Transcriptomic Analysis of Quinoa Reveals a Group of Germin-Like Proteins Induced by Trichoderma

Symbiotic strains of fungi in the genus Trichoderma affect growth and pathogen resistance of many plant species, but the interaction is not known in molecular detail. Here we describe the transcriptomic response of two cultivars of the crop Chenopodium quinoa to axenic co-cultivation with Trichoderma harzianum BOL-12 and Trichoderma afroharzianum T22. The response of C. quinoa roots to BOL-12 and T22 in the early phases of interaction was studied by RNA sequencing and RT-qPCR verification. Interaction with the two fungal strains induced partially overlapping gene expression responses. Comparing the two plant genotypes, a broad spectrum of putative quinoa defense genes were found activated in the cultivar Kurmi but not in the Real cultivar. In cultivar Kurmi, relatively small effects were observed for classical pathogen response pathways but instead a C. quinoa-specific clade of germin-like genes were activated. Germin-like genes were found to be more rapidly induced in cultivar Kurmi as compared to Real. The same germin-like genes were found to also be upregulated systemically in the leaves. No strong correlation was observed between any of the known hormone-mediated defense response pathways and any of the quinoa-Trichoderma interactions. The differences in responses are relevant for the capabilities of applying Trichoderma agents for crop protection of different cultivars of C. quinoa.

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Transcriptomic analysis of quinoa reveals a group of germin-like proteins induced by Trichoderma

10.1101/2021.04.14.439738 ◽

2021 ◽

Author(s):

Oscar Miguel Rollano-Penaloza ◽

Allan G. Rasmusson ◽

Susanne Widell ◽

Patricia Mollinedo

Keyword(s):

Gene Expression ◽

Broad Spectrum ◽

Trichoderma Harzianum ◽

Strong Correlation ◽

Crop Protection ◽

Chenopodium Quinoa ◽

Pathogen Resistance ◽

Transcriptomic Response ◽

Pathogen Response ◽

Early Phases

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Transcriptomic Analysis of Quinoa Reveals A Group of Germin-Like Proteins Induced By Trichoderma

10.21203/rs.3.rs-435518/v1 ◽

2021 ◽

Author(s):

Oscar Miguel Rollano-Peñaloza ◽

Patricia Mollinedo ◽

Susanne Widell ◽

Allan G. Rasmusson

Keyword(s):

Gene Expression ◽

Broad Spectrum ◽

Negative Impact ◽

Crop Protection ◽

Chenopodium Quinoa ◽

Pathogen Resistance ◽

Genetic Compatibility ◽

Transcriptomic Response ◽

Pathogen Response ◽

Early Phases

Abstract Background: Fungi in the Trichoderma genus affect growth and pathogen resistance of many plant species with different outcomes. Most plant-Trichoderma interactions result in a beneficial relationship. However, Trichoderma fungi may have a negative impact on certain plants depending on their genotype. Thus, plant-Trichoderma interactions outcome might depend on their genetic compatibility, which is not known in molecular detail. Results: Here we describe the transcriptomic response of two cultivars of Chenopodium quinoa to axenic co-cultivation with Trichoderma harzianum BOL-12 and Trichoderma afroharzianum T22. The response of C. quinoa roots to BOL-12 and T22 in the early phases of interaction was studied by RNA sequencing and RT-qPCR verification. Interaction with the two fungal strains induced partially overlapping gene expression responses. Comparing the two plant genotypes, a broad spectrum of putative quinoa defense genes were found activated in cultivar Kurmi but not in the Real cultivar. In cultivar Kurmi, relatively small effects were observed for classical pathogen response pathways but instead a C. quinoa-specific clade of putative defensive germin-like genes were activated. Germin-like genes were found to be more rapidly induced in cultivar Kurmi as compared to Real. The same germin-like genes were found to be upregulated systemically in Kurmi leaves. No strong correlation was observed between any of the known hormone-mediated defense response pathways and any of the quinoa-Trichoderma interactions. Conclusions: C. quinoa triggers a set of germin-like defensive genes in response to Trichoderma interaction. Quinoa germin-like gene expression is cultivar-specific upon interaction with Trichoderma and was found to be expressed also systemically. The observed differences of quinoa response to Trichoderma for each quinoa cultivar are relevant for the application of Trichoderma agents for quinoa crop protection.

