scholarly journals Genome-wide identification and expression analysis of the VQ gene family in Cicer arietinum and Medicago truncatula

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8471 ◽  
Author(s):  
Lei Ling ◽  
Yue Qu ◽  
Jintao Zhu ◽  
Dan Wang ◽  
Changhong Guo
Keyword(s):  
Cicer Arietinum ◽  
Medicago Truncatula ◽  
Stress Responses ◽  
Pcr Analysis ◽  
Biotic And Abiotic Stress ◽  
Systematic Analysis ◽  
Genome Wide ◽  
Specific Proteins ◽  
Solid Foundation ◽  
In Silico Analyses

Valine-glutamine (VQ) proteins are plant-specific proteins that play crucial roles in plant development as well as biotic and abiotic stress responses. VQ genes have been identified in various plants; however, there are no systematic reports in Cicer arietinum or Medicago truncatula. Herein, we identified 19 and 32 VQ genes in C. arietinum and M. truncatula, respectively. A total of these VQ genes were divided into eight groups (I–VIII) based on phylogenetic analysis. Gene structure analyses and motif patterns revealed that these VQ genes might have originated from a common ancestor. In silico analyses demonstrated that these VQ genes were expressed in different tissues. qRT-PCR analysis indicated that the VQ genes were differentially regulated during multiple abiotic stresses. This report presents the first systematic analysis of VQ genes from C. arietinum and M. truncatula and provides a solid foundation for further research of the specific functions of VQ proteins.

scholarly journals SWEET Gene Family in Medicago truncatula: Genome-Wide Identification, Expression and Substrate Specificity Analysis

Plants ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 338 ◽  
Author(s):  
Bin Hu ◽  
Hao Wu ◽  
Weifeng Huang ◽  
Jianbo Song ◽  
Yong Zhou ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Stress Responses ◽  
Active Sites ◽  
Developmental Stages ◽  
Rna Seq ◽  
Transmembrane Helices ◽  
Functional Roles ◽  
Genome Wide ◽  
Solid Foundation ◽  
As Stress

SWEET (Sugars Will Eventually be Exported Transporter) proteins mediate the translocation of sugars across cell membranes and play crucial roles in plant growth and development as well as stress responses. In this study, a total of 25 SWEET genes were identified from the Medicago truncatula genome and were divided into four clades based on the phylogenetic analysis. The MtSWEET genes are distributed unevenly on the M. truncatula chromosomes, and eight and 12 MtSWEET genes are segmentally and tandemly duplicated, respectively. Most MtSWEET genes contain five introns and encode proteins with seven transmembrane helices (TMHs). Besides, nearly all MtSWEET proteins have relatively conserved membrane domains, and contain conserved active sites. Analysis of microarray data showed that some MtSWEET genes are specifically expressed in disparate developmental stages or tissues, such as flowers, developing seeds and nodules. RNA-seq and qRT-PCR expression analysis indicated that many MtSWEET genes are responsive to various abiotic stresses such as cold, drought, and salt treatments. Functional analysis of six selected MtSWEETs in yeast revealed that they possess diverse transport activities for sucrose, fructose, glucose, galactose, and mannose. These results provide new insights into the characteristics of the MtSWEET genes, which lay a solid foundation for further investigating their functional roles in the developmental processes and stress responses of M. truncatula.

scholarly journals Genome-Wide Characterization and Expression Analysis Provide Basis to the Biological Function of Cotton FBA Genes

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhong-Qing Li ◽  
Yao Zhang ◽  
He Li ◽  
Ting-Ting Su ◽  
Cheng-Gong Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Function Analysis ◽  
Pcr Analysis ◽  
Functional Domain ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Identification And Characterization

