scholarly journals Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

2020 ◽  
Author(s):  
Juan Niu ◽  
Yaliang Shi ◽  
Kunyong Huang ◽  
Yicheng Zhong ◽  
Jing Chen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Differentially Expressed ◽  
Wall Structure ◽  
Mrna Levels ◽  
Galactose Metabolism ◽  
Pests And Diseases ◽  
Fruit Cracking ◽  
Resistant Varieties ◽  
Fruit Decay

Abstract Background: Akebia trifoliata (Thunb.) Koid may have applications as a new source of biofuels owing to its high seed count, seed oil content, and in-field yields. However, the pericarp of A. trifoliata cracks longitudinally during fruit ripening, which increases the incidence of pests and diseases and can lead to fruit decay and deterioration, resulting in significant losses in yield. Few studies have evaluated the mechanisms underlying A. trifoliata fruit cracking. Results: In this study, by observing the cell wall structure of the pericarp, we found that the cell wall became thinner and looser and showed substantial breakdown in the pericarp of cracking fruit compared with that in non-cracking fruit. Moreover, integrative analyses of transcriptome and proteome profiles at different stages of fruit ripening demonstrated changes in the expression of various genes and proteins after cracking. Furthermore, the mRNA levels of 20 differentially expressed genes were analyzed, and parallel reaction monitoring analysis of 20 differentially expressed proteins involved in cell wall metabolism was conducted. Among the molecular targets, pectate lyases and pectinesterase, which are involved in pentose and glucuronate interconversion, and β-galactosidase 2, which is involved in galactose metabolism, were significantly upregulated in cracking fruits than in non-cracking fruits. This suggested that they might play crucial roles in A. trifoliata fruit cracking. Conclusions: Our findings provided new insights into potential genes influencing the fruit cracking trait in A. trifoliata and established a basis for further research on the breeding of cracking-resistant varieties to increase seed yields for biorefineries.

scholarly journals Integrity transcriptome and proteome analyses provide new insights into the mechanisms regulating pericarp cracking in Akebia trifoliata fruit

2020 ◽  
Author(s):  
Juan Niu ◽  
Yaliang Shi ◽  
Kunyong Huang ◽  
Yicheng Zhong ◽  
Jing Chen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Mrna Levels ◽  
Galactose Metabolism ◽  
Pectate Lyases ◽  
Fruit Cracking ◽  
Tandem Mass Tag ◽  
High Yields

Abstract Background: Akebia trifoliata (Thunb.) Koidz, a perennial wild woody liana, can be used as biofuel to generate bioenergy, as well as a traditional Chinese medicine plant,and new potential edible fruit crop, due to its high yields in fields, wide adaptability, high economic, medicinal and nutritive values, and tolerance tocultivation conditions. However, the pericarp of A. trifoliata cracks longitudinallyalong the ventral suture during fruit ripening, which is a serious problem that limits its usefulness and causes significant losses in yield and commercial value. Furthermore, there have been no known investigations on fruit cracking and its molecular mechanisms in A. trifoliata . Results: In this study, the dynamic structural changes in fruit pericarps were observed, revealing that the cell wall of fruit pericarp became thinner, and had reduced integrity, and that the cell walls began to degrade in the cracking fruits compared to those observed in non-cracking fruits. Moreover, analyses of the complementary RNA- sequencing-based transcriptomes and tandem mass tag-based proteomes at different development stages during fruit ripening were performed, and the expression of various genes and proteins was found to be changed after cracking, The mRNA levels of 20 differentially expressed genes and 17 differentially abundant proteins (DAPs) involved in cell wall metabolism were further analyzed; 20 DAPs were also validated through parallel reaction monitoring analysis. Among these, pectate lyases and pectinesterase involved in pentose and glucuronate interconversions, β-galactosidases 2 involved in galactose metabolism, were significantly up-regulated in cracking fruits compared to levels in non-cracking fruits, suggesting that they might play crucial roles in A. trifoliata fruit cracking. Conclusions: This study provides new insights into the molecular basis of fruit cracking in A. trifoliata fruits and important clues for further studies on the genetic improvement of A. trifoliata and the breeding of non-cracking varieties.