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Dissecting the Role of Thyrotropin in the DNA Damage Response in Human Thyrocytes after 131I, γ Radiation and H2O2

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/clinem/dgz185 ◽

2019 ◽

Vol 105 (3) ◽

pp. 839-853

Author(s):

Aglaia Kyrilli ◽

David Gacquer ◽

Vincent Detours ◽

Anne Lefort ◽

Frédéric Libert ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Dna Damage ◽

Dna Damage Response ◽

Iodide Uptake ◽

Transcriptomic Response ◽

Uptake Inhibition ◽

Γ Radiation ◽

Damage Response

Abstract Background The early molecular events in human thyrocytes after 131I exposure have not yet been unravelled. Therefore, we investigated the role of TSH in the 131I-induced DNA damage response and gene expression in primary cultured human thyrocytes. Methods Following exposure of thyrocytes, in the presence or absence of TSH, to 131I (β radiation), γ radiation (3 Gy), and hydrogen peroxide (H2O2), we assessed DNA damage, proliferation, and cell-cycle status. We conducted RNA sequencing to profile gene expression after each type of exposure and evaluated the influence of TSH on each transcriptomic response. Results Overall, the thyrocyte responses following exposure to β or γ radiation and to H2O2 were similar. However, TSH increased 131I-induced DNA damage, an effect partially diminished after iodide uptake inhibition. Specifically, TSH increased the number of DNA double-strand breaks in nonexposed thyrocytes and thus predisposed them to greater damage following 131I exposure. This effect most likely occurred via Gα q cascade and a rise in intracellular reactive oxygen species (ROS) levels. β and γ radiation prolonged thyroid cell-cycle arrest to a similar extent without sign of apoptosis. The gene expression profiles of thyrocytes exposed to β/γ radiation or H2O2 were overlapping. Modulations in genes involved in inflammatory response, apoptosis, and proliferation were observed. TSH increased the number and intensity of modulation of differentially expressed genes after 131I exposure. Conclusions TSH specifically increased 131I-induced DNA damage probably via a rise in ROS levels and produced a more prominent transcriptomic response after exposure to 131I.

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Multi-species transcriptome meta-analysis of the response to retinoic acid in vertebrates and comparative analysis of the effects of retinol and retinoic acid on gene expression in LMH cells

BMC Genomics ◽

10.1186/s12864-021-07451-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Clemens Falker-Gieske ◽

Andrea Mott ◽

Sören Franzenburg ◽

Jens Tetens

Keyword(s):

Gene Expression ◽

Retinoic Acid ◽

Cellular Response ◽

Homo Sapiens ◽

Meta Analysis ◽

Early Response ◽

Rna Seq ◽

Transcriptomic Response ◽

Time Points ◽

Lmh Cells

Abstract Background Retinol (RO) and its active metabolite retinoic acid (RA) are major regulators of gene expression in vertebrates and influence various processes like organ development, cell differentiation, and immune response. To characterize a general transcriptomic response to RA-exposure in vertebrates, independent of species- and tissue-specific effects, four publicly available RNA-Seq datasets from Homo sapiens, Mus musculus, and Xenopus laevis were analyzed. To increase species and cell-type diversity we generated RNA-seq data with chicken hepatocellular carcinoma (LMH) cells. Additionally, we compared the response of LMH cells to RA and RO at different time points. Results By conducting a transcriptome meta-analysis, we identified three retinoic acid response core clusters (RARCCs) consisting of 27 interacting proteins, seven of which have not been associated with retinoids yet. Comparison of the transcriptional response of LMH cells to RO and RA exposure at different time points led to the identification of non-coding RNAs (ncRNAs) that are only differentially expressed (DE) during the early response. Conclusions We propose that these RARCCs stand on top of a common regulatory RA hierarchy among vertebrates. Based on the protein sets included in these clusters we were able to identify an RA-response cluster, a control center type cluster, and a cluster that directs cell proliferation. Concerning the comparison of the cellular response to RA and RO we conclude that ncRNAs play an underestimated role in retinoid-mediated gene regulation.

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Detoxification and Immune Transcriptomic Response of the Gill Tissue of Bay Scallop (Argopecten irradians) Following Exposure to the Algicide Palmitoleic Acid

Biomolecules ◽

10.3390/biom8040139 ◽

2018 ◽

Vol 8 (4) ◽

pp. 139 ◽

Cited By ~ 3

Author(s):

Cheng Chi ◽

Sib Giri ◽

Jin Jun ◽

Hyoun Kim ◽

Sang Kim ◽

...

Keyword(s):

