scholarly journals Characterization of MATE Gene Family And Its Role In Drought, Heat, And Salt Tolerance In Wheat (Triticum Aestivum L.)

2021 ◽  
Author(s):  
Joseph Noble Amoah ◽  
Yong Weon Seo
Keyword(s):  
Salt Stress ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Stress Conditions ◽  
Crop Species ◽  
Expression Levels ◽  
Cis Acting ◽  
Genome Wide ◽  
A Genome

Abstract To explore the response of multidrug and toxic compound extrusion (MATE) proteins to drought, heat, and salt stress in wheat, a genome-wide identification and expression study was performed. 20 MATE genes located on 4 of the 12 chromosomes were identified and categorized into four (I-1V) subfamilies, based on phylogenetic analysis. Wheat MATE family expansion was primarily driven by whole-genome duplication (WGD) and tandem events. In the same subfamily, gene exon-intron structures and motif composition are more similar. TaMATE genes had cis-acting elements that were implicated in stress and defense response. Tae-miR5175e was identified as the highly expressed miRNA that targets TaMATEs by miRNA prediction. When compared to controls, the relative expression patterns of seven TaMATE genes were substantially elevated during drought stress. TaMATE2, 10, 13, and 14 expression levels considerably elevated after 15 days (d) of heat stress, whereas TaMATE2, 14, 18, and 20 expression levels were highly upregulated following 15 d of salt stress treatment, indicating the crucial role of TaMATEs under these abiotic stress conditions. Furthermore, drought, heat, and salt stress decreased wheat water content, but increased malondialdehyde (MDA), electrolyte leakage (EL), and proline content, whereas the expression of the 7 putative MATE genes was correlated with physio-biochemical indicators of these stress conditions. The findings contribute to a better understanding of the complexities of MATEs and present a theoretical base for future MATE gene discovery and application in wheat and other crop species.

scholarly journals Identification and Analysis of the AP2 Subfamily Transcription Factors in the Pecan (Carya illinoinensis)

2021 ◽  
Vol 22 (24) ◽  
pp. 13568
Author(s):  
Zhengfu Yang ◽  
Hongmiao Jin ◽  
Junhao Chen ◽  
Caiyun Li ◽  
Jiani Wang ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Expression Patterns ◽  
Carya Illinoinensis ◽  
Expression Levels ◽  
Cis Acting ◽  
Similar Expression ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Ethylene Responsive Factor

The AP2 transcriptional factors (TFs) belong to the APETALA2/ ethylene-responsive factor (AP2/ERF) superfamily and regulate various biological processes of plant growth and development, as well as response to biotic and abiotic stresses. However, genome-wide research on the AP2 subfamily TFs in the pecan (Carya illinoinensis) is rarely reported. In this paper, we identify 30 AP2 subfamily genes from pecans through a genome-wide search, and they were unevenly distributed on the pecan chromosomes. Then, a phylogenetic tree, gene structure and conserved motifs were further analyzed. The 30 AP2 genes were divided into euAP2, euANT and basalANT three clades. Moreover, the cis-acting elements analysis showed many light responsive elements, plant hormone-responsive elements and abiotic stress responsive elements are found in CiAP2 promoters. Furthermore, a qPCR analysis showed that genes clustered together usually shared similar expression patterns in euAP2 and basalANT clades, while the expression pattern in the euANT clade varied greatly. In developing pecan fruits, CiAP2-5, CiANT1 and CiANT2 shared similar expression patterns, and their expression levels decreased with fruit development. CiANT5 displayed the highest expression levels in developing fruits. The subcellular localization and transcriptional activation activity assay demonstrated that CiANT5 is located in the nucleus and functions as a transcription factor with transcriptional activation activity. These results help to comprehensively understand the pecan AP2 subfamily TFs and lay the foundation for further functional research on pecan AP2 family genes.

scholarly journals Genome-Wide Identification and Characterization of PIN-FORMED (PIN) Gene Family Reveals Role in Developmental and Various Stress Conditions in Triticum aestivum L.

2021 ◽  
Vol 22 (14) ◽  
pp. 7396
Author(s):  
Manu Kumar ◽  
Bhagwat Singh Kherawat ◽  
Prajjal Dey ◽  
Debanjana Saha ◽  
Anupama Singh ◽  
...  
Keyword(s):  
Gene Family ◽  
Auxin Transport ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Stress Conditions ◽  
Biotic And Abiotic Stress ◽  
Developmental Processes ◽  
Qrt Pcr ◽  
Genome Wide

