis of target genes of differently expressed ncRNAs indicated that some target genes are involved in the synthesis pathway of terpene, including diterpene and sesquiterpene. We also found many target genes related to secondary metabolites, including 2-C-Methyl-d-erythritol 2,4-cyclodiphosphate Synthase (SmMCS) and several CYP450s. Furthermore, most target genes may be related to the resistance of pathogens, such as receptor kinases, disease-resistant proteins, and pentatricopeptide repeat-containing proteins. Conclusions: The present study exhibited the tissue-specific expression patterns of ncRNAs preliminarily in S. miltiorrhiza, which may reflect that the formation of white root or red root is related to regulation by ncRNAs. It would provide a basis for further research about the regulation mechanism in the tanshinone synthesis process.

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A network of transcriptional repressors mediates auxin response specificity

10.1101/448860 ◽

2018 ◽

Author(s):

Jekaterina Truskina ◽

Jingyi Han ◽

Carlos S. Galvan-Ampudia ◽

Stéphanie Lainé ◽

Géraldine Brunoud ◽

...

Keyword(s):

Target Genes ◽

Expression Patterns ◽

Open Chromatin ◽

Transcriptional Repressors ◽

In Planta ◽

Auxin Response ◽

Specific Expression ◽

Developmental Patterns ◽

Auxin Signalling ◽

Response Specificity

INTRODUCTORY PARAGRAPHThe regulation of signalling capacity plays a pivotal role in setting developmental patterns in both plants and animals (1). The hormone auxin is a key signal for plant growth and development that acts through the AUXIN RESPONSE FACTOR (ARF) transcription factors (2). A subset of these ARFs comprises transcriptional activators of target genes in response to auxin, and are essential for regulating auxin signalling throughout the plant lifecycle (3). While ARF activators show tissue-specific expression patterns, it is unknown how their expression patterns are established. Chromatin modifications and accessibility studies revealed the chromatin of loci encoding ARF activators is constitutively open for transcription. Using a high-throughput yeast one-hybrid (Y1H) approach, we discovered a network of transcriptional regulators of ARF activator genes from Arabidopsis thaliana. Expression analyses demonstrated that the majority of these regulators act as repressors of ARF transcription in planta. Our observations support a scenario where the default configuration of open chromatin enables a network of transcriptional repressors to shape the expression pattern of ARF activators and provide specificity in auxin signalling output throughout development.

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Genome-Wide Identification of GH3 Genes in Brassica Oleracea and Identification of a Promoter Region for Anther-Specific Expression of a GH3 Gene

10.21203/rs.3.rs-58799/v1 ◽

2020 ◽

Author(s):

Hankuil Yi ◽

Jiseong Jeong ◽

Sunhee Park ◽

Jeong Hui Im

Keyword(s):

Brassica Oleracea ◽

Promoter Region ◽

Expression Patterns ◽

Leaf Primordia ◽

Start Codon ◽

Male Sterile ◽

Specific Expression ◽

Genome Wide ◽

Tapetal Cells ◽

Floral Abscission

Abstract Background:The Gretchen Hagen 3 (GH3) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors. GH3 genes, especially Group Ⅲ subgroup 6 GH3 genes, and their expression patterns in economically important kale-type Brassica oleracea have not been systematically identified. Results:As a first step to understand regulation and molecular functions of Group Ⅲ subgroup 6 GH3 genes, thirty-four GH3 genes including four subgroup 6 genes were identified In B. oleracea var. oleracea, using TO1000. Synteny found around subgroup 6 GH3 genes in TO1000 and Arabidopsis indicated that these genes are evolutionarily related. Although expression of four subgroup 6 GH3 genes in TO1000 is not induced by auxin, gibberellic acid, and jasmonic acid, the genes show different organ-dependent expression patterns. Only one TO1000 subgroup 6 GH3 gene, Bo2g011210, is expressed in anthers when microspores, polarized microspores, and bicellular pollens are present, similar to two out of four syntenic Arabidopsis subgroup 6 GH3 genes. Detailed analyses of promoter activities of Bo2g011210 further showed that Bo2g011210 is expressed in tapetal cells and pollens in anther, and also expressed in leaf primordia and floral abscission zones. Conclusions:Sixty-two base pair (bp) region (-340 ~ -279 bp upstream from start codon) and about 450 bp region (-1489 to -1017 bp) in Bo2g011210 promoter were found to be important for expressions in anther and expressions in leaf primordia and floral abscission zones, respectively. The identified anther-specific promoter region will be useful to develop male sterile transgenic Brassica plants.

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Genome-wide identification and expression analysis of PUB genes in cotton

10.21203/rs.2.10518/v3 ◽

2020 ◽

Author(s):

Xuke Lu ◽

Na Shu ◽

Delong Wang ◽

Junjuan Wang ◽

Xiugui Chen ◽

...

Keyword(s):

Expression Analysis ◽

Abiotic Stresses ◽

Expression Patterns ◽

Structure Evolution ◽

Homologous Gene ◽

Segmental Duplications ◽

Gene Pairs ◽

Genome Wide ◽

Cotton Species ◽

Tandem Duplications

Abstract Background: The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stress, but few reports about PUBs in cotton were available. Therefore research on PUBs is of great importance and is a necessity when studying the mechanism of stress tolerance in cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from four sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), respectively. Prediction analysis of subcellular localization showed that the PUBs in cotton were widely distributed in cells, but primarily in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) on the basis of phylogenetic analysis, and the intron/exon structure was comparatively conserved within each subfamily. Location analysis showed that cotton PUBs were unevenly anchored on all chromosomes, varying from 1 to 14 per chromosome. Through multiple sequence alignment, 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs shared in A2 and D5 were found; however no tandem duplication region in A2 or D5 was found. Additionally, 105, 14 and 17 homologous gene pairs were found in the intra-subgenome of At and Dt, the At subgenome and the Dt subgenome of allotetraploid cotton, respectively. Functional analysis of GhPUB85A and GhPUB45D showed that these genes positively responded to abiotic stresses, but the expression patterns were different. In addition, although the expression levels of these two homologous genes were similar, their contributions were different when responding to stresses, specifically showing different responses to abiotic stresses and functional differences between the two subgenomes of G. hirsutum. Conclusion: This study reports the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs were highly conserved throughout the evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses (including those induced by salt, drought, hot and cold) to varying degrees.

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