scholarly journals Genome-Wide Identification and Analysis of HAK/KUP/KT Potassium Transporters Gene Family in Wheat (Triticum aestivum L.)

2018 ◽  
Vol 19 (12) ◽  
pp. 3969 ◽  
Author(s):  
Xiyong Cheng ◽  
Xiaodan Liu ◽  
Weiwei Mao ◽  
Xurui Zhang ◽  
Shulin Chen ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Triticum Aestivum L ◽  
Pcr Analysis ◽  
Chromosomal Distribution ◽  
Wheat Seedlings ◽  
Expression Levels ◽  
Transporter Family ◽  
Genome Wide ◽  
A Genome ◽  
Potassium Transporters

In plants, the HAK (high-affinity K+)/KUP (K+ uptake)/KT (K+ transporter) family represents a large group of potassium transporters that play important roles in plant growth and environmental adaptation. Although HAK/KUP/KT genes have been extensively investigated in many plant species, they remain uncharacterized in wheat, especially those involved in the response to environmental stresses. In this study, 56 wheat HAK/KUP/KT (hereafter called TaHAKs) genes were identified by a genome-wide search using recently released wheat genomic data. Phylogenetic analysis grouped these genes into four clusters (Ι, II, III, IV), containing 22, 19, 7 and 8 genes, respectively. Chromosomal distribution, gene structure, and conserved motif analyses of the 56 TaHAK genes were subsequently performed. In silico RNA-seq data analysis revealed that TaHAKs from clusters II and III are constitutively expressed in various wheat tissues, while most genes from clusters I and IV have very low expression levels in the examined tissues at different developmental stages. qRT-PCR analysis showed that expression levels of TaHAK genes in wheat seedlings were significantly up- or downregulated when seedlings were exposed to K+ deficiency, high salinity, or dehydration. Furthermore, we functionally characterized TaHAK1b-2BL and showed that it facilitates K+ transport in yeast. Collectively, these results provide valuable information for further functional studies of TaHAKs, and contribute to a better understanding of the molecular basis of wheat development and stress tolerance.

scholarly journals The Sugar Transporter family in wheat (Triticum aestivum. L): genome-wide identification, classification, and expression profiling during stress in seedlings

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11371
Author(s):  
Hongzhan Liu ◽  
Chaoqiong Li ◽  
Lin Qiao ◽  
Lizong Hu ◽  
Xueqin Wang ◽  
...  
Keyword(s):  
Plant Growth ◽  
Stress Tolerance ◽  
Expression Profiles ◽  
Gene Clusters ◽  
Triticum Aestivum L ◽  
Pcr Analysis ◽  
Sugar Transporter ◽  
Wheat Seedlings ◽  
Transporter Family ◽  
Genome Wide

The sugar transporter protein (STP) plays a crucial role in regulating plant growth and stress tolerance. We performed genome-wide identification and expression analysis of the STP gene family to investigate the STPSs’ potential roles in the growth of wheat seedlings under stress. Here, a total of 81 TaSTP genes containing the Sugar_tr conserved motif were identified within the wheat genome. Bioinformatic studies including phylogenetic tree, chromosome position, and tandem repeat were performed to analyze the identified genes. The 81 TaSTP genes can be classified into five main groups according to their structural and phylogenetic features, with several subgroups, which were located separately on chromosomes A, B, and D. Moreover, six gene clusters were formed with more than three genes each. The results of three comparative syntenic maps of wheat associated with three representative species suggested that STP genes have strong relationships in monocots. qRT-PCR analysis confirmed that most TaSTP genes displayed different expression profiles after seedlings were subjected to six days of different stress (10% PEG6000, 150 mM NaCl, and their combination, respectively), suggesting that these genes may be involved in regulating plant growth and stress tolerance. In conclusion, 81 TaSTP genes were identified and their expressions changed under stress, indicating TaSTP’s potential roles in wheat growth monosaccharide distribution is regulated.

