scholarly journals Molecular characterization and expression analysis of pitaya (Hylocereus polyrhizus) HpLRR genes in response to Neoscytalidium dimidiatum infection

2020 ◽  
Author(s):  
Min Xu ◽  
Cheng-Li Liu ◽  
Yu Fu ◽  
Zhi-Wen Liao ◽  
Pan-Yang Guo ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Expression Analysis ◽  
Stress Responses ◽  
Transcriptional Level ◽  
Biotic And Abiotic Stress ◽  
Comprehensive Overview ◽  
Canker Disease ◽  
Resistance Proteins ◽  
Neoscytalidium Dimidiatum ◽  
Hylocereus Polyrhizus

Abstract Background: Canker disease caused by Neoscytalidium dimidiatum is a devastating disease resulting in a major loss to the pitaya industry. However, resistance proteins in plants play crucial roles to against pathogen infection. Among resistance proteins, the leucine-rich repeat (LRR) protein is a major family that plays crucial roles in plant growth, development, and biotic and abiotic stress responses, especially in disease defense. Results: In the present study, a transcriptomics analysis identified a total of 272 LRR genes, 233 of which had coding sequences (CDSs), in the plant pitaya ( Hylocereus polyrhizus ) in response to fungal Neoscytalidium dimidiatum infection. These genes were divided into various subgroups based on specific domains and phylogenetic analysis. Molecular characterization, functional annotation of proteins, and an expression analysis of the LRR genes were conducted. Additionally, four LRR genes (CL445.Contig4_All, Unigene28_All, CL28.Contig2_All, and Unigene2712_All, which were selected because they had the four longest CDSs were further assessed using quantitative reverse transcription PCR (qRT-PCR) at different fungal infection stages in different pitaya species ( Hylocereus polyrhizus and Hylocereus undatus ), in different pitaya tissues, and after treatment with salicylic acid (SA), methyl jasmonate (MeJA), and abscisic acid (ABA) hormones. The associated protein functions and roles in signaling pathways were identified. Conclusions: This study provides a comprehensive overview of the Hp LRR family genes at transcriptional level in pitaya in response to N. dimidiatum infection, it will be helpful to understand the molecular mechanism of pitaya canker disease, and lay a strong foundation for further research.

Molecular characterization and expression analysis of pitaya (Hylocereus polyrhizus) HpLRR genes in response to Neoscytalidium dimidiatum infection

2020 ◽  
Author(s):  
Min Xu ◽  
Cheng-Li Liu ◽  
Yu Fu ◽  
Zhi-Wen Liao ◽  
Pan-Yang Guo ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Expression Analysis ◽  
Stress Responses ◽  
Transcriptional Level ◽  
Biotic And Abiotic Stress ◽  
Comprehensive Overview ◽  
Canker Disease ◽  
Resistance Proteins ◽  
Neoscytalidium Dimidiatum ◽  
Hylocereus Polyrhizus

Abstract Background: Canker disease caused by Neoscytalidium dimidiatum is a devastating disease resulting in a major loss to the pitaya industry. However, resistance proteins in plants play crucial roles to against pathogen infection. Among resistance proteins, the leucine-rich repeat (LRR) protein is a major family that plays crucial roles in plant growth, development, and biotic and abiotic stress responses, especially in disease defense. Results: In the present study, a transcriptomics analysis identified a total of 272 LRR genes, 233 of which had coding sequences (CDSs), in the plant pitaya ( Hylocereus polyrhizus ) in response to fungal Neoscytalidium dimidiatum infection. These genes were divided into various subgroups based on specific domains and phylogenetic analysis. Molecular characterization, functional annotation of proteins, and an expression analysis of the LRR genes were conducted. Additionally, four LRR genes (CL445.Contig4_All, Unigene28_All, CL28.Contig2_All, and Unigene2712_All, which were selected because they had the four longest CDSs were further assessed using quantitative reverse transcription PCR (qRT-PCR) at different fungal infection stages in different pitaya species ( Hylocereus polyrhizus and Hylocereus undatus ), in different pitaya tissues, and after treatment with salicylic acid (SA), methyl jasmonate (MeJA), and abscisic acid (ABA) hormones. The associated protein functions and roles in signaling pathways were identified. Conclusions: This study provides a comprehensive overview of the Hp LRR family genes at transcriptional level in pitaya in response to N. dimidiatum infection, it will be helpful to understand the molecular mechanism of pitaya canker disease, and lay a strong foundation for further research.