Fructose-1,6-biphosphate aldolase (FBA) is a multifunctional enzyme in plants, which participates in the process of Calvin-Benson cycle, glycolysis and gluconeogenesis. Despite the importance of FBA genes in regulating plant growth, development and abiotic stress responses, little is known about their roles in cotton. In the present study, we performed a genome-wide identification and characterization of FBAs in Gossypium hirsutum. Totally seventeen GhFBA genes were identified. According to the analysis of functional domain, phylogenetic relationship, and gene structure, GhFBA genes were classified into two subgroups. Furthermore, nine GhFBAs were predicted to be in chloroplast and eight were located in cytoplasm. Moreover, the promoter prediction showed a variety of abiotic stresses and phytohormone related cis-acting elements exist in the 2k up-stream region of GhFBA. And the evolutionary characteristics of cotton FBA genes were clearly presented by synteny analysis. Moreover, the results of transcriptome and qRT-PCR analysis showed that the expression of GhFBAs were related to the tissue distribution, and further analysis suggested that GhFBAs could respond to various abiotic stress and phytohormonal treatments. Overall, our systematic analysis of GhFBA genes would not only provide a basis for the understanding of the evolution of GhFBAs, but also found a foundation for the further function analysis of GhFBAs to improve cotton yield and environmental adaptability.

scholarly journals Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12617
Author(s):  
Yarui Wei ◽  
Shuliang Zhao ◽  
Na Liu ◽  
Yuxing Zhang
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Systemic Acquired Resistance ◽  
Acquired Resistance ◽  
Signal Transduction Pathway ◽  
Promoter Regions ◽  
Systematic Analysis ◽  
Genome Wide ◽  
Pathogenesis Related ◽  
Genome Level

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) plays a master regulatory role in the salicylic acid (SA) signal transduction pathway and plant systemic acquired resistance (SAR). Members of the NPR1-like gene family have been reported to the associated with biotic/abiotic stress in many plants, however the genome-wide characterization of NPR1-like genes has not been carried out in Chinese pear (Pyrus bretschneideri Reld). In this study, a systematic analysis was conducted on the characteristics of the NPR1-like genes in P. bretschneideri Reld at the whole-genome level. A total nine NPR1-like genes were detected which eight genes were located on six chromosomes and one gene was mapped to scaffold. Based on the phylogenetic analysis, the nine PbrNPR1-like proteins were divided into three clades (Clades I–III) had similar gene structure, domain and conserved motifs. We sorted the cis-acting elements into three clades, including plant growth and development, stress responses, and hormone responses in the promoter regions of PbrNPR1-like genes. The result of qPCR analysis showed that expression diversity of PbrNPR1-like genes in various tissues. All the genes were up-regulated after SA treatment in leaves except for Pbrgene8896. PbrNPR1-like genes showed circadian rhythm and significantly different expression levels after inoculation with Alternaria alternata. These findings provide a solid insight for understanding the functions and evolution of PbrNPR1-like genes in Chinese pear.

scholarly journals Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)

2019 ◽  
Author(s):  
Yongbin Wang ◽  
Zhenfeng Jiang ◽  
Zhenxiang Li ◽  
Yuanling Zhao ◽  
Weiwei Tan ◽  
...  
Keyword(s):  
Glycine Max ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Biological Functions ◽  
Conserved Domain ◽  
Genome Wide ◽  
Development Processes

Background. VQ proteins, the plant-specific transcription factors, are involved in the regulation of plant growth, development, and stress responses; however, few articles systematic reported VQ genes in the soybean. Methods. In total, we identified 75 GmVQ genes, which were classified into 7 groups (Ⅰ-Ⅶ). Conserved domain analysis indicated that VQ gene family members all contained the VQ domains. The VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed cis-elements related to stress responses, phytohormone responses and controlling physical and reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were expressed in nine tissues suggested their putative function in many aspects of plant growth and development, and response to stresses in Glycine max. Results. The present study provided basic information for further analysis of the biological functions of GmVQ proteins in various development processes.

scholarly journals Probabilistic data integration identifies reliable gametocyte-specific proteins and transcripts in malaria parasites