scholarly journals F-Box Genes in the Wheat Genome and Expression Profiling in Wheat at Different Developmental Stages

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1154
Author(s):  
Min Jeong Hong ◽  
Jin-Baek Kim ◽  
Yong Weon Seo ◽  
Dae Yeon Kim
Keyword(s):  
Developmental Stages ◽  
Brachypodium Distachyon ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
Post Translational Modification ◽  
Genome Wide ◽  
A Genome ◽  
High Sequence Homology ◽  
Wide Scale

Genes of the F-box family play specific roles in protein degradation by post-translational modification in several biological processes, including flowering, the regulation of circadian rhythms, photomorphogenesis, seed development, leaf senescence, and hormone signaling. F-box genes have not been previously investigated on a genome-wide scale; however, the establishment of the wheat (Triticum aestivum L.) reference genome sequence enabled a genome-based examination of the F-box genes to be conducted in the present study. In total, 1796 F-box genes were detected in the wheat genome and classified into various subgroups based on their functional C-terminal domain. The F-box genes were distributed among 21 chromosomes and most showed high sequence homology with F-box genes located on the homoeologous chromosomes because of allohexaploidy in the wheat genome. Additionally, a synteny analysis of wheat F-box genes was conducted in rice and Brachypodium distachyon. Transcriptome analysis during various wheat developmental stages and expression analysis by quantitative real-time PCR revealed that some F-box genes were specifically expressed in the vegetative and/or seed developmental stages. A genome-based examination and classification of F-box genes provide an opportunity to elucidate the biological functions of F-box genes in wheat.

scholarly journals Genome-Wide Identification, Expression Profile, and Alternative Splicing Analysis of CAMTA Family Genes in Cucumber (Cucumis sativus L.)

Agronomy ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1827
Author(s):  
Rong Gao ◽  
Yanyan Luo ◽  
Fahong Yun ◽  
Xuetong Wu ◽  
Peng Wang ◽  
...  
Keyword(s):  
Stress Response ◽  
Growth And Development ◽  
Chemical Properties ◽  
Pcr Analysis ◽  
Transcription Activator ◽  
Cucumis Sativus L ◽  
Expression Levels ◽  
Calmodulin Binding ◽  
Genome Wide ◽  
A Genome

The calmodulin-binding transcription activator (CAMTA), as one of the most distinctive families of transcription factors, plays an important role in plant growth and development and in the stress response. However, it is currently unknown whether CAMTA exists in cucumbers and what its function is. In this study, we first identified four CAMTA genes in the cucumber genome using a genome-wide search method. Subsequently, we analyzed their physical and chemical properties, gene structure, protein domains, and phylogenetic relationships. The results show that the structure of CsCAMTAs is similar to that of other plants, and a phylogenetic analysis divides them into three groups. The analysis of cis-acting elements shows that most CsCAMTAs contain a variety of hormones and stress-related elements. The RT-PCR analysis shows that CsCAMTAs have different expression levels in different tissues and can be induced by IAA, ABA, MeJA, NaCl, and PEG. Finally, we analyzed the expression pattern of CsCAMTAs’ alternative spliceosomes under salt and drought stress. The results show that the expression levels of the different spliceosomes are affected by the type of stress and the duration of stress. These data indicate that CsCAMTAs participate in growth and development and in the stress response in cucumbers, a finding which lays the foundation for future CsCAMTAs’ functional research.

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 Genome-wide Identification and Analysis of CCT Genes in Wheat (Triticum Aestivum L.)