scholarly journals Integrity transcriptome and proteome analyses provide new insights into the mechanisms regulating peel cracking in Akebia trifoliata fruit

2019 ◽  
Author(s):  
Juan Niu ◽  
Yaliang Shi ◽  
Kunyong Huang ◽  
Yicheng Zhong ◽  
Jing Chen ◽  
...  
Keyword(s):  
Cell Wall ◽  
Candidate Genes ◽  
Fruit Ripening ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Sugar Metabolism ◽  
Potential Candidate ◽  
Proteomics Data ◽  
Galactose Metabolism ◽  
Fruit Cracking

Abstract Background Akebia trifoliata (Thunb.) Koidz, can be used as a new potential candidate biofuel and bioenergy crop due to its high productivity, adaptability and tolerance to cultivation conditions. However, the pericarp of A. trifoliata cracks open longitudinally and disperses its seeds along the ventral suture during fruit ripening, which is a serious problem that limits the usefulness of its biofuel feedstocks and causes significant losses of yield and commercial value. However, there have been no known previous investigations of the fruit cracking and its molecular mechanisms in A. trifoliata.Results The dynamic structural changes of the fruit peels were observed. In the non-cracking stage of growth, the exocarp was dense, had an orderly arrangement, and the cuticle was complete and distributed continuously. However, the cells became thinner, had reduced integrity, lost cell wall structures, and there was cell wall break down, in the fruit cracking stage. Moreover, analysis of the complementary RNA sequencing based transcriptomes and tandem mass tag based proteomes at different development stages of the fruit ripening, were performed to detect the genes and proteins related to the fruit cracking in A. trifoliata. A total of 20 differentially expressed genes and 17 differentially abundant proteins were identified from the transcriptomics and proteomics data that contribute to the fruit cracking, by participating in the biosynthesis of the phenylpropanoid pathway, galactose metabolism, pentose, and glucuronate interconversions, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism. Several candidate genes and proteins related to pentose and glucuronate interconversions (pectate lyases and pectinesterase) and galactose metabolism (β-galactosidases 1 and β-galactosidases 2) may play key roles in A. trifoliata fruit cracking.Conclusions Complementary transcriptome and proteome level analyses indicated that a complex molecular network was controlling the fruit cracking process. This study provides new insights into the molecular basis of fruit cracking in A. trifoliata fruits. The candidate genes/proteins identified in this study may be useful for the genetic improvement of A. trifoliata and other crops.

scholarly journals LncRNA regulates tomato fruit cracking by coordinating gene expression via a  hormone-redox-cell wall network

2020 ◽  
Author(s):  
Lingzi Xue ◽  
Mintao Sun ◽  
Zhen Wu ◽  
Lu Yu ◽  
Qinghui Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Abiotic Stress ◽  
Regulatory Networks ◽  
Tomato Fruit ◽  
Fruit Production ◽  
Differentially Expressed ◽  
Oxidoreductase Activity ◽  
Fruit Cracking ◽  
Stress Signals

Abstract Background Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, ‘LA1698’ (cracking-resistant, CR) and ‘LA2683’ (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 ( Peroxide, POD ), Solyc01g008710.3 ( Mannan endo-1,4-beta-mannosidase, MAN ), Solyc08g077910.3 ( Expanded, EXP ), Solyc09g075330.3 ( Pectinesterase , PE ), Solyc07g055990.3 ( Xyloglucan endotransglucosylase-hydrolase 7, XTH7 ), Solyc12g011030.2 ( X yloglucan endotransglucosylase-hydrolase 9 , XTH9 ), Solyc10g080210.2 ( Polygalacturonase-2, PG2 ), Solyc08g081010.2 ( Gamma-glutamylcysteine synthetase, gamma-GCS ), Solyc09g008720.2 ( Ethylene receptor , ER ), Solyc11g042560.2 ( Ethylene-responsive transcription factor 4, ERF4 ) etc. In addition, the lncRNAs (XLOC_16662 and XLOC_033910, etc) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs ( EXP, PG, XTH ), as well as some lncRNAs ( XLOC_16662 and XLOC_033910, etc.).