PIN-FORMED (PIN) genes play a crucial role in regulating polar auxin distribution in diverse developmental processes, including tropic responses, embryogenesis, tissue differentiation, and organogenesis. However, the role of PIN-mediated auxin transport in various plant species is poorly understood. Currently, no information is available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the PIN gene family in wheat to understand the evolution of PIN-mediated auxin transport and its role in various developmental processes and under different biotic and abiotic stress conditions. In this study, we performed genome-wide analysis of the PIN gene family in common wheat and identified 44 TaPIN genes through a homology search, further characterizing them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses led to the classification of TaPIN genes into seven different groups, providing evidence of an evolutionary relationship with Arabidopsis thaliana and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, transmembrane domains, and three-dimensional (3D) structure were also examined using various computational approaches. Cis-elements analysis of TaPIN genes showed that TaPIN promoters consist of phytohormone, plant growth and development, and stress-related cis-elements. In addition, expression profile analysis also revealed that the expression patterns of the TaPIN genes were different in different tissues and developmental stages. Several members of the TaPIN family were induced during biotic and abiotic stress. Moreover, the expression patterns of TaPIN genes were verified by qRT-PCR. The qRT-PCR results also show a similar expression with slight variation. Therefore, the outcome of this study provides basic genomic information on the expression of the TaPIN gene family and will pave the way for dissecting the precise role of TaPINs in plant developmental processes and different stress conditions.

scholarly journals Calcium-Dependent Protein Kinase Genes in Glycyrrhiza Uralensis Appear to be Involved in Promoting the Biosynthesis of Glycyrrhizic Acid and Flavonoids under Salt Stress

Molecules ◽  
2019 ◽  
Vol 24 (9) ◽  
pp. 1837 ◽  
Author(s):  
Xuechen Tong ◽  
Aiping Cao ◽  
Fei Wang ◽  
Xifeng Chen ◽  
Shuangquan Xie ◽  
...  
Keyword(s):  
Salt Stress ◽  
Glycyrrhizic Acid ◽  
Expression Patterns ◽  
Glycyrrhiza Uralensis ◽  
Calcium Signal ◽  
Cis Acting ◽  
Calcium Dependent ◽  
Genome Wide ◽  
A Genome ◽  
Dependent Protein

As calcium signal sensors, calcium-dependent protein kinases (CPKs) play vital roles in stimulating the production of secondary metabolites to participate in plant development and response to environmental stress. However, investigations of the Glycyrrhiza uralensis CPK family genes and their multiple functions are rarely reported. In this study, a total of 23 GuCPK genes in G. uralensis were identified, and their phylogenetic relationships, evolutionary characteristics, gene structure, motif distribution, and promoter cis-acting elements were analyzed. Ten GuCPKs showed root-specific preferential expressions, and GuCPKs indicated different expression patterns under treatments of CaCl2 and NaCl. In addition, under 2.5 mM of CaCl2 and 30 mM of NaCl treatments, the diverse, induced expression of GuCPKs and significant accumulations of glycyrrhizic acid and flavonoids suggested the possible important function of GuCPKs in regulating the production of glycyrrhizic acid and flavonoids. Our results provide a genome-wide characterization of CPK family genes in G. uralensis, and serve as a foundation for understanding the potential function and regulatory mechanism of GuCPKs in promoting the biosynthesis of glycyrrhizic acid and flavonoids under salt stress.

scholarly journals Genome-wide identification of the GATA transcription factor family and their expression patterns under temperature and salt stress in Aspergillus oryzae

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chunmiao Jiang ◽  
Gongbo Lv ◽  
Jinxin Ge ◽  
Bin He ◽  
Zhe Zhang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Expression Patterns ◽  
Interaction Network ◽  
Protein Protein Interaction ◽  
Genome Wide ◽  
Gata Transcription Factor ◽  
Starting Point ◽  
Evolutionary Features ◽  
First Time

AbstractGATA transcription factors (TFs) are involved in the regulation of growth processes and various environmental stresses. Although GATA TFs involved in abiotic stress in plants and some fungi have been analyzed, information regarding GATA TFs in Aspergillusoryzae is extremely poor. In this study, we identified and functionally characterized seven GATA proteins from A.oryzae 3.042 genome, including a novel AoSnf5 GATA TF with 20-residue between the Cys-X2-Cys motifs which was found in Aspergillus GATA TFs for the first time. Phylogenetic analysis indicated that these seven A. oryzae GATA TFs could be classified into six subgroups. Analysis of conserved motifs demonstrated that Aspergillus GATA TFs with similar motif compositions clustered in one subgroup, suggesting that they might possess similar genetic functions, further confirming the accuracy of the phylogenetic relationship. Furthermore, the expression patterns of seven A.oryzae GATA TFs under temperature and salt stresses indicated that A. oryzae GATA TFs were mainly responsive to high temperature and high salt stress. The protein–protein interaction network of A.oryzae GATA TFs revealed certain potentially interacting proteins. The comprehensive analysis of A. oryzae GATA TFs will be beneficial for understanding their biological function and evolutionary features and provide an important starting point to further understand the role of GATA TFs in the regulation of distinct environmental conditions in A.oryzae.

