Identification of differentially expressed genes from Trichoderma harzianum during growth on cell wall of Fusarium solani as a tool for biotechnological application

AbstractPisum sativum (pea) yields have declined significantly over the last decades, predominantly due to susceptibility to root rot diseases. One of the main causal agents of root rot is the fungus Fusarium solani f. sp. pisi (Fsp), leading to yield losses ranging from 15 to 60%. Determining and subsequently incorporating the genetic basis for resistance in new cultivars offers one of the best solutions to control this pathogen; however, no green-seeded pea cultivars with complete resistance to Fsp have been identified. To date, only partial levels of resistance to Fsp has been identified among pea genotypes. SNPs mined from Fsp-responsive differentially expressed genes (DEGs) identified in a preceding study were utilized to identify QTLs associated with Fsp resistance using composite interval mapping in two recombinant inbred line (RIL) populations segregating for partial root rot resistance. A total of 769 DEGs with single nucleotide polymorphisms (SNPs) were identified, and the putative SNPs were evaluated for being polymorphic across four partially resistant and four susceptible P. sativum genotypes. The SNPs with validated polymorphisms were used to screen two RIL populations using two phenotypic criteria: root disease severity and plant height. One QTL, WB.Fsp-Ps 5.1 that mapped to chromosome V explained 14.76 % of the variance with a confidence interval of 10.36 cM. The other four QTLs located on chromosomes II, III, and V, explained 5.26–8.05 % of the variance. The use of SNPs derived from Fsp-responsive DEGs for QTL mapping proved to be an efficient way to identify molecular markers associated with Fsp resistance in pea. These QTLs are potential candidates for marker-assisted selection and gene pyramiding to obtain high levels of partial resistance in pea cultivars to combat root rot caused by Fsp.

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Identification of differentially expressed genes from Trichoderma atroviride strain SS003 in the presence of cell wall of Cronartium ribicola

Genes & Genomics ◽

10.1007/s13258-016-0512-5 ◽

2017 ◽

Vol 39 (5) ◽

pp. 473-484

Author(s):

Nai-Yong Liu ◽

Ze-Ran Bao ◽

Jing Li ◽

Xin-Yu Ao ◽

Jia-Ying Zhu ◽

...

Keyword(s):

Cell Wall ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

Cronartium Ribicola ◽

Trichoderma Atroviride

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Differentially expressed genes in mycorrhized and nodulated roots of common bean are associated with defense, cell wall architecture, N metabolism, and P metabolism

PLoS ONE ◽

10.1371/journal.pone.0182328 ◽

2017 ◽

Vol 12 (8) ◽

pp. e0182328 ◽

Cited By ~ 9

Author(s):

Kalpana Nanjareddy ◽

Manoj-Kumar Arthikala ◽

Brenda-Mariana Gómez ◽

Lourdes Blanco ◽

Miguel Lara

Keyword(s):

Cell Wall ◽

Common Bean ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

N Metabolism ◽

Cell Wall Architecture

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Identification of Root Rot Resistance QTLs in Pea Using Fusarium solani f. sp. pisi-Responsive Differentially Expressed Genes

Frontiers in Genetics ◽

10.3389/fgene.2021.629267 ◽

2021 ◽

Vol 12 ◽

Author(s):

Bruce A. Williamson-Benavides ◽

Richard M. Sharpe ◽

Grant Nelson ◽

Eliane T. Bodah ◽

Lyndon D. Porter ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Fusarium Solani ◽