scholarly journals Genome wide identification and functional characterization of strawberry pectin methylesterases related to fruit softening

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Cheng Xue ◽  
Si-Cong Guan ◽  
Jian-Qing Chen ◽  
Chen-Jin Wen ◽  
Jian-Fa Cai ◽  
...  
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Genetic Manipulation ◽  
Functional Characterization ◽  
Hydrolytic Enzyme ◽  
Wall Structure ◽  
Fruit Softening ◽  
Fruit Firmness ◽  
Strawberry Fruit ◽  
Cell Wall Modification

Abstract Background Pectin methylesterase (PME) is a hydrolytic enzyme that catalyzes the demethylesterification of homogalacturonans and controls pectin reconstruction, being essential in regulation of cell wall modification. During fruit ripening stage, PME-mediated cell wall remodeling is an important process to determine fruit firmness and softening. Strawberry fruit is a soft fruit with a short postharvest life, due to a rapid loss of firm texture. Hence, preharvest improvement of strawberry fruit rigidity is a prerequisite for extension of fruit refreshing time. Although PME has been well characterized in model plants, knowledge regarding the functionality and evolutionary property of PME gene family in strawberry remain limited. Results A total of 54 PME genes (FvPMEs) were identified in woodland strawberry (Fragaria vesca ‘Hawaii 4’). Phylogeny and gene structure analysis divided these FvPME genes into four groups (Group 1–4). Duplicate events analysis suggested that tandem and dispersed duplications effectively contributed to the expansion of the PME family in strawberry. Through transcriptome analysis, we identified FvPME38 and FvPME39 as the most abundant-expressed PMEs at fruit ripening stages, and they were positively regulated by abscisic acid. Genetic manipulation of FvPME38 and FvPME39 by overexpression and RNAi-silencing significantly influences the fruit firmness, pectin content and cell wall structure, indicating a requirement of PME for strawberry fruit softening. Conclusion Our study globally analyzed strawberry pectin methylesterases by the approaches of phylogenetics, evolutionary prediction and genetic analysis. We verified the essential role of FvPME38 and FvPME39 in regulation of strawberry fruit softening process, which provided a guide for improving strawberry fruit firmness by modifying PME level.

scholarly journals LncRNA regulates tomato fruit cracking by coordinating gene expression via a  hormone-redox-cell wall network

2020 ◽  
Author(s):  
Lingzi Xue ◽  
Mintao Sun ◽  
Zhen Wu ◽  
Lu Yu ◽  
Qinghui Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Abiotic Stress ◽  
Regulatory Networks ◽  
Tomato Fruit ◽  
Fruit Production ◽  
Differentially Expressed ◽  
Oxidoreductase Activity ◽  
Fruit Cracking ◽  
Stress Signals

Abstract Background Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, ‘LA1698’ (cracking-resistant, CR) and ‘LA2683’ (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 ( Peroxide, POD ), Solyc01g008710.3 ( Mannan endo-1,4-beta-mannosidase, MAN ), Solyc08g077910.3 ( Expanded, EXP ), Solyc09g075330.3 ( Pectinesterase , PE ), Solyc07g055990.3 ( Xyloglucan endotransglucosylase-hydrolase 7, XTH7 ), Solyc12g011030.2 ( X yloglucan endotransglucosylase-hydrolase 9 , XTH9 ), Solyc10g080210.2 ( Polygalacturonase-2, PG2 ), Solyc08g081010.2 ( Gamma-glutamylcysteine synthetase, gamma-GCS ), Solyc09g008720.2 ( Ethylene receptor , ER ), Solyc11g042560.2 ( Ethylene-responsive transcription factor 4, ERF4 ) etc. In addition, the lncRNAs (XLOC_16662 and XLOC_033910, etc) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs ( EXP, PG, XTH ), as well as some lncRNAs ( XLOC_16662 and XLOC_033910, etc.).

