Genome-Wide Identification and Expression Analyses of AnSnRK2 Gene Family under Osmotic Stress in Ammopiptanthus nanus

Sucrose non-fermenting-1 (SNF1)-related protein kinase 2’s (SnRK2s) are plant-specific serine/threonine protein kinases and play crucial roles in the abscisic acid signaling pathway and abiotic stress response. Ammopiptanthus nanus is a relict xerophyte shrub and extremely tolerant of abiotic stresses. Therefore, we performed genome-wide identification of the AnSnRK2 genes and analyzed their expression profiles under osmotic stresses including drought and salinity. A total of 11 AnSnRK2 genes (AnSnRK2.1-AnSnRK2.11) were identified in the A. nanus genome and were divided into three groups according to the phylogenetic tree. The AnSnRK2.6 has seven introns and others have eight introns. All of the AnSnRK2 proteins are highly conserved at the N-terminus and contain similar motif composition. The result of cis-acting element analysis showed that there were abundant hormone- and stress-related cis-elements in the promoter regions of AnSnRK2s. Moreover, the results of quantitative real-time PCR exhibited that the expression of most AnSnRK2s was induced by NaCl and PEG-6000 treatments, but the expression of AnSnRK2.3 and AnSnRK2.6 was inhibited, suggesting that the AnSnRK2s might play key roles in stress tolerance. The study provides insights into understanding the function of AnSnRK2s.

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Genome-Wide Identification and Characterization of WOX Genes in Cucumis sativus

Genome ◽

10.1139/gen-2020-0029 ◽

2021 ◽

Author(s):

Ni Han ◽

Rui Tang ◽

Xueqian Chen ◽

Zhixuan Xu ◽

Zhonghai Ren ◽

...

Keyword(s):

Cucumis Sativus ◽

Stress Responses ◽

Expression Profiles ◽

Duplication Event ◽

Amino Acid Sequences ◽

Event Analysis ◽

Promoter Regions ◽

Element Analysis ◽

Genome Wide ◽

Wox Genes

WUSCHEL-related homeobox (WOX) proteins are plant-specific transcription factors that are profoundly involved in regulation of plant development and stress responses. In this study, we totally identified 11 WOX transcription factor family members in cucumber (Cucumis sativus, CsWOXs) genome and classified them into three clades with nine subclades based on phylogenetic analysis results. Alignment of amino acid sequences revealed that all WOX members in cucumber contained the typical homeodomain, which consists of 60-66 amino acids and is folded into a helix-turn-helix structure. Gene duplication event analysis indicated that CsWOX1a and CsWOX1b were a segment duplication pair, which might affect the number of WOX members in cucumber genome. The expression profiles of CsWOX genes in different tissues demonstrated that the members sorted into the ancient clade (CsWOX13a and CsWOX13b) were constitutively expressed at higher levels in comparison to the others. Cis-element analysis in promoter regions suggested that the expression of CsWOX genes was associated with phytohormone pathways and stress responses, which was further supported by RNA-seq data. Taken together, our results provide new insights into the evolution of cucumber WOX genes and improve our understanding about the biological functions of CsWOX family.

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Genome-Wide Identification and Expression Analyses of CONSTANS-Like Family Genes in Cucumber (Cucumis sativus L.)

Journal of Plant Growth Regulation ◽

10.1007/s00344-021-10420-4 ◽

2021 ◽

Author(s):

Zhen Tian ◽

Xiaodong Qin ◽

Hui Wang ◽

Ji Li ◽

Jinfeng Chen

Keyword(s):

Floral Induction ◽

Structural Characteristics ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Biological Functions ◽

Promoter Regions ◽

Cucumis Sativus L ◽

Cis Acting ◽

Genome Wide ◽

Induction Process

AbstractThe CONSTANS-like (COL) gene family is one of the plant-specific transcription factor families that play important roles in plant growth and development. However, the knowledge of COLs related in cucumber is limited, and their biological functions, especially in the photoperiod-dependent flowering process, are still unclear. In this study, twelve CsaCOL genes were identified in the cucumber genome. Phylogenetic and conserved motif analyses provided insights into the evolutionary relationship between the CsaCOLs. Further, the comparative genome analysis revealed that COL genes are conserved in different plant species, especially collinearity gene pairs related to CsaCOL5. Ten kinds of cis-acting elements were vividly detected in CsaCOLs promoter regions, including five light-responsive elements, which echo the diurnal rhythm expression patterns of seven CsaCOL genes under SD and LD photoperiod regimes. Combined with the expression data of developmental stage, three CsaCOL genes are involved in the flowering network and play pivotal roles for the floral induction process. Our results provide useful information for further elucidating the structural characteristics, expression patterns, and biological functions of COL family genes in many plants