scholarly journals Molecular characterization and expression analysis of pitaya (Hylocereus polyrhizus) HpLRR genes in response to Neoscytalidium dimidiatuminfection

2019 ◽  
Author(s):  
Min Xu ◽  
Cheng-Li Liu ◽  
Yu Fu ◽  
Zhi-Wen Liao ◽  
Pan-Yang Guo ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Expression Analysis ◽  
Stress Responses ◽  
Transcriptional Level ◽  
Biotic And Abiotic Stress ◽  
Comprehensive Overview ◽  
Canker Disease ◽  
Resistance Proteins ◽  
Neoscytalidium Dimidiatum ◽  
Hylocereus Polyrhizus

Abstract Background: Canker disease caused by Neoscytalidium dimidiatum is a devastating disease resulting in a major loss to the pitaya industry. However, resistance proteins in plants play crucial roles to against pathogen infection. Among resistance proteins, the leucine-rich repeat (LRR) proteins are a major family that play crucial roles in plant growth, development, and biotic and abiotic stress responses, especially in disease defence. Results: In the present study, a transcriptomics analysis identified a total of 272 LRR genes, 233 of which had coding sequences (CDSs), in the plant pitaya ( Hylocereus polyrhizus )in response to fungal Neoscytalidium dimidiatum infection. These genes were divided into various subgroups based on specific domains and phylogenetic analysis. Molecular characterization, functional annotation of proteins, and an expression analysis of the LRR genes were conducted. Additionally, four LRR genes (CL445.Contig4_All, Unigene28_All, CL28.Contig2_All, and Unigene2712_All, which were selected because they had the four longest CDSs were further assessed using quantitative reverse transcription PCR (qRT-PCR) at different fungal infection stages in different pitaya species ( Hylocereus polyrhizus and Hylocereus undatus ), in different pitaya tissues, and after treatment with salicylic acid (SA), methyl jasmonate (MeJA), and abscisic acid (ABA) hormones. The associated protein functions and roles in signaling pathways were identified. Conclusions: This study provides a comprehensive overview of the Hp LRR family genes at transcriptional level in pitaya in response to N. dimidiatum infection and provides a basis for further in-depth functional studies.

scholarly journals Molecular characterization and expression analysis of pitaya (Hylocereus polyrhizus) HpLRR genes in response to Neoscytalidium dimidiatuminfection

2019 ◽  
Author(s):  
Min Xu ◽  
Cheng-Li Liu ◽  
Yu Fu ◽  
Zhi-Wen Liao ◽  
Pan-Yang Guo ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Expression Analysis ◽  
Stress Responses ◽  
Transcriptional Level ◽  
Biotic And Abiotic Stress ◽  
Comprehensive Overview ◽  
Canker Disease ◽  
Resistance Proteins ◽  
Reverse Transcription Pcr ◽  
Hylocereus Polyrhizus

Abstract Background:Canker disease caused by Neoscytalidium dimidiatumis a devastating disease resulting in a major loss to the pitaya industry. However, resistance proteins in plants play crucial roles to against pathogen infection. Among resistance proteins, the leucine-rich repeat (LRR) protein is a major family that plays crucial roles in plant growth, development, and biotic and abiotic stress responses, especially in disease defense. Results: In the present study, a transcriptomics analysis identified a total of 272 LRR genes, 233 of which had coding sequences (CDSs), in the plant pitaya (Hylocereus polyrhizus) in response to fungal Neoscytalidium dimidiatuminfection. These genes were divided into various subgroups based on specific domains and phylogenetic analysis. Molecular characterization, functional annotation of proteins, and an expression analysis of the LRR genes were conducted. Additionally, four LRR genes (CL445.Contig4_All, Unigene28_All, CL28.Contig2_All, and Unigene2712_All, which were selected because they had the four longest CDSs were further assessed using quantitative reverse transcription PCR (qRT-PCR) at different fungal infection stages in different pitaya species (Hylocereus polyrhizus and Hylocereus undatus), in different pitaya tissues, and after treatment with salicylic acid (SA), methyl jasmonate (MeJA), and abscisic acid(ABA) hormones. The associated protein functions and roles in signaling pathways were identified. Conclusions: This study provides a comprehensive overview of the HpLRR family genes at transcriptional level in pitaya in response toN. dimidiatuminfection, it will be helpful to understand the molecular mechanism of pitaya canker disease, and lay a strong foundation for further research.