scholarly journals LncRNA regulates tomato fruit cracking by coordinating gene expression via a  hormone-redox-cell wall network

2020 ◽  
Author(s):  
Lingzi Xue ◽  
Mintao Sun ◽  
Zhen Wu ◽  
Lu Yu ◽  
Qinghui Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Abiotic Stress ◽  
Regulatory Networks ◽  
Tomato Fruit ◽  
Fruit Production ◽  
Differentially Expressed ◽  
Oxidoreductase Activity ◽  
Fruit Cracking ◽  
Stress Signals

Abstract Background Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, ‘LA1698’ (cracking-resistant, CR) and ‘LA2683’ (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 ( Peroxide, POD ), Solyc01g008710.3 ( Mannan endo-1,4-beta-mannosidase, MAN ), Solyc08g077910.3 ( Expanded, EXP ), Solyc09g075330.3 ( Pectinesterase , PE ), Solyc07g055990.3 ( Xyloglucan endotransglucosylase-hydrolase 7, XTH7 ), Solyc12g011030.2 ( X yloglucan endotransglucosylase-hydrolase 9 , XTH9 ), Solyc10g080210.2 ( Polygalacturonase-2, PG2 ), Solyc08g081010.2 ( Gamma-glutamylcysteine synthetase, gamma-GCS ), Solyc09g008720.2 ( Ethylene receptor , ER ), Solyc11g042560.2 ( Ethylene-responsive transcription factor 4, ERF4 ) etc. In addition, the lncRNAs (XLOC_134491 and XLOC_036966) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs (EXP, PG, XTH), as well as some lncRNAs ( XLOC_134491 and XLOC_104931, etc.). Keywords Tomato, LncRNA, mRNA, Transcriptome, Network, Fruit cracking

scholarly journals Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015

2018 ◽  
Author(s):  
Cong Liu ◽  
Dongying Fan ◽  
Yanfang Li ◽  
Yue Chen ◽  
Lili Huang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Glyoxylate Cycle ◽  
Tca Cycle ◽  
Differentially Expressed ◽  
Wall Structure ◽  
Control Group ◽  
Retinol Dehydrogenase ◽  
Nitrogenous Compounds ◽  
Function And Pathway Analysis ◽  
Valsa Mali

Apple canker is a devastating branch disease caused by Valsa mali (Vm). The endophytic actinomycete Saccharothrix yanglingensis Hhs.015 (Sy Hhs.015) can effectively inhibit the growth of Vm. To reveal the mechanism, by which Vm respond to Sy Hhs.015, the transcriptome of Vm was analyzed using RNA-seq technology. Compared with the control group, 1476 genes were significantly differentially expressed in the treatment group, of which 851 genes were up-regulated and 625 genes were down-regulated. Combined gene function and pathway analysis of differentially expressed genes (DEGs) revealed that Sy Hhs.015 affected the carbohydrate metabolic pathway, which is utilized by Vm for energy production. Approximately 82% of the glycoside hydrolase genes were down-regulated, including three pectinase genes (PGs), which are key pathogenic factors. The cell wall structure of Vm was disrupted by Sy Hhs.015 and cell wall-related genes were found to be down-regulated. Of the peroxisome associated genes, those encoding catalase (CAT) and superoxide dismutase (SOD) which scavenge reactive oxygen species (ROS), as well as those encoding AMACR and ACAA1 which are related to the β-oxidation of fatty acids, were down-regulated. MS and ICL, key genes in glyoxylate cycle, were also down-regulated. In response to the stress of Sy Hhs.015 exposure, Vm increased amino acid metabolism to synthesize the required nitrogenous compounds, while alpha-keto acids, which involved in the TCA cycle, could be used to produce energy by deamination or transamination. Retinol dehydrogenase, associated with cell wall dextran synthesis, and sterol 24-C-methyltransferase, related to cell membrane ergosterol synthesis, were up-regulated. The genes encoding glutathione S-transferase, (GST), which has antioxidant activity and ABC transporters which have an efflux function, were also up-regulated. These results show that the response of Vm to Sy Hhs.015 exposure is a complicated and highly regulated process, and provide a theoretical basis for both clarifying the biocontrol mechanism of Sy Hhs.015 and the response of Vm to stress.

