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

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.

HSEAT: A Tool for Plant Heat Shock Element Analysis, Motif Identification and Analysis

2020 ◽  
Vol 15 (3) ◽  
pp. 196-203 ◽  
Author(s):  
Sarah Rizwan Qazi ◽  
Noor ul Haq ◽  
Shakeel Ahmad ◽  
Samina N. Shakeel
Keyword(s):  
Heat Shock ◽  
Differential Expression ◽  
Promoter Region ◽  
Analysis Tool ◽  
Promoter Regions ◽  
Heat Shock Element ◽  
Element Analysis ◽  
Cis Acting ◽  
Plant Genes ◽  
Hsp Genes

Background: Previous methods used to discover cis-regulatory motifs in promoter region of plant genes possess very limited performance, especially for analysis of novel and rare motifs. Different plant genes have differential expression under different environmental or experimental conditions and modular regulation of cis-regulatory sequences in promoter regions of the same or different genes. It has previously been revealed that Heat Shock Proteins (HSPs) creation is correlated with plant tolerance under heat and other stress conditions. Regulation of these HSP genes is controlled by interactions between heat shock factors (HSFs) with cis-acting motifs present in the promoter region of the genes. Differential expression of these HSP genes is because of their unique promoter architecture, cis-acting sequences and their interaction with HSFs. Objective: A versatile promoter analysis tool was proposed for identification and analysis of promoters of HSPs. Methods: Heat Shock Element Analysis Tool (HSEAT) has been implemented in java programming language using pattern recognition approach. This tool has build-in MS access database for storing different motifs. Results: HSEAT has been designed to detect different types of Heat Shock Elements (HSEs) in promoter regions of plant HSPs with integration of complete analysis of plant promoters to the tool. HSEAT is user-friendly, interactive application to discover various types of HSEs e.g. TTC Rich Types, Gap Types and Prefect HSE as well as STRE in HSPs. Here we examined and evaluated some known HSP promoters from different plants using this tool with already available tools. Conclusion: HSEAT has extensive potential to explore conserved or semi-conserved motifs or potential binding sites of different transcription factors for other stress regulating genes. This tool can be found at https://sourceforge.net/projects/heast/.

scholarly journals Genome-Wide Identification and Expression Analysis of MAPK and MAPKK Gene Family in Pomegranate (Punica Granatum L.)

Agronomy ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1015
Author(s):  
Yuan Ren ◽  
Dapeng Ge ◽  
Jianmei Dong ◽  
Linhui Guo ◽  
Zhaohe Yuan
Keyword(s):  
Gene Family ◽  
Punica Granatum ◽  
Mitogen Activated Protein Kinase ◽  
Phylogenetic Groups ◽  
Element Analysis ◽  
Multiple Sequence ◽  
Cis Acting ◽  
Genome Wide ◽  
A Genome ◽  
Mitogen Activated Protein

Mitogen-activated protein kinase (MAPK) cascade is involved in the regulation of a series of biological processes in organisms, which are composed of MAPKKKs, MAPKKs, and MAPKs. Although genome-wide analyses of it has been well described in some species, little is known about MAPK and MAPKK genes in pomegranates. In this study, we identified 18 PgMAPKs, 9 PgMAPKKs through a genome-wide search. Chromosome localization showed that 27 genes are distributed on 7 chromosomes with different densities. Multiple sequence alignment and phylogenetic analysis revealed that PgMAPKs and PgMAPKKs could be divided into 4 subfamilies (groups A, B, C, and D), respectively. In addition, exon-introns structural analysis of each candidate gene has indicated high levels of conservation within and between phylogenetic groups. Cis-acting element analysis predicted that PgMAPKs and PgMAPKKs were widely involved in the growth, development, stress and hormone response of pomegranate. Expression profile analyses of PgMAPKs and PgMAPKKs were performed in different tissues (root, leaf, flower and fruit), and PgMAPK13 was significantly expressed in all tissues. To our knowledge, this is the first genome-wide analysis of the MAPK and MAPKK gene family in pomegranate. This study provides valuable information for understanding the classification and functions of pomegranate MAPK signal.

scholarly journals Genome-Wide Identification of the NHX Gene Family in Punica granatum L. and Their Expressional Patterns under Salt Stress

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 264
Author(s):  
Jianmei Dong ◽  
Cuiyu Liu ◽  
Yuying Wang ◽  
Yujie Zhao ◽  
Dapeng Ge ◽  
...  
Keyword(s):  
Salt Stress ◽  
Gene Family ◽  
Tertiary Structure ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Punica Granatum ◽  
Conserved Motifs ◽  
Cis Acting ◽  
Gene Structures ◽  
Punica Granatum L

Most cultivated lands are suffering from soil salinization, which is a global problem affecting agricultural development and economy. High NaCl concentrations in the soil result in the accumulation of toxic Cl− and Na+ in plants. Na+/H+ antiporter (NHX) can regulate Na+ compartmentalization or efflux to reduce Na+ toxicity. This study aims to identify the NHX genes in pomegranate (Punica granatum L.) from the genome sequences and investigate their expression patterns under different concentrations of NaCl stress. In this study, we used the sequences of PgNHXs to analyze the physicochemical properties, phylogenetic evolution, conserved motifs, gene structures, cis-acting elements, protein tertiary structure and expression pattern. A total of 10 PgNHX genes were identified, and divided into three clades. Conserved motifs and gene structures showed that most of them had an amiloride-binding site (FFI/LY/FLLPPI), except for the members of clade III. There were multiple cis-acting elements involved in abiotic stress in PgNHX genes. Additionally, protein-protein interaction network analysis suggested that PgNHXs might play crucial roles in keeping a balance of Na+ in cells. The qRT-PCR analysis suggested that PgNHXs had tissue-specific expressional patterns under salt stress. Overall, our findings indicated that the PgNHXs could play significant roles in response to salt stress. The theoretical foundation was established in the present study for the further functional characterization of the NHX gene family in pomegranate.