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Genome-wide identification and analysis of the CNGC gene family in maize

PeerJ ◽

10.7717/peerj.5816 ◽

2018 ◽

Vol 6 ◽

pp. e5816 ◽

Cited By ~ 4

Author(s):

Lidong Hao ◽

Xiuli Qiao

Keyword(s):

Gene Family ◽

Expression Profiles ◽

Gene Families ◽

Regulatory Elements ◽

Vital Role ◽

Signal Pathways ◽

Cis Acting ◽

Genome Wide ◽

Gramineous Plant ◽

Gated Channel

As one of the non-selective cation channel gene families, the cyclic nucleotide-gated channel (CNGC) gene family plays a vital role in plant physiological processes that are related to signal pathways, plant development, and environmental stresses. However, genome-wide identification and analysis of the CNGC gene family in maize has not yet been undertaken. In the present study, twelve ZmCNGC genes were identified in the maize genome, which were unevenly distributed on chromosomes 1, 2, 4, 5, 6, 7, and 8. They were classified into five major groups: Groups I, II, III, IVa, and IVb. Phylogenetic analysis showed that gramineous plant CNGC genes expanded unequally during evolution. Group IV CNGC genes emerged first, whereas Groups I and II appeared later. Prediction analysis of cis-acting regulatory elements showed that 137 putative cis-elements were related to hormone-response, abiotic stress, and organ development. Furthermore, 120 protein pairs were predicted to interact with the 12 ZmCNGC proteins and other maize proteins. The expression profiles of the ZmCNGC genes were expressed in tissue-specific patterns. These results provide important information that will increase our understanding of the CNGC gene family in maize and other plants.

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Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays

PeerJ ◽

10.7717/peerj.9551 ◽

2020 ◽

Vol 8 ◽

pp. e9551

Author(s):

Lidong Hao ◽

Shubing Shi ◽

Haibin Guo ◽

Ming Li ◽

Pan Hu ◽

...

Keyword(s):

Transcription Factors ◽

Plant Growth ◽

Growth And Development ◽

Expression Profiles ◽

Vital Role ◽

Ethylene Response Factor ◽

Plant Growth And Development ◽

Element Analysis ◽

Genome Wide ◽

Genes Expression

The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize.

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Genome-Wide Identification of WRKY Genes in Artemisia annua: Characterization of a Putative Ortholog of AtWRKY40

Plants ◽

10.3390/plants9121669 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1669

Author(s):

Angelo De Paolis ◽

Sofia Caretto ◽

Angela Quarta ◽

Gian-Pietro Di Sansebastiano ◽

Irene Sbrocca ◽

...

Keyword(s):

Artemisia Annua ◽

Antimalarial Activity ◽

Regulatory Elements ◽

Promoter Regions ◽

Cis Acting ◽

Protein Motifs ◽

Genome Wide ◽

A Genome ◽

Rapid Amplification

Artemisia annua L. is well-known as the plant source of artemisinin, a sesquiterpene lactone with effective antimalarial activity. Here, a putative ortholog of the Arabidopsis thaliana WRKY40 transcription factor (TF) was isolated via reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends in A. annua and named AaWRKY40. A putative nuclear localization domain was identified in silico and experimentally confirmed by using protoplasts of A. annua transiently transformed with AaWRKY40-GFP. A genome-wide analysis identified 122 WRKY genes in A. annua, and a manually curated database was obtained. The deduced proteins were categorized into the major WRKY groups, with group IIa containing eight WRKY members including AaWRKY40. Protein motifs, gene structure, and promoter regions of group IIa WRKY TFs of A. annua were characterized. The promoter region of AaWRKY group IIa genes contained several abiotic stress cis-acting regulatory elements, among which a highly conserved W-box motif was identified. Expression analysis of AaWRKY40 compared to AaWRKY1 in A. annua cell cultures treated with methyl jasmonate known to enhance artemisinin production, suggested a possible involvement of AaWRKY40 in terpenoid metabolism. Further investigation is necessary to study the role of AaWRKY40 and possible interactions with other TFs in A. annua.