scholarly journals Identification of Candidate Genes Involved in Fruit Ripening and Crispness Retention Through Transcriptome Analyses of a ‘Honeycrisp’ Population

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1335
Author(s):  
Hsueh-Yuan Chang ◽  
Cindy B. S. Tong
Keyword(s):  
Cell Wall ◽  
Fruit Ripening ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Phenotypic Differences ◽  
Genes Encoding ◽  
A Cell ◽  
Phenotypic Groups

Crispness retention is a postharvest trait that fruit of the ’Honeycrisp’ apple and some of its progeny possess. To investigate the molecular mechanisms of crispness retention, progeny individuals derived from a ’Honeycrisp’ × MN1764 population with fruit that either retain crispness (named “Retain”), lose crispness (named “Lose”), or that are not crisp at harvest (named “Non-crisp”) were selected for transcriptomic comparisons. Differentially expressed genes (DEGs) were identified using RNA-Seq, and the expression levels of the DEGs were validated using nCounter®. Functional annotation of the DEGs revealed distinct ripening behaviors between fruit of the “Retain” and “Non-crisp” individuals, characterized by opposing expression patterns of auxin- and ethylene-related genes. However, both types of genes were highly expressed in the fruit of “Lose” individuals and ’Honeycrisp’, which led to the potential involvements of genes encoding auxin-conjugating enzyme (GH3), ubiquitin ligase (ETO), and jasmonate O-methyltransferase (JMT) in regulating fruit ripening. Cell wall-related genes also differentiated the phenotypic groups; greater numbers of cell wall synthesis genes were highly expressed in fruit of the “Retain” individuals and ’Honeycrisp’ when compared with “Non-crisp” individuals and MN1764. On the other hand, the phenotypic differences between fruit of the “Retain” and “Lose” individuals could be attributed to the functioning of fewer cell wall-modifying genes. A cell wall-modifying gene, MdXTH, was consistently identified as differentially expressed in those fruit over two years in this study, so is a major candidate for crispness retention.

scholarly journals Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015

2018 ◽  
Author(s):  
Cong Liu ◽  
Dongying Fan ◽  
Yanfang Li ◽  
Yue Chen ◽  
Lili Huang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Glyoxylate Cycle ◽  
Tca Cycle ◽  
Differentially Expressed ◽  
Wall Structure ◽  
Control Group ◽  
Retinol Dehydrogenase ◽  
Nitrogenous Compounds ◽  
Function And Pathway Analysis ◽  
Valsa Mali

Apple canker is a devastating branch disease caused by Valsa mali (Vm). The endophytic actinomycete Saccharothrix yanglingensis Hhs.015 (Sy Hhs.015) can effectively inhibit the growth of Vm. To reveal the mechanism, by which Vm respond to Sy Hhs.015, the transcriptome of Vm was analyzed using RNA-seq technology. Compared with the control group, 1476 genes were significantly differentially expressed in the treatment group, of which 851 genes were up-regulated and 625 genes were down-regulated. Combined gene function and pathway analysis of differentially expressed genes (DEGs) revealed that Sy Hhs.015 affected the carbohydrate metabolic pathway, which is utilized by Vm for energy production. Approximately 82% of the glycoside hydrolase genes were down-regulated, including three pectinase genes (PGs), which are key pathogenic factors. The cell wall structure of Vm was disrupted by Sy Hhs.015 and cell wall-related genes were found to be down-regulated. Of the peroxisome associated genes, those encoding catalase (CAT) and superoxide dismutase (SOD) which scavenge reactive oxygen species (ROS), as well as those encoding AMACR and ACAA1 which are related to the β-oxidation of fatty acids, were down-regulated. MS and ICL, key genes in glyoxylate cycle, were also down-regulated. In response to the stress of Sy Hhs.015 exposure, Vm increased amino acid metabolism to synthesize the required nitrogenous compounds, while alpha-keto acids, which involved in the TCA cycle, could be used to produce energy by deamination or transamination. Retinol dehydrogenase, associated with cell wall dextran synthesis, and sterol 24-C-methyltransferase, related to cell membrane ergosterol synthesis, were up-regulated. The genes encoding glutathione S-transferase, (GST), which has antioxidant activity and ABC transporters which have an efflux function, were also up-regulated. These results show that the response of Vm to Sy Hhs.015 exposure is a complicated and highly regulated process, and provide a theoretical basis for both clarifying the biocontrol mechanism of Sy Hhs.015 and the response of Vm to stress.