2020 ◽  
Author(s):  
Hongwei Zhang ◽  
Xinxia Liang ◽  
Shuo Zhou ◽  
Haibo Wang
Keyword(s):  
Gene Clusters ◽  
Triticum Aestivum L ◽  
Suppressor Gene ◽  
Pcr Analysis ◽  
Genome Wide Analysis ◽  
Real Time Quantitative Pcr ◽  
Genome Wide ◽  
A Genome ◽  
Mads Box Gene ◽  
And Function

Abstract Background: The vernalization, in which the plants must undergo a prolonged winter cold exposure to flower, is mainly controlled by a suppressive MADS-box gene FLC in Arabidopsis. However, different from Arabidopsis, the CCT-domain containing gene VRN2 is the critical vernalization-related suppressor gene in cereals. Based on this apparent diversity of vernalization in different plants, and involvement of VRN2 with vernalization in cereals, we conducted a genome-wide analysis of CCT genes in wheat, and the relationship between vernalization and these genes were also revealed.Results: A genome-wide analysis of the CCT genes in common wheat was performed by employing a hidden Markov model-based method, and 127 sequences, which assigned to 40 clusters, were obtained in three subgenomes. Specially, two of the gene clusters are duplicated, and distinguishingly located near telomere. Furthermore, these sequences were classified into eight groups by a phylogenetic analysis procedure using the UPGMA method, and this taxonomy is concordant to the classification based on CCT interruptions and domain organization which roughly divided the proteins into four divergently related subfamilies. Moreover, the expression of several CCT genes is continually downregulated during and after vernalization, but no continually upregulated CCT genes were revealed, as indicated by transcriptome sequencing and real-time quantitative PCR analysis.Conclusion: This study improves our understanding of the structure and function of CCT genes, suggests many vernalization-related CCT genes, and may guide future investigations on CCT genes and vernalization in wheat.

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

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.

scholarly journals A target expression threshold dictates invader defense and autoimmunity by CRISPR-Cas13

2021 ◽  
Author(s):  
Elena Vialetto ◽  
Yanying Yu ◽  
Scott P. Collins ◽  
Katharina G. Wandera ◽  
Lars Barquist ◽  
...  
Keyword(s):  
Immune Activation ◽  
Rna Degradation ◽  
Lytic Bacteriophage ◽  
Immune Systems ◽  
Expression Levels ◽  
Additional Requirement ◽  
Genome Wide ◽  
A Genome ◽  
Rna Targeting ◽  
Target Transcript

Immune systems must recognize and clear foreign invaders without eliciting autoimmunity. CRISPR-Cas immune systems in prokaryotes manage this task by following two criteria: extensive guide:target complementarity and a defined target-flanking motif. Here we report an additional requirement for RNA-targeting CRISPR-Cas13 systems: expression of the target transcript exceeding a threshold. This finding is based on targeting endogenous non-essential transcripts, which rarely elicited dormancy through collateral RNA degradation. Instead, eliciting dormancy required over-expressing targeted transcripts above a threshold. A genome-wide screen confirmed target expression levels as the principal determinant of cytotoxic autoimmunity and revealed that the threshold shifts with the guide:target pair. This expression threshold ensured defense against a lytic bacteriophage yet allowed tolerance of a targeted beneficial gene expressed from an invading plasmid. These findings establish target expression levels as a third criterion for immune activation by RNA-targeting CRISPR-Cas systems, buffering against autoimmunity and distinguishing pathogenic and benign invaders.

scholarly journals A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

PLoS Genetics ◽  
2011 ◽  
Vol 7 (2) ◽  
pp. e1001316 ◽  
Author(s):  
Athma A. Pai ◽  
Jordana T. Bell ◽  
John C. Marioni ◽  
Jonathan K. Pritchard ◽  
Yoav Gilad
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Expression Levels ◽  
Genome Wide ◽  
A Genome ◽  
Methylation Patterns ◽  
Genome Wide Study ◽  
Gene Expression Levels

scholarly journals Genome-wide survey of the F-box/Kelch (FBK) members and molecular identification of a novel FBK gene TaAFR in wheat