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.

Exploring microRNAs, Target mRNAs and their Functions in Leguminous PlantArachis hypogaea

MicroRNA ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 135-146 ◽  
Author(s):  
Anjana Rajendiran ◽  
Saravanan Vijayakumar ◽  
Archana Pan
Keyword(s):  
Comparative Genomics ◽  
Stress Responses ◽  
Unsaturated Fatty Acids ◽  
Enrichment Analysis ◽  
Antibiotic Biosynthesis ◽  
Pathway Enrichment Analysis ◽  
Transcriptional Level ◽  
Biological Databases ◽  
Biotic And Abiotic Stress ◽  
Genome Survey

Background:MicroRNAs (miRNAs) are a class of small non-coding, endogenous RNAs that regulate gene expression at post-transcriptional level. In plants, miRNAs are usually of 18-24 nucleotide in length and play humongous role by aiding in development, growth, defense, biotic and abiotic stress responses, etc.Objective:Arachis hypogaea is an economically important oil seed crop and human dietary source cultivated mostly in tropical and subtropical regions. In the present study, an initiative was taken to uncover miRNAs, their targets and functions in this important plant species. </P><P> Method: Comparative genomics strategy coupled with bioinformatics approaches was deployed for the identification of miRNAs, their corresponding targets and functions by exploiting biological databases and tools.Results:The study was able to identify 34 conserved miRNA candidates, belonging to 17 miRNA families, contributed by 23 and 3 precursor miRNAs from A. hypogaea Expressed Sequence Tags (EST) and Genome Survey Sequences (GSS), respectively. As well, 495 EST and 917 unigene sequences were predicted as targets for the identified miRNAs. Herein, psRNAtarget server and TargetFinder tool were used to predict unigene targets, whereas comparative genomics strategy was used for identifying EST targets. Functional annotation of the identified targets revealed that the identified miRNAs regulate mRNAs that participate in key biological and metabolic processes. Pathway enrichment analysis using KEGG database also revealed that they regulate important metabolic pathways including antibiotic biosynthesis, biosynthesis of unsaturated fatty acids, amino acids metabolism and flavonoid biosynthesis.Conclusion:The outcome of the study would aid experimental biologists to focus on these miRNAs to facilitate improved crop development and yield.

scholarly journals A comprehensive overview of miRNA targeting drought stress resistance in plants

2023 ◽  
Vol 83 ◽  
Author(s):  
S. M. S. Shah ◽  
F. Ullah
Keyword(s):  
Drought Stress ◽  
Stress Responses ◽  
Crop Production ◽  
Genetic Alterations ◽  
Cereal Crops ◽  
Transcriptional Level ◽  
Gene Expressions ◽  
Comprehensive Overview ◽  
Defense Systems ◽  
The Given

Abstract MicroRNAs (miRNAs) are essential nonprotein-coding genes. In a range of organisms, miRNAs has been reported to play an essential role in regulating gene expressions at post-transcriptional level. They participate in most of the stress responsive processes in plants. Drought is an ultimate abiotic stress that affects the crop production. Therefore understanding drought stress responses are essential to improve the production of agricultural crops. Throughout evolution, plants have developed their own defense systems to cope with the adversities of environmental stresses. Among defensive mechanisms include the regulations of gene expression by miRNAs. Drought stress regulates the expression of some of the functionally conserved miRNAs in different plants. The given properties of miRNAs provide an insight to genetic alterations and enhancing drought resistance in cereal crops. The current review gives a summary to regulatory mechanisms in plants as well as miRNAs response to drought stresses in cereal crops. Some possible approaches and guidelines for the exploitation of drought stress miRNA responses to improve cereal crops are also described.

scholarly journals Transcriptomic de novo analysis of pitaya (Hylocereus polyrhizus) canker disease caused by Neoscytalidium dimidiatum