2017 ◽  
Author(s):  
Lisette Meerstein-Kessel ◽  
Robin van der Lee ◽  
Will Stone ◽  
Kjerstin Lanke ◽  
David A Baker ◽  
...  
Keyword(s):  
Transcript Abundance ◽  
Data Sets ◽  
Asexual Blood Stage ◽  
Systematic Analysis ◽  
Humoral Immune ◽  
Proteomic Data ◽  
Genome Wide ◽  
Field Samples ◽  
Specific Proteins ◽  
Specific Antigens

AbstractPlasmodium gametocytes are the sexual forms of the malaria parasite essential for transmission to mosquitoes. To better understand how gametocytes differ from asexual blood-stage parasites, we performed a systematic analysis of available ‘omics data for P. falciparum and other Plasmodium species. 18 transcriptomic and proteomic data sets were evaluated for the presence of curated “gold standards” of 41 gametocyte-specific versus 46 non-gametocyte genes and integrated using Bayesian probabilities, resulting in gametocyte-specificity scores for all P. falciparum genes.To illustrate the utility of the gametocyte score, we explored newly predicted gametocyte-specific genes as potential biomarkers of gametocyte carriage and exposure. We analyzed the humoral immune response in field samples against 30 novel gametocyte-specific antigens and found five antigens to be differentially recognized by gametocyte carriers as compared to malaria-infected individuals without detectable gametocytes. We also validated the gametocyte-specificity of 15 identified gametocyte transcripts on culture material and samples from naturally infected individuals, resulting in eight transcripts that were >1000-fold higher expressed in gametocytes compared to asexual parasites and whose transcript abundance allowed gametocyte detection in naturally infected individuals. Our integrated genome-wide gametocyte-specificity scores provide a comprehensive resource to identify targets and monitor P. falciparum gametocytemia.

scholarly journals Genome-wide Identification and Expression Analysis of Autophagy-related Genes (ATGs) in Medicago Truncatula

2020 ◽  
Author(s):  
Mingkang Yang ◽  
Liping Wang ◽  
Xu Guo ◽  
Chuanglie Lin ◽  
Wei Huang ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expression Analysis ◽  
Interaction Network ◽  
Degradation Process ◽  
Abiotic Stress Response ◽  
Biotic And Abiotic Stress ◽  
Comprehensive Overview ◽  
Genome Wide ◽  
Evolutionarily Conserved ◽  
Gene Structures

Abstract Background: Autophagy is a highly conserved degradation process of cytoplasmic constituents in eukaryotes. Autophagy is known to be involved in the regulation of plant growth and development, as well as biotic and abiotic stress response. Although autophagy-related genes (ATGs) have been identified and characterized in many plant species, little is known about the autophagy process in Medicago truncatula. Results: In this study, 39 ATGs were identified in M. truncatula (MtATGs), and the gene structures and conserved domains of MtATGs were systematically characterized. In addition, many cis-elements which are related to hormone and stress responsiveness were identified in the promoters of MtATGs. Furthermore, phylogenetic analysis and interaction network analysis suggested that the function of MtATGs is evolutionarily conserved in Arabidopsis and M. truncatula. Gene expression analysis showed that most MtATGs were largely induced during seed development, but repressed by nodulation. Moreover, MtATGs were up-regulated in response to salt and drought stresses.Conclusion: These results provide a comprehensive overview of the MtATGs, which provided important clues for further functional analysis of autophagy in M. truncatula.

Genome-wide identification of citrus calmodulin-like genes and their expression in response to arbuscular mycorrhizal fungi colonization and drought

2021 ◽  
Author(s):  
Bo Shu ◽  
YaChao Xie ◽  
Fei Zhang ◽  
Dejian Zhang ◽  
Chunyan Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Arbuscular Mycorrhizal Fungi ◽  
Stress Responses ◽  
Mycorrhizal Fungi ◽  
Expression Patterns ◽  
Arbuscular Mycorrhizal ◽  
Biotic And Abiotic Stress ◽  
Genome Wide ◽  
A Genome