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Genome-Wide Identification and Expression Analyses of the Chitinases under Cold and Osmotic stress in Ammopiptanthus nanus

Genes ◽

10.3390/genes10060472 ◽

2019 ◽

Vol 10 (6) ◽

pp. 472 ◽

Cited By ~ 5

Author(s):

Cao ◽

Wang ◽

Li ◽

Shi ◽

Gao ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Low Temperature ◽

Osmotic Stress ◽

Fungal Pathogens ◽

Glycosyl Hydrolase ◽

Class Iii ◽

Abiotic Stress Response ◽

Ammopiptanthus Nanus ◽

Genome Wide

Chitinase is a kind of hydrolase with chitin as a substrate and is proposed to play an essential role in plant defense system by functioning against fungal pathogens through degrading chitin. Recent studies indicated chitinase is also involved in abiotic stress response in plants, helping plants to survive in stressful environments. A. nanus, a rare evergreen broad-leaved shrub distrusted in deserts in Central Asia, exhibits a high level of tolerance to drought and low temperature stresses. To identify the chitinase gene involved in drought and low temperature responses in A. nanus, we performed genome-wide identification, classification, sequence alignment, and spatio-temporal gene expression analysis of the chitinases in A. nanus under osmotic and low temperature stress. A total of 32 chitinase genes belonging to glycosyl hydrolase 18 (GH18) and GH19 families were identified from A. nanus. Class III chitinases appear to be amplified quantitatively in A. nanus, and their genes carry less introns, indicating their involvement in stress response in A. nanus. The expression level of the majority of chitinases varied in leaves, stems, and roots, and regulated under environmental stress. Some chitinases, such as EVM0022783, EVM0020238, and EVM0003645, are strongly induced by low temperature and osmotic stress, and the MYC/ICE1 (inducer of CBF expression 1) binding sites in promoter regions may mediate the induction of these chitinases under stress. These chitinases might play key roles in the tolerance to these abiotic stress in A. nanus and have potential for biotechnological applications. This study provided important data for understanding the biological functions of chitinases in A. nanus.

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Genome-wide characterization of SPL gene family in Codonopsis pilosula reveals the novel roles of CpSPL2 and CpSPL10 in promoting the accumulation of secondary metabolites and growth of C. pilosula hairy root

10.21203/rs.3.rs-81496/v1 ◽

2020 ◽

Author(s):

Jing Yang ◽

Zhonglong Guo ◽

Yao Cao ◽

Rui Chen ◽

Wentao Wang ◽

...

Keyword(s):

Secondary Metabolites ◽

Hairy Root ◽

Expression Patterns ◽

Light Stress ◽

The Novel ◽

Promoter Regions ◽

Cis Acting ◽

Codonopsis Pilosula ◽

Genome Data ◽

Genome Wide

Abstract Background SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors play critical roles in regulating diverse aspects of plant growth and development, including vegetative phase change, plant architecture, anthocyanin accumulation, lateral root growth, etc. Codonopsis pilosula is a famous medicinal plant and its dried root, named Dangshen, is one of the most widely used traditional Chinese medicine. However, little information about SPL genes in this species has been reported. Results In the present study, 15 SPL genes were identified based on the genome data of Codonopsis pilosula. Ten of the 15 CpSPLs were predicted to be the targets of miR156. Phylogenetic analysis clustered CpSPLs into seven groups (G1-G7) along with 16 SPLs from Arabidopsis thaliana. CpSPLs in the same group share similar gene structure and conserved motif composition. Cis-acting elements responding to light, stress, and phytohormone widely exist in their promoter regions. Our qRT-PCR results indicated that 15 CpSPLs were differentially expressed in different tissues (root, stem, leaf, flower, and calyx), different developmental periods (1, 2 and 3 months after germination), and various conditions (NaCl, MeJA and ABA treatment). Compared with the control, overexpression of CpSPL2 or CpSPL10 significantly promoted not only the growth of hairy roots, but also the accumulation of total saponins and lobetyolin. Conclusions The SPL genes in the C. pilosula genome were identified and their expression patterns were analyzed. The novel roles of CpSPL2 and CpSPL10 in promoting the accumulation of secondary metabolites and growth of C. pilosula hairy root were revealed. Our results established a foundation for further investigation of CpSPLs and provided novel insights into their biological functions.

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Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells

10.1101/122135 ◽

2017 ◽

Cited By ~ 4

Author(s):

Anish Dattani ◽

Damian Kao ◽

Yuliana Mihaylova ◽

Prasad Abnave ◽

Samantha Hughes ◽

...