Root Rot ◽

Gene Pyramiding ◽

The United States ◽

Interval Mapping ◽

Differentially Expressed ◽

Nucleotide Polymorphisms ◽

Resistance Qtls ◽

Single Nucleotide

Pisum sativum (pea) yields in the United States have declined significantly over the last decades, predominantly due to susceptibility to root rot diseases. One of the main causal agents of root rot is the fungus Fusarium solani f. sp. pisi (Fsp), leading to yield losses ranging from 15 to 60%. Determining and subsequently incorporating the genetic basis for resistance in new cultivars offers one of the best solutions to control this pathogen; however, no green-seeded pea cultivars with complete resistance to Fsp have been identified. To date, only partial levels of resistance to Fsp has been identified among pea genotypes. SNPs mined from Fsp-responsive differentially expressed genes (DEGs) identified in a preceding study were utilized to identify QTLs associated with Fsp resistance using composite interval mapping in two recombinant inbred line (RIL) populations segregating for partial root rot resistance. A total of 769 DEGs with single nucleotide polymorphisms (SNPs) were identified, and the putative SNPs were evaluated for being polymorphic across four partially resistant and four susceptible P. sativum genotypes. The SNPs with validated polymorphisms were used to screen two RIL populations using two phenotypic criteria: root disease severity and plant height. One QTL, WB.Fsp-Ps 5.1 that mapped to chromosome 5 explained 14.8% of the variance with a confidence interval of 10.4 cM. The other four QTLs located on chromosomes 2, 3, and 5, explained 5.3–8.1% of the variance. The use of SNPs derived from Fsp-responsive DEGs for QTL mapping proved to be an efficient way to identify molecular markers associated with Fsp resistance in pea. These QTLs are potential candidates for marker-assisted selection and gene pyramiding to obtain high levels of partial resistance in pea cultivars to combat root rot caused by Fsp.

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A transcriptomic analysis of sugarcane response to Leifsonia xyli subsp. xyli infection

PLoS ONE ◽

10.1371/journal.pone.0245613 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0245613

Author(s):

Kai Zhu ◽

Li-Tao Yang ◽

Cheng-Xi Li ◽

Prakash Lakshmanan ◽

Yong-Xiu Xing ◽

...

Keyword(s):

Cell Wall ◽

Protein Phosphorylation ◽

Differentially Expressed Genes ◽

Plant Pathogen ◽

Significant Inhibition ◽

Differentially Expressed ◽

Down Regulation ◽

Sugarcane Varieties ◽

Obligate Pathogen ◽

Plant Pathogen Interactions

Sugarcane ratoon stunting disease (RSD) caused by Leifsonia xyli subsp. xyli (Lxx) is a common destructive disease that occurs around the world. Lxx is an obligate pathogen of sugarcane, and previous studies have reported some physiological responses of RSD-affected sugarcane. However, the molecular understanding of sugarcane response to Lxx infection remains unclear. In the present study, transcriptomes of healthy and Lxx-infected sugarcane stalks and leaves were studied to gain more insights into the gene activity in sugarcane in response to Lxx infection. RNA-Seq analysis of healthy and diseased plants transcriptomes identified 107,750 unigenes. Analysis of these unigenes showed a large number of differentially expressed genes (DEGs) occurring mostly in leaves of infected plants. Sugarcane responds to Lxx infection mainly via alteration of metabolic pathways such as photosynthesis, phytohormone biosynthesis, phytohormone action-mediated regulation, and plant-pathogen interactions. It was also found that cell wall defense pathways and protein phosphorylation/dephosphorylation pathways may play important roles in Lxx pathogeneis. In Lxx-infected plants, significant inhibition in photosynthetic processes through large number of differentially expressed genes involved in energy capture, energy metabolism and chloroplast structure. Also, Lxx infection caused down-regulation of gibberellin response through an increased activity of DELLA and down-regulation of GID1 proteins. This alteration in gibberellic acid response combined with the inhibition of photosynthetic processes may account for the majority of growth retardation occurring in RSD-affected plants. A number of genes associated with plant-pathogen interactions were also differentially expressed in Lxx-infected plants. These include those involved in secondary metabolite biosynthesis, protein phosphorylation/dephosphorylation, cell wall biosynthesis, and phagosomes, implicating an active defense response to Lxx infection. Considering the fact that RSD occurs worldwide and a significant cause of sugarcane productivity, a better understanding of Lxx resistance-related processes may help develop tools and technologies for producing RSD-resistant sugarcane varieties through conventional and/or molecular breeding.

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Global Analysis of Gene Expression Profiles in Glutinous Rice 89-1 (Oryza sativa L.) Seedlings Exposed to Chilling Stress

Plant Molecular Biology Reporter ◽

10.1007/s11105-020-01278-z ◽

2021 ◽

Author(s):

Xiaoxue Pan ◽

Hong Wu ◽

Mingyu Hu ◽

Zhongwei Wang ◽

Xiaoying Jiang ◽

...