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

Plants ◽  
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.

scholarly journals The Potential Role of Genetic Assimilation during Maize Domestication

2017 ◽  
Author(s):  
Anne Lorant ◽  
Sarah Pedersen ◽  
Irene Holst ◽  
Matthew B. Hufford ◽  
Klaus Winter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Zea Mays ◽  
Potential Role ◽  
Expression Patterns ◽  
Genetic Assimilation ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms ◽  
Maize Domestication

ABSTRACTDomestication research has largely focused on identification of morphological and genetic differences between extant populations of crops and their wild relatives. Little attention has been paid to the potential effects of environment despite substantial known changes in climate from the time of domestication to modern day. Recent research, in which maize and teosinte (i.e., wild maize) were exposed to environments similar to the time of domestication, resulted in a plastic induction of domesticated phenotypes in teosinte and little response to environment in maize. These results suggest that early agriculturalists may have selected for genetic mechanisms that cemented domestication phenotypes initially induced by a plastic response of teosinte to environment, a process known as genetic assimilation. To better understand this phenomenon and the potential role of environment in maize domestication, we examined differential gene expression in maize (Zea mays ssp. mays) and teosinte (Zea mays ssp. parviglumis) between past and present conditions. We identified a gene set of over 2000 loci showing a change in expression across environmental conditions in teosinte and invariance in maize. In fact, overall we observed both greater plasticity in gene expression and more substantial re-wiring of expression networks in teosinte across environments when compared to maize. While these results suggest genetic assimilation played at least some role in domestication, genes showing expression patterns consistent with assimilation are not significantly enriched for previously identified domestication candidates, indicating assimilation did not have a genome-wide effect.

scholarly journals Genome-wide identification and expression analysis of the xyloglucan endotransglucosylase/hydrolase gene family in poplar

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Yuan Gao ◽  
Kai Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Stress Responses ◽  
Tissue Specificity ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Rna Seq ◽  
Salt Stress Response ◽  
Populus Simonii ◽  
Cis Acting ◽  
Genome Wide

Abstract Background Xyloglucan endotransglucosylase/hydrolase (XTH) family plays an important role in cell wall reconstruction and stress resistance in plants. However, the detailed characteristics of XTH family genes and their expression pattern under salt stress have not been reported in poplar. Results In this study, a total of 43 PtrXTH genes were identified from Populus simonii × Populus nigra, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). The promoters of the PtrXTH genes contain mutiple cis-acting elements related to growth and development and stress responses. Collinearity analysis revealed that the XTH genes from poplar has an evolutionary relationship with other six species, including Eucalyptus robusta, Solanum lycopersicum, Glycine max, Arabidopsis, Zea mays and Oryza sativa. Based on RNA-Seq analysis, the PtrXTH genes have different expression patterns in the roots, stems and leaves, and many of them are highly expressed in the roots. In addition, there are11 differentially expressed PtrXTH genes in the roots, 9 in the stems, and 7 in the leaves under salt stress. In addition, the accuracy of RNA-Seq results was verified by RT-qPCR. Conclusion All the results indicated that XTH family genes may play an important role in tissue specificity and salt stress response. This study will lay a theoretical foundation for further study on molecular function of XTH genes in poplar.

scholarly journals Genome-wide Identification and Expression Analysis of the Eyloglucan Endotransglucosylase/hydrolase Gene Family in Poplar

2021 ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Yuan Gao ◽  
Kai Zhao ◽  
...  
Keyword(s):  
Salt Stress ◽  
Plant Cell Wall ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Rna Seq ◽  
Promoter Regions ◽  
Salt Stress Response ◽  
Populus Simonii ◽  
Cis Acting ◽  
Genome Wide

Abstract Background: Xyloglucan endotransglucosylase/hydrolase (XTH) plays an important role in the process of plant cell wall reconstruction, and also involved in plants stress resistance. However, its characteristics of XTH family genes have not been reported in poplar. Results: In this study, we found 43 PtrXTH genes from Populus simonii × Populus nigra, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). The promoter regions of the PtrXTH genes contain many cis-acting elements related to growth and development and adverse stresses responses. Collinearity analysis revealed that the XTH family from poplarhave an evolutionary relationship with other five species, including Eucalyptus robusta, Solanum lycopersicum, Glycine max, Arabidopsis, Zea mays and Oryza sativa. Through RNA-Seq analysis, we found that the PtrXTH genes have different expression patterns in the roots, stems and leaves, and many of them are highly expressed in the roots. In addition, we found 11 differentially expressed PtrXTH genes in the roots, 9 in the stems, and 7 in the leaves under salt stress, and verified the accuracy of RNA-Seq analysis by RT-qPCR.Conclusion: All the results indicated that XTH family genes may play an important role in tissue specificity and salt stress response. This study laid a theoretical foundation for further study on the functions of XTH genes in poplar.

scholarly journals Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L.