2021 ◽  
Author(s):  
Chunru Wei ◽  
Weiquan Zhao ◽  
Runqiao Fan ◽  
Yuyu Meng ◽  
Yiming Yang ◽  
...  
Keyword(s):  
Developmental Stages ◽  
In Silico Analysis ◽  
Digital Pcr ◽  
Plant Responses ◽  
Plant Signaling ◽  
Biotic Stresses ◽  
Genome Wide ◽  
Cereal Species ◽  
A Genome ◽  
Genome Wide Survey

F-box proteins play critical roles in plant responses to biotic/abiotic stresses. In the present study, a total of 68 wheat F-box/Kelch ( TaFBK ) gene sequences encoding for 74 proteins were obtained in a genome-wide survey against EnsemblPlants. The 74 TaFBK proteins were divided into 5 categories based on their domain structures. The FBK proteins from wheat, Arabidopsis, and three other cereal species were grouped into 7 clades, and the number of Kelch domains present was their key clustering criterion. Sixty-eight TaFBK genes were unevenly distributed on 21 chromosomes. Most of TaFBKs were predicted to localize in the nucleus and cytoplasm. In silico analysis of a digital PCR revealed that TaFBKs were expressed at multiple developmental stages and tissues, and in response to drought and/or heat stresses. The TaFBK19 gene, a homologous to the Attenuated Far-Red Response ( AFR ) genes in other plant species, and hence named TaAFR , was selected for further analysis. The gene was isolated from the wheat line TcLr15 and its expression evaluated by quantitative real-time PCR. TaAFR transcripts were primarily detected in wheat leaves, and its expression was found to be regulated by various abiotic and biotic stresses as well as plant signaling hormones. Of particular interest, TaAFR expression was differentially regulated in the compatible vs incompatible wheat leaf rust reaction. Subcellular localization studies showed that TaAFR accumulates in the nucleus and cytoplasm. Three TaAFR-interacting proteins were identified experimentally: Skp1/ASK1-like protein (Skp1), ADP-ribosylation factor 2-like isoform X1 (ARL2) and phenylalanine ammonia-lyase (PAL). Further analysis revealed that the Skp1 protein interacted specifically with the F-box domain of TaAFR, while ARL2 and PAL were recognized by the Kelch domain. The data presented herein provides a solid foundation from which the function and metabolic network of TaAFR and other wheat FBKs can be further explored.

scholarly journals Genome-wide investigation of the AP2/ERF gene family in  ginger: evolution and expression profiles during rhizome and inflorescence development

2021 ◽  
Author(s):  
Haitao Xing ◽  
Yusong Jiang ◽  
Xiaoling Long ◽  
Xiaoli Wu ◽  
Yun Ren ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Whole Genome Sequence ◽  
Chromosomal Distribution ◽  
Inflorescence Development ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Erf Transcription Factors

Abstract Background:AP2/ERF transcription factors perform indispensable functions in various biological processes, such as plant growth, development, biotic and abiotic stresses responses. The AP2/ERF transcription factor family has been identified in many plants, and several AP2/ERF transcription factors from Arabidopsis (Arabidopsis thaliana) have been functionally characterized. However, little research has been conducted on the AP2/ERF genes of ginger (Zingiber officinale), which is an important edible and medicinal horticultural plant. The recently published whole genome sequence of ginger allowed us to study the tissue and expression profiles of AP2/ERF genes in ginger on a genome-wide basis.Results:In this study, 163 AP2/ERF genes of ginger (ZoAP2/ERF) were identified and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. According to the number conserved domains and gene structure, the AP2/ERF genes were divided into three subfamilies by phylogenetic analysis, namely, AP2 (35 members), ERF (125 members) and RAV (3 members). A total of 10 motifs were detected in ginger AP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes.Conclusion:A comprehensive analysis of AP2/ERF gene expression patterns in different tissues and rhizome development stages by transcriptom sequence and quantitative real-time PCR (qRT-PCR) showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminarily identified. This systematic analysis establishes a foundation for further studies of the functional characteristics of ZoAP2/ERF genes and improvement of ginger.

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