Keyword(s):

Cell Wall ◽

Oryza Sativa ◽

Differentially Expressed Genes ◽

Oryza Sativa L ◽

Expression Profiles ◽

Global Analysis ◽

Chilling Stress ◽

Cold Treatment ◽

Differentially Expressed ◽

Glutinous Rice

AbstractRice (Oryza sativa) is a tropical cereal crop that is severely affected by chilling stress at the seedling stage, although glutinous rice 89-1 (Gr89-1) in Chongqing, China, shows tolerance to low temperatures and overwintering ability. However, little research has been conducted on the mechanisms regulating chilling stress in Gr89-1. In this study, a comprehensive of transcriptional profiles of Gr89-1 seedlings at the three-leaf stage was conducted after a 4 °C treatment for 2, 6, 12, 24, or 48 h. Overall, 2993 differentially expressed genes were detected in Gr89-1 seedlings upon cold exposure. Gene Ontology testing and pathway analysis revealed differentially expressed genes involved in transcriptional regulation, carbohydrate metabolism, plant hormone signal, and cell wall composition. A total of 243 transcription factors were differentially expressed during the cold treatment; in particular, the AP2/EREBP, bHLH, NAC, WRKY, C2H2, and TIFY families were generally upregulated after cold treatment, whereas the mTERF and GNAT families were downregulated. Chilling stress changed the starch and sucrose metabolism, coupled with the accumulation of sucrose and trehalose level, and increases in jasmonic acid level in Gr89-1 seedlings. Furthermore, a number of the cell wall-related genes identified in the present study were also differentially expressed during the cold treatment. The genes and pathways identified in the current study increase our understanding of the mechanisms underlying cold resistance in rice seedlings.

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Identification of differentially expressed genes in response to mercury I and II stress in Trichoderma harzianum

Gene ◽

10.1016/j.gene.2012.06.091 ◽

2012 ◽

Vol 506 (2) ◽

pp. 325-330 ◽

Cited By ~ 23

Author(s):

Ivana Puglisi ◽

Roberto Faedda ◽

Vincenzo Sanzaro ◽

Angela R. Lo Piero ◽

Goffredo Petrone ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Trichoderma Harzianum ◽

Differentially Expressed

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The bacteriostatic effect and mechanism of berberine on Methicillin resistant Staphylococcus aureus in vitro

10.21203/rs.2.9640/v2 ◽

2020 ◽

Author(s):

Lei Wang ◽

Fangfang Zhou ◽

Minyi Xu ◽

Pei Lu ◽

Ming Lin ◽

...

Keyword(s):