Calmodulin-like (CML) proteins represent a diverse family of protein in plants, and play significant roles in biotic and abiotic stress responses. However, the involvement of citrus CMLs in plant responses to drought stress (abiotic stress) and arbuscular mycorrhizal fungi (AMF) colonization remain relatively unknown. We characterized the citrus CML genes by analyzing the EF-hand domains and a genome-wide search, and identified a total of 38 such genes, distributed across at least nine chromosomes. Six tandem duplication clusters were observed in the CsCMLs, and 12 CsCMLs exhibited syntenic relationships with Arabidopsis thaliana CMLs. Gene expression analysis showed that 29 CsCMLs were expressed in the roots, and exhibited differential expression patterns. The regulation of CsCMLs expression was not consistent with the cis-elements identified in their promoters. CsCML2, 3, and 5 were upregulated in response to drought stress, and AMF colonization repressed the expression of CsCML7, 9, 12, 13,20, 27, 28, and 35,and induced that of CsCML1, 2, 3, 5, 8, 10, 11, 14, 15, 16, 18, 25, 30, 33, and 37. Furthermore, AMF colonization and drought stress exerted a synergistic effect, evident from the enhanced repression of CsCML7, 9, 12, 13, 27, 28, and 35 and enhanced expression of CsCML2, 3, and 5 under AMF colonization and drought stress. The present study provides valuable insights into the CsCML gene family and its responses to AMF colonization and drought stress.

Identification of Ubiquitin Ligase From Grapevine Ring C3H2C3E3 and Characterization of Drought Resistance Function of VyRCHC114

2020 ◽  
Author(s):  
Yihe Yu ◽  
Shengdi Yang ◽  
Lu Bian ◽  
Keke Yu ◽  
Xiangxuan Meng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Ubiquitin Ligase ◽  
Stress Responses ◽  
Phylogenetic Trees ◽  
Expression Profiles ◽  
E3 Ubiquitin Ligase ◽  
Pcr Analysis ◽  
Biotic And Abiotic Stress ◽  
Element Analysis

Abstract Background: RING is one of the largest E3 ubiquitin ligase families and C3H2C3 type is the largest subfamily of RING, playing an important role in plants’ development and growth and their biotic and abiotic stress responses. Results: A total of 143 RING C3H2C3-type genes (RCHCs) were discovered from the grapevine genome and separated into groups (I-XI) according to their phylogenetic analysis, with these genes named according to their positions on chromosomes. Gene replication analysis showed that tandem duplications play a predominant role in the expansion of VyRCHCs family together. Structural analysis showed that most VyRCHCs(67.13%) had no more than 2 introns, while genes clustered together based on phylogenetic trees had similar motifs and evolutionarily conserved structures. Cis-acting element analysis showed the diversity of VyRCHCs regulation. The expression profiles of eight DEGs in RNA-Seq after drought stress were similar to those in qRT-PCR analysis. The in vitro ubiquitin experiment showed that VyRCHC114 had E3 ubiquitin ligase activity, overexpression of VyRCHC114 in Arabidopsis improved drought tolerance, moreover, the transgenic plant survival rate increased by 30%, accompanied by changing of electrolyte leakage, chlorophyll content and the activities of SOD, POD, APX and CAT were changed. AtCOR15a, AtRD29A, AtERD15 and AtP5CS1 were expressed quantitatively, the results showed that they participated in the drought stress response may be regulated by the expression of VyRCHC114.Conclusions: Valuable new information on the evolution of grapevine RCHCs and its relevance for studying the functional characteristics of grapevine VyRCHC114 genes under drought stress emerged from this research.

scholarly journals Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement

2020 ◽  
Vol 21 (19) ◽  
pp. 7180
Author(s):  
Hongfeng Wang ◽  
Hongjiao Jiang ◽  
Yiteng Xu ◽  
Yan Wang ◽  
Lin Zhu ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Feedback Regulation ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Model Legume ◽  
Genome Wide ◽  
A Genome

Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.

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