scholarly journals LncRNA regulates tomato fruit cracking by coordinating gene expression via a  hormone-redox-cell wall network

2020 ◽  
Author(s):  
Lingzi Xue ◽  
Mintao Sun ◽  
Zhen Wu ◽  
Lu Yu ◽  
Qinghui Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Abiotic Stress ◽  
Regulatory Networks ◽  
Tomato Fruit ◽  
Fruit Production ◽  
Differentially Expressed ◽  
Oxidoreductase Activity ◽  
Fruit Cracking ◽  
Stress Signals

Abstract Background Fruit cracking occurs easily under unsuitable environmental conditions and is one of the main types of damage that occurs in fruit production. It is widely accepted that plants have developed defence mechanisms and regulatory networks that respond to abiotic stress, which involves perceiving, integrating and responding to stress signals by modulating the expression of related genes. Fruit cracking is also a physiological disease caused by abiotic stress. It has been reported that a single or several genes may regulate fruit cracking. However, almost none of these reports have involved cracking regulatory networks. Results Here, RNA expression in 0 h, 8 h and 30 h saturated irrigation-treated fruits from two contrasting tomato genotypes, ‘LA1698’ (cracking-resistant, CR) and ‘LA2683’ (cracking-susceptible, CS), was analysed by mRNA and lncRNA sequencing. The GO pathways of the differentially expressed mRNAs were mainly enriched in the ‘hormone metabolic process’, ‘cell wall organization’, ‘oxidoreductase activity’ and ‘catalytic activity’ categories. According to the gene expression analysis, significantly differentially expressed genes included Solyc02g080530.3 ( Peroxide, POD ), Solyc01g008710.3 ( Mannan endo-1,4-beta-mannosidase, MAN ), Solyc08g077910.3 ( Expanded, EXP ), Solyc09g075330.3 ( Pectinesterase , PE ), Solyc07g055990.3 ( Xyloglucan endotransglucosylase-hydrolase 7, XTH7 ), Solyc12g011030.2 ( X yloglucan endotransglucosylase-hydrolase 9 , XTH9 ), Solyc10g080210.2 ( Polygalacturonase-2, PG2 ), Solyc08g081010.2 ( Gamma-glutamylcysteine synthetase, gamma-GCS ), Solyc09g008720.2 ( Ethylene receptor , ER ), Solyc11g042560.2 ( Ethylene-responsive transcription factor 4, ERF4 ) etc. In addition, the lncRNAs (XLOC_134491 and XLOC_036966) regulated the expression of their neighbouring genes, and genes related to tomato cracking were selected to construct a lncRNA-mRNA network influencing tomato cracking. Conclusions This study provides insight into the responsive network for water-induced cracking in tomato fruit. Specifically, lncRNAs regulate the hormone-redox-cell wall network, including plant hormone (auxin, ethylene) and ROS (H 2 O 2 ) signal transduction and many cell wall-related mRNAs (EXP, PG, XTH), as well as some lncRNAs ( XLOC_134491 and XLOC_104931, etc.). Keywords Tomato, LncRNA, mRNA, Transcriptome, Network, Fruit cracking

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