Keyword(s):

Stem Cells ◽

Rna Polymerase Ii ◽

Histone Modifications ◽

Cell Function ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Proximal Region ◽

Body Parts ◽

Promoter Regions ◽

Genome Wide

AbstractPlanarian flatworms have an indefinite capacity to regenerate missing or damaged body parts owing to a population of pluripotent adult stems cells called neoblasts (NBs). Currently, little is known about the importance of the epigenetic status of NBs and how histone modifications regulate homeostasis and cellular differentiation. We have developed an improved and optimized ChIP-seq protocol for NBs in Schmidtea mediterranea and have generated genome-wide profiles for the active marks H3K4me3 and H3K36me3, and suppressive marks H3K4me1 and H3K27me3. The genome-wide profiles of these marks were found to correlate well with NB gene expression profiles. We found that genes with little transcriptional activity in the NB compartment but which switch on in post-mitotic progeny during differentiation are bivalent, being marked by both H3K4me3 and H3K27me3 at promoter regions. In further support of this hypothesis bivalent genes also have a high level of paused RNA Polymerase II at the promoter-proximal region. Overall, this study confirms that epigenetic control is important for the maintenance of a NB transcriptional program and makes a case for bivalent promoters as a conserved feature of animal stem cells and not a vertebrate specific innovation. By establishing a robust ChIP-seq protocol and analysis methodology, we further promote planarians as a promising model system to investigate histone modification mediated regulation of stem cell function and differentiation.

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Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum)

PeerJ ◽

10.7717/peerj.7664 ◽

2019 ◽

Vol 7 ◽

pp. e7664

Author(s):

Weiguo Qian ◽

Xiaomin Yang ◽

Jiawen Li ◽

Rui Luo ◽

Xiufeng Yan ◽

...

Keyword(s):

Function Analysis ◽

Expression Profiles ◽

Critical Role ◽

Water Channel ◽

Gene Expression Profiles ◽

Salt Resistance ◽

Abiotic Stress Response ◽

Salt Cress ◽

Genome Wide ◽

Eutrema Salsugineum

Aquaporins (AQPs) serve as water channel proteins and belong to major intrinsic proteins (MIPs) family, functioning in rapidly and selectively transporting water and other small solutes across biological membranes. Importantly, AQPs have been shown to play a critical role in abiotic stress response pathways of plants. As a species closely related to Arabidopsis thaliana, Eutrema salsugineum has been proposed as a model for studying salt resistance in plants. Here we surveyed 35 full-length AQP genes in E. salsugineum, which could be grouped into four subfamilies including 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), nine NOD-like intrinsic proteins (NIPs), and three small basic intrinsic proteins (SIPs) by phylogenetic analysis. EsAQPs were comprised of 237–323 amino acids, with a theoretical molecular weight (MW) of 24.31–31.80 kDa and an isoelectric point (pI) value of 4.73–10.49. Functional prediction based on the NPA motif, aromatic/arginine (ar/R) selectivity filter, Froger’s position and specificity-determining position suggested quite differences in substrate specificities of EsAQPs. EsAQPs exhibited global expressions in all organs as shown by gene expression profiles and should be play important roles in response to salt, cold and drought stresses. This study provides comprehensive bioinformation on AQPs in E. salsugineum, which would be helpful for gene function analysis for further studies.

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In silico characterization and comparison of the fruit ripening related beta‐ amylase (BAM) gene family in banana genome A and B

Indonesian Journal of Biotechnology ◽

10.22146/ijbiotech.65142 ◽

2021 ◽

Vol 26 (4) ◽

pp. 175

Author(s):

Erdianty Setiabudi ◽

Karlia Meitha ◽

Fenny Martha Dwivany

Keyword(s):

Gene Family ◽

Functional Characterization ◽

Genomic Analysis ◽

Starch Metabolism ◽

Promoter Regions ◽

Element Analysis ◽

Cis Acting ◽

Global Food Security ◽

Metabolism Regulation ◽

Functional Genomic Analysis

Banana is one of the most important commodities for maintaining global food security. Primary metabolic processes during the ripening of banana greatly affect post‐harvest quality, particularly in starch metabolism. The beta‐ amylase (BAM) gene family is known as a group of genes that plays an important role in starch metabolism regulation. In this study, we focused on the characterization and comparative analysis of the BAM gene family in DH Pahang and Pisang Klutuk Wulung (PKW) varieties, these being the AA and BB genomes, respectively. The sequences of BAM gene family were retrieved from the database of Musa acuminata ’DH Pahang’ and Musa balbisiana ’PKW’ genome, then structural and functional characterization was performed, followed by identification of cis‐acting elements in the BAM promoter regions. The results showed that the BAM gene family structure was relatively conserved in both genomes, and a putative BAM11 gene was found, the function of which has not been studied in other plants. Cis‐acting element analysis showed that they were distinct in the copy number and types of elements that were responsive to various phytohormones. This study suggested that the BAM genes involved in ripening are spatiotemporally regulated. However, further functional genomic analysis is required to describe the specific role and regulation of BAM genes during ripening in banana.

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