Cell Wall ◽

Rna Sequencing ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

Control Group ◽

High Concentration ◽

Bacteriostatic Effect ◽

Low Concentration ◽

Transmission Electron ◽

Cell Wall Hydrolysis

Abstract Background: To observe the bacteriostatic effect of berberine (BBR) and BBR combined with gentamicin (GEN), levofloxacin (LEV) and amikacin (AMI) on Methicillin resistant Staphylococcus aureus (MRSA), while also exploring the bacteriostatic mechanism of BBR on MRSA. Methods: The minimal inhibitory concentration (MIC) of BBR, GEN, LEV and AMI on 26 clinical MRSA strains was determined by broth microdilution, while the MICs of BBR combined with GEN, LEV and AMI against MRSA were determined using a microdilution checkerboard. Time-killing curves were used to determine the kinetics of BBR combined with antibiotics for MRSA. We used conductivity tests to assess the changes in membrane permeability in response to BBR on MRSA, while also investigating the changes in MRSA morphology by transmission electron microscopy. RNA-sequencing was used to analyze the expression of differentially expressed genes in reference strain USA300 after its treatment with BBR at different concentrations.Results: The MICs range of BBR on 26 strains of MRSA was 32-256 µg/mL. BBR combined with GEN, LEV and AMI had obvious bacteriostatic effect on MASA. After co-culturing MRSA with BBR at 512 ug/mL, 64 ug/mL and 8 ug/mL, respectively, the electrical conductivity increased, compared with the control group, by 8.14%, 13.08% and 12.01%, respectively. Using transmission electron microscopy, we found that low concentration of BBR (8 ug/mL) had no significant effect on MRSA structure (keeping intact), medium concentration of BBR (64 ug/mL) thinned the cell wall of MRSA, while high concentration of BBR (512 ug/mL) induced the destruction and dissolution of MRSA cell wall structure and the leakage of bacterial contents, leading to bacterial lysis. RNA-sequencing results showed that there were 754 differentially expressed genes in the high concentration group compared with the normal control group. Compared with the low concentration group, there were 590 differentially expressed genes in the high concentration group. Compared with the control group, only 19 genes were differentially expressed in the low concentration group. The up-regulated genes are mainly related to the cell wall hydrolysis regulatory genes, while the down-regulated genes are mainly related to the serine protease family.Conclusions: BBR displayed an excellent bacteriostatic effect on MRSA. BBR combined with GEN and AMI significantly enhanced the bacteriostatic effect on MRSA, while BBR combined with LEV showed no significant change in the bacteriostatic effect on MRSA. BBR inhibited bacteria by destroying and dissolving the structure of MRSA cell wall. RNA-sequencing results further demonstrated that the expression of cell wall hydrolysis genes ssaA, lytM and virulence factor serine protease genes were significantly differentially expressed when high concentration BBR treated on MRSA.

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The bacteriostatic effect and mechanism of berberine on Methicillin resistant Staphylococcus aureus in vitro

10.21203/rs.2.9640/v1 ◽

2019 ◽

Author(s):

Lei Wang ◽

Fangfang Zhou ◽

Minyi Xu ◽

Wei Gong ◽

Shuiying Ji

Keyword(s):

Cell Wall ◽

Rna Sequencing ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

Control Group ◽

High Concentration ◽

Bacteriostatic Effect ◽

Low Concentration ◽

Kinetics Of

Abstract Background: To observe the bacteriostatic effect of berberine on MRSA, while also exploring the bacteriostatic mechanism of BBR on MRSA. Methods: The MIC of BBR, gentamicin, levofloxacin，amikacin was determined by broth microdilution, while the MICs of BBR combined with gentamicin, levofloxacin，amikacin against MRSA were determined using microdilution checkerboard. Time-killing test were used to determine the kinetics of BBR combined with antibiotics for MRSA. We used conductivity to assess the changes in membrane permeability in response to BBR on MRSA, while also investigating the changes in MRSA morphology by TEM. RNA-sequencing was used to analyze the expression of differentially expressed genes in USA300 after its treatment with BBR. Results: The MICs range of BBR on MRSA was 32-256 µg/mL. The range of FICIs of BBR combined with gentamicin, levofloxacin，amikacin were 0.53-1.06, 0.62-1.5, 0.16-1.25. After co-culturing MRSA with BBR at 512 ug/mL, 64 ug/mL,8 ug/mL, respectively, the conductivity of these group increased by 8.14%,13.08% and 12.01%, respectively. Using TEM, we found that low-concentration of BBR had no significant effect on MRSA structure, medium-concentration of BBR thinned the cell wall of MRSA, while high-concentration of BBR destroyed cell wall, leading to bacterial lysis. RNA-sequencing results showed that there were 754 differentially expressed genes in the high-concentration group compared with the control group, of which 561 genes were up-regulated and 193 genes were down-regulated. Compared with the low-concentration group, there were 590 differentially expressed genes, of which 402 genes were up-regulated and 188 genes were down-regulated. Compared with the control group, 19 genes were differentially expressed in the low-concentration group, of which 11 genes were up-regulated,8 genes were down-regulated. Conclusions: BBR displayed an excellent bacteriostatic effect on MRSA. BBR combined with antibiotics significantly enhanced the bacteriostatic effect on MRSA. BBR inhibited bacteria by destroying the structure of cell wall. RNA-sequencing results demonstrated that the expression of cell wall hydrolysis genes and virulence factor were significantly differentially expressed on MRSA.

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