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Min Xu ◽  
Cheng-Li Liu ◽  
Juan Luo ◽  
Zhao Qi ◽  
Zhen Yan ◽  
...  
Keyword(s):  
De Novo ◽  
Canker Disease ◽  
Neoscytalidium Dimidiatum ◽  
Hylocereus Polyrhizus

scholarly journals Membrane Lipid Remodeling in Response to Salinity

2019 ◽  
Vol 20 (17) ◽  
pp. 4264 ◽  
Author(s):  
Qi Guo ◽  
Lei Liu ◽  
Bronwyn J. Barkla
Keyword(s):  
Salt Stress ◽  
Stress Responses ◽  
Membrane Lipids ◽  
Signaling Molecules ◽  
Membrane Lipid ◽  
Biotic And Abiotic Stress ◽  
Comprehensive Overview ◽  
Plant Salt Tolerance ◽  
Induced Changes ◽  
Plant Membranes

Salinity is one of the most decisive environmental factors threatening the productivity of crop plants. Understanding the mechanisms of plant salt tolerance is critical to be able to maintain or improve crop yield under these adverse environmental conditions. Plant membranes act as biological barriers, protecting the contents of cells and organelles from biotic and abiotic stress, including salt stress. Alterations in membrane lipids in response to salinity have been observed in a number of plant species including both halophytes and glycophytes. Changes in membrane lipids can directly affect the properties of membrane proteins and activity of signaling molecules, adjusting the fluidity and permeability of membranes, and activating signal transduction pathways. In this review, we compile evidence on the salt stress responses of the major membrane lipids from different plant tissues, varieties, and species. The role of membrane lipids as signaling molecules in response to salinity is also discussed. Advances in mass spectrometry (MS)-based techniques have largely expanded our knowledge of salt-induced changes in lipids, however only a handful studies have investigated the underlying mechanisms of membrane lipidome regulation. This review provides a comprehensive overview of the recent works that have been carried out on lipid remodeling of plant membranes under salt treatment. Challenges and future perspectives in understanding the mechanisms of salt-induced changes to lipid metabolisms are proposed.

scholarly journals Homo- and Hetero-Dimers of CAD Enzymes Regulate Lignification and Abiotic Stress Response in Moso Bamboo

2021 ◽  
Vol 22 (23) ◽  
pp. 12917
Author(s):  
Naresh Vasupalli ◽  
Dan Hou ◽  
Rahul Mohan Singh ◽  
Hantian Wei ◽  
Long-Hai Zou ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Expression Analysis ◽  
Stress Responses ◽  
Lignin Biosynthesis ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Moso Bamboo ◽  
Biosynthesis Pathway ◽  
Abiotic Stress Response ◽  
Biotic And Abiotic Stress

Lignin biosynthesis enzymes form complexes for metabolic channelling during lignification and these enzymes also play an essential role in biotic and abiotic stress response. Cinnamyl alcohol dehydrogenase (CAD) is a vital enzyme that catalyses the reduction of aldehydes to alcohols, which is the final step in the lignin biosynthesis pathway. In the present study, we identified 49 CAD enzymes in five Bambusoideae species and analysed their phylogenetic relationships and conserved domains. Expression analysis of Moso bamboo PheCAD genes in several developmental tissues and stages revealed that among the PheCAD genes, PheCAD2 has the highest expression level and is expressed in many tissues and PheCAD1, PheCAD6, PheCAD8 and PheCAD12 were also expressed in most of the tissues studied. Co-expression analysis identified that the PheCAD2 positively correlates with most lignin biosynthesis enzymes, indicating that PheCAD2 might be the key enzyme involved in lignin biosynthesis. Further, more than 35% of the co-expressed genes with PheCADs were involved in biotic or abiotic stress responses. Abiotic stress transcriptomic data (SA, ABA, drought, and salt) analysis identified that PheCAD2, PheCAD3 and PheCAD5 genes were highly upregulated, confirming their involvement in abiotic stress response. Through yeast two-hybrid analysis, we found that PheCAD1, PheCAD2 and PheCAD8 form homo-dimers. Interestingly, BiFC and pull-down experiments identified that these enzymes form both homo- and hetero- dimers. These data suggest that PheCAD genes are involved in abiotic stress response and PheCAD2 might be a key lignin biosynthesis pathway enzyme. Moreover, this is the first report to show that three PheCAD enzymes form complexes and that the formation of PheCAD homo- and hetero- dimers might be tissue specific.

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