scholarly journals Comprehensive Genomic Characterization and Expression Analysis of the Lipoxygenase Gene Family in Watermelon under Hormonal Treatments

Agriculture ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 429
Author(s):  
Jianping Liu ◽  
Yong Zhou ◽  
Jingwen Li ◽  
Feng Wang ◽  
Youxin Yang
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Protein Structures ◽  
Promoter Regions ◽  
Element Analysis ◽  
Cis Element ◽  
Genome Wide ◽  
Genomic Characterization ◽  
Gene Structures ◽  
Lipoxygenase Gene Family

Lipoxygenases (LOXs) are non-haem iron-containing dioxygenases and play vital roles in a variety of plant biological processes. Here, we first carried out the genome-wide identification of LOX genes in watermelon. A total of 16 LOX genes were identified, which could be classified into two categories according to phylogenetic analysis: the 9-LOXs (ClLOX1–4, 12, and 15) and 13-LOXs (ClLOX5–11, 13, 14, and 16). Furthermore, the protein structures, intrachromosomal distributions, and gene structures were thoroughly analyzed. Cis-element analysis of the promoter regions indicated that the expression of ClLOX genes may be influenced by stress and plant hormones. Bioinformatic and expression analyses revealed that the expression of ClLOX genes is tissue-specific and hormone-responsive. The detected LOX genes exhibited distinctive expression patterns in various tissues. Different ClLOX genes showed different responses to methyl jasmonate (MeJA), salicylic acid (SA), and ethylene (ET) treatments, particularly ClLOX7, which exhibited the most active response to the above treatments. This study provides valuable information for a better understanding of the functions of LOX genes and further exploration of the LOX gene family in watermelon.

scholarly journals Functional Genomic Analysis of the AUXIN/INDOLE-3-ACETIC ACID Gene Family Members in Arabidopsis thaliana

2005 ◽  
Vol 17 (12) ◽  
pp. 3282-3300 ◽  
Author(s):  
Paul J. Overvoorde ◽  
Yoko Okushima ◽  
José M. Alonso ◽  
April Chan ◽  
Charlie Chang ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Acetic Acid ◽  
Gene Family ◽  
Family Members ◽  
Genomic Analysis ◽  
Functional Genomic ◽  
Functional Genomic Analysis ◽  
Indole 3 Acetic Acid

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

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 882
Author(s):  
Yueming Tang ◽  
Fengzhong Lu ◽  
Wenqi Feng ◽  
Yuan Liu ◽  
Yang Cao ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Related Protein ◽  
Quantitative Real Time Pcr ◽  
Abiotic Stress Response ◽  
Promoter Regions ◽  
Element Analysis ◽  
Cis Acting ◽  
Ammopiptanthus Nanus ◽  
Genome Wide ◽  
Motif Composition

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.

scholarly journals Functional Genomic Analysis Supports Conservation of Function Among Cellulose Synthase-Like A Gene Family Members and Suggests Diverse Roles of Mannans in Plants

2007 ◽  
Vol 143 (4) ◽  
pp. 1881-1893 ◽  
Author(s):  
Aaron H. Liepman ◽  
C. Joseph Nairn ◽  
William G.T. Willats ◽  
Iben Sørensen ◽  
Alison W. Roberts ◽  
...  
Keyword(s):  
Gene Family ◽  
Family Members ◽  
Genomic Analysis ◽  
Cellulose Synthase ◽  
Functional Genomic ◽  
Functional Genomic Analysis

scholarly journals Genome-wide identification, characterization and expression analysis of the expansin gene family under drought stress in tea (Camellia sinensis L.)

2021 ◽  
Vol 8 (1) ◽  
pp. 32-44
Author(s):  
Kuntala Bordoloi ◽  
Pallabika Dihingia ◽  
Debasish Krishnatreya ◽  
Niraj Agarwala
Keyword(s):  
Drought Stress ◽  
Stress Response ◽  
Network Analysis ◽  
Gene Family ◽  
Gene Structure ◽  
Promoter Regions ◽  
Cis Acting ◽  
Expansin Gene ◽  
Tea Plants ◽  
Public Datasets

During several developmental processes, expansins contribute to cell enlargement by promoting cell wall loosening. To explore the biological roles of expansins during drought stress response and to characterize different expansins in tea, we performed a detailed analysis of the expansin gene family covering phylogeny, gene structure, profiling of gene expression and co-expression network analysis. We identified a total of 40 expansin genes in the tea genome belonging to 3 subfamilies, out of which 29 tea expansins belong to EXPA, 9 to EXLA and 2 to EXPB subfamilies. A minimum of 3 and a maximum of 13 exons are present in the gene structure of expansins. Presence of drought stress responsive cis-acting elements in the upstream of promoter regions of 40% of the identified expansins shows that the putative expansins may have been involved in tea plant’s response to drought stress. At least 15 out of the 40 expansin genes are found to be differentially expressed in response to drought in each of the drought stress related public datasets analysed in-silico. TEA022767 belonging to EXPA subfamily is seen to be upregulated during drought stress, as revealed from the analysis of all three publicly available bio-projects. Co-expression network analysis shows that TEA022767 and TEA032954 form a connecting link between two expression correlation groups that further signifies their role in drought stress response in tea. This study helps to interpret and to understand the biological roles of diverse expansin genes in tea plants under drought stress conditions.

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