Gene Expression ◽

Cytochrome P450 ◽

Palmitoleic Acid ◽

Molecular Mechanisms ◽

Functional Enrichment ◽

Alexandrium Tamarense ◽

Read Length ◽

Related Factor ◽

Transcriptomic Response ◽

Bay Scallop

Palmitoleic acid (PA) is an effective algicide against Alexandrium tamarense. However, the toxicological mechanism of PA exposure is unclear. The transcript abundance and differentially expressed genes (DEGs) in gills of bay scallop were investigated following 80 mg/L PA exposure up to 48 h using the Illumina HiSeq 4000 deep-sequencing platform with the recommended read length of 100 bp. De novo assembly of paired-end reads yielded 62,099 unigenes; 5414 genes were identified as being significantly increased, and 4452 were decreased. Based on gene ontology classification and enrichment analysis, the ‘cellular process’, ‘metabolic process’, ‘response to stimulus’, and ‘catalytic process’ with particularly high functional enrichment were revealed. The DEGs, which are related to detoxification and immune responses, revealed that acid phosphatase, fibrinogen C domain-containing protein, cyclic AMP-responsive element-binding protein, glutathione reductase, ATP-binding cassette, nuclear factor erythroid 2-related factor, NADPH2:quinone reductase, and cytochrome P450 4F22, 4B1, and 2C8-related gene expression decreased. In contrast, some genes related to glutathione S-transferase, C-type lectin, superoxide dismutase, toll-like receptors, and cytochrome P450 2C14, 2U1, 3A24 and 4A2 increased. The results of current research will be a valuable resource for the investigation of gene expression stimulated by PA, and will help understanding of the molecular mechanisms underlying the scallops’ response to PA exposure.

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Gene Expression during the Early Phases of Bone Repair in the Horse: Effects of Electromagnetic Field Exposure

Electricity and Magnetism in Biology and Medicine ◽

10.1007/978-1-4615-4867-6_205 ◽

1999 ◽

pp. 857-859

Author(s):

Patrizia Zucchini ◽

Ruggero Cadossi ◽

Valerio Cané ◽

Sergio Ferrari

Keyword(s):

Gene Expression ◽

Electromagnetic Field ◽

Bone Repair ◽

Field Exposure ◽

Early Phases

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Expression of genes SBP and leginsulin in contrasting soybean seed coats

Ciência Rural ◽

10.1590/0103-8478cr20140172 ◽

2016 ◽

Vol 46 (10) ◽

pp. 1695-1700

Author(s):

Carlos André Bahry ◽

Paulo Dejalma Zimmer

Keyword(s):

Gene Expression ◽

Seed Quality ◽

Soybean Seed ◽

Future Research ◽

Expression Of Genes ◽

New Information ◽

Soybean Genotypes ◽

Phases Of Development ◽

Seed Coats ◽

Early Phases

ABSTRACT: Evaluation of differential candidate gene expression in contrasting soybean seeds is an auxiliary tool in the partial elucidation of processes involved in seeds formation, as well as it contributes to the generation of new information that can be used in future research or in the development of r genetic superior constitutions. The aim of this study was to evaluate the expression of two candidate genes, SBP and leginsulin genes, possibly involved in seed quality, in contrasting coats of four soybean genotypes. Two cultivars of yellow soybeans were used, BMX Potência RR and CD 202, and two lines of black soybean, TP and IAC. Gene expression was evaluated using qPCR in seven stages of development from seed coats for four genotypes, at 25, 30, 35, 40, 45, 50, and 55 days after anthesis. The design was completely randomized, with three replications. Data were subjected to analysis of variance and means compared by Tukey's test at 5% probability. SBP and leginsulin gene have higher expression in the early phases of development from seed coats of BMX Potência RR cultivar, followed by the IAC line. These genotypes are therefore of interest for further research involving these genes.

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Genomic and Molecular Perspectives of Host-pathogen Interaction and Resistance Strategies against White Rust in Oilseed Mustard

Current Genomics ◽

10.2174/1389202921999200508075410 ◽

2020 ◽

Vol 21 (3) ◽

pp. 179-193

Author(s):

Chatterjee Anupriya ◽

Nirwan Shradha ◽

Bandyopadhyay Prasun ◽

Agnihotri Abha ◽

Sharma Pankaj ◽

...

Keyword(s):

Crop Protection ◽

Resistance Mechanism ◽

Pathogen Resistance ◽

Susceptibility Genes ◽

Rust Disease ◽

Disease Response ◽

White Rust ◽

Oilseed Brassicas ◽

Insight Into

: Oilseed brassicas stand as the second most valuable source of vegetable oil and the third most traded one across the globe. However, the yield can be severely affected by infections caused by phytopathogens. White rust is a major oomycete disease of oilseed brassicas resulting in up to 60% yield loss globally. So far, success in the development of oomycete resistant Brassicas through conventional breeding has been limited. Hence, there is an imperative need to blend conventional and frontier biotechnological means to breed for improved crop protection and yield. : This review provides a deep insight into the white rust disease and explains the oomycete-plant molecular events with special reference to Albugo candida describing the role of effector molecules, A. candida secretome, and disease response mechanism along with nucleotide-binding leucine-rich repeat receptor (NLR) signaling. Based on these facts, we further discussed the recent progress and future scopes of genomic approaches to transfer white rust resistance in the susceptible varieties of oilseed brassicas, while elucidating the role of resistance and susceptibility genes. Novel genomic technologies have been widely used in crop sustainability by deploying resistance in the host. Enrichment of NLR repertoire, over-expression of R genes, silencing of avirulent and disease susceptibility genes through RNA interference and CRSPR-Cas are technologies which have been successfully applied against pathogen-resistance mechanism. The article provides new insight into Albugo and Brassica genomics which could be useful for producing high yielding and WR resistant oilseed cultivars across the globe.

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