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Su ◽  
Ali Raza ◽  
Liu Zeng ◽  
Ang Gao ◽  
Yan Lv ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Stress Conditions ◽  
Motif Analysis ◽  
Genome Wide Analysis ◽  
Group I ◽  
Genome Wide ◽  
A Genome

Abstract Background Lipid phosphate phosphatases (LPP) are critical for regulating the production and degradation of phosphatidic acid (PA), an essential signaling molecule under stress conditions. Thus far, the LPP family genes have not been reported in rapeseed (Brassica napus L.). Results In this study, a genome-wide analysis was carried out to identify LPP family genes in rapeseed that respond to different stress conditions. Eleven BnLPPs genes were identified in the rapeseed genome. Based on phylogenetic and synteny analysis, BnLPPs were classified into four groups (Group I-Group IV). Gene structure and conserved motif analysis showed that similar intron/exon and motifs patterns occur in the same group. By evaluating cis-elements in the promoters, we recognized six hormone- and seven stress-responsive elements. Further, six putative miRNAs were identified targeting three BnLPP genes. Gene ontology analysis disclosed that BnLPP genes were closely associated with phosphatase/hydrolase activity, membrane parts, phosphorus metabolic process, and dephosphorylation. The qRT-PCR based expression profiles of BnLPP genes varied in different tissues/organs. Likewise, several gene expression were significantly up-regulated under NaCl, PEG, cold, ABA, GA, IAA, and KT treatments. Conclusions This is the first report to describe the comprehensive genome-wide analysis of the rapeseed LPP gene family. We identified different phytohormones and abiotic stress-associated genes that could help in enlightening the plant tolerance against phytohormones and abiotic stresses. The findings unlocked new gaps for the functional verification of the BnLPP gene family during stresses, leading to rapeseed improvement.

scholarly journals Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor superfamily in Dimocarpus longan Lour

2019 ◽  
Author(s):  
Shuting Zhang ◽  
Chen Zhu ◽  
Yumeng Lyu ◽  
Yan Chen ◽  
Zihao Zhang ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Molecular Evolution ◽  
Expression Patterns ◽  
Cis Acting ◽  
Young Fruit ◽  
Genome Wide ◽  
A Genome ◽  
Dimocarpus Longan ◽  
Ethylene Responsive Factor ◽  
Early Somatic Embryogenesis

Abstract Backgroud: APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors perform indispensable roles in various biological processes, and it has been identified in many plants. However, little is known about the AP2/ERF superfamily in longan (Dimocarpus longan Lour.). The release of the whole-genome sequence of longan provided us an opportunity to perform a genome-wide investigation of AP2/ERF superfamily. Results: In the present study, we performed a genome-wide survey of AP2/ERF superfamily longan (DlAP2/ERF), including the gene structure, motif composition, phylogenetic, cis-acting element, single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), alternative splicing (AS) events and the expression patterns. In total, 125 DlAP2/ERF genes were identified and classified into four families, including AP2 (19 members), ERF (101 members), RAV (four members) and Soliost (one member) in the longan genome. The AP2 and soloist genes possessed one to ten introns, while 87 genes within the ERF and RAV family had no introns. A large number of hormone signaling and stress response cis-acting elements were also identified. Besides, a large number of SNPs existed in the DlAP2/ERF superfamily, they may be deverse in the early somatic embryogenesis and stem of longan. However, the numbers of InDels was far less than SNPs. In addition, the AP2 family members existed a large number of AS events in different developmental processes of longan. Expression patterns analysis revealed that the AP2 family may promote the early somatic embryogenesis of longan, and DlAP2/ERF genes were specifically expressed in various organs such as seed, root, flower and young-fruit. The DlAP2/ERF genes can response to exogenous phytohormones, such as 2,4-Dichlorophenoxyacetic acid (2,4-D), Abscisic acid (ABA), Methyl jasmonate (MeJA) and Salicylic acid (SA). Protein interactions prediction indicated that the Baby Boom (BBM) protein may interacted with LALF/AGL15 network and was up-regulated expression at the transcriptional level in the early somatic embryogenesis of longan. Conclusions: A comprehensive analysis of molecular evolution and expression patterns showed that AP2/ERF superfamily played an important role in longan, especially in the early somatic embryogenesis, seed, root, flower and young-fruit. This systematic analysis provided the foundation for further functional characterization of AP2/ERF superfamily with an aim of longan improvement.

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