A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening

AbstractBackgroundGrape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition.ResultsTo better understand the effect of “place” on transcript abundance during the late stages of berry ripening, Cabernet Sauvignon berries grown in Bordeaux and Reno were compared at similar sugar levels (19 to 26 °Brix (total soluble solids)). Day temperatures were warmer and night temperatures were cooler in Reno. °Brix was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-Seq analysis identified 5528 differentially expressed genes between Bordeaux and Reno grape skins at 22°Brix. Weighted Gene Coexpression Network Analysis for all expressed transcripts for all four °Brix levels measured indicated that the majority (75%) of transcript expression differed significantly between the two locations. Top gene ontology categories for the common transcript sets were translation, photosynthesis, DNA metabolism and catabolism. Top gene ontology categories for the differentially expressed genes at 22°Brix involved response to stimulus, biosynthesis and response to stress. Some differentially expressed genes encoded terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. Bordeaux berries had higher transcript abundance with differentially expressed genes associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with differentially expressed genes involved in water deprivation, cold response, ABA signaling and iron homeostasis.ConclusionsTranscript abundance profiles in the berry skins at maturity were highly dynamic. RNA-Seq analysis identified a smaller (25% of total) common core set of ripening genes that appear not to depend on rootstock, vineyard management, plant age, soil and climatic conditions. Much of the gene expression differed between the two locations and could be associated with multiple differences in environmental conditions that may have affected the berries in the two locations; some of these genes may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result.

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A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.

10.21203/rs.2.10248/v4 ◽

2020 ◽

Author(s):

Grant R. Cramer ◽

Noé Cochetel ◽

Ryan Ghan ◽

Agnès Destrac-Irvine ◽

Serge Delrot

Keyword(s):

Circadian Clock ◽

Seed Dormancy ◽

Transcript Abundance ◽

Cabernet Sauvignon ◽

Berry Development ◽

Rna Seq ◽

Cold Response ◽

Berry Ripening ◽

Berry Skins ◽

Late Stages

Abstract Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis. Conclusions Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.

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A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.

10.21203/rs.2.10248/v3 ◽

2019 ◽

Author(s):

Grant R. Cramer ◽

Noé Cochetel ◽

Ryan Ghan ◽

Agnès Destrac-Irvine ◽

Serge Delrot

Keyword(s):

Circadian Clock ◽

Seed Dormancy ◽

Transcript Abundance ◽

Cabernet Sauvignon ◽

Berry Development ◽

Rna Seq ◽

Cold Response ◽

Berry Ripening ◽

Berry Skins ◽

Late Stages

Abstract Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis. Conclusions Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.

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A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.

10.21203/rs.2.10248/v2 ◽

2019 ◽

Author(s):

Grant R. Cramer ◽

Noé Cochetel ◽

Ryan Ghan ◽

Agnès Destrac-Irvine ◽

Serge Delrot

Keyword(s):

Circadian Clock ◽

Seed Dormancy ◽

Transcript Abundance ◽

Cabernet Sauvignon ◽

Berry Development ◽

Rna Seq ◽

Cold Response ◽

Berry Ripening ◽

Berry Skins ◽

Late Stages

Abstract Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis. Conclusions Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.

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A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.

10.21203/rs.2.10248/v1 ◽

2019 ◽

Author(s):

Grant R. Cramer ◽

Noé Cochetel ◽

Ryan Ghan ◽

Agnès Destrac-Irvine ◽

Serge Delrot

Keyword(s):

Circadian Clock ◽

Seed Dormancy ◽

Transcript Abundance ◽

Cabernet Sauvignon ◽

Berry Development ◽

Rna Seq ◽

Cold Response ◽

Berry Ripening ◽

Berry Skins ◽

Late Stages

Abstract Background: Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results: To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis. Conclusions: Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.

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A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.

10.21203/rs.2.10248/v5 ◽

2020 ◽

Author(s):

Grant R. Cramer ◽

Noé Cochetel ◽

Ryan Ghan ◽

Agnès Destrac-Irvine ◽

Serge Delrot

Keyword(s):

Circadian Clock ◽

Seed Dormancy ◽

Transcript Abundance ◽

Cabernet Sauvignon ◽

Berry Development ◽

Rna Seq ◽

Cold Response ◽

Berry Ripening ◽

Berry Skins ◽

Late Stages

Abstract Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis. Conclusions Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.

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RNA-Seq profiling of microdissected glomeruli identifies potential biomarkers for human IgA nephropathy

AJP Renal Physiology ◽

10.1152/ajprenal.00037.2020 ◽

2020 ◽

Vol 319 (5) ◽

pp. F809-F821

Author(s):

Sehoon Park ◽

Seung Hee Yang ◽

Chang Wook Jeong ◽

Kyung Chul Moon ◽

Dong Ki Kim ◽

...

Keyword(s):

Gene Ontology ◽

Iga Nephropathy ◽

Differentially Expressed Genes ◽

Mesangial Cells ◽

Principal Component ◽

Differentially Expressed ◽

Rna Seq ◽

Ontology Term ◽

Transcriptomic Profiling

Few studies have examined gene expression changes occurring in the glomeruli of IgA nephropathy (IgAN) using a sensitive transcriptomic profiling method such as RNA sequencing (RNA-Seq). We collected glomeruli from biopsy specimens from patients with IgAN with relatively preserved kidney function (estimated glomerular filtration rate ≥ 60 mL·min−1·1.73 m−2 and urine protein-to-creatinine ratio < 3 g/g) and from normal kidney cortexes by hand microdissection and performed RNA-Seq. Differentially expressed genes were identified, and gene ontology term annotation and pathway analysis were performed. Immunohistochemical labeling and primary mesangial cell cultures were performed to confirm the findings of RNA-Seq analysis. Fourteen patients with IgAN and ten controls were included in this study. Glomerulus-specific genes were highly abundant. Principal component analysis showed clear separation between the IgAN and control groups. There were 2,497 differentially expressed genes, of which 1,380 were upregulated and 1,117 were downregulated (false discovery rate < 0.01). The enriched gene ontology terms included motility/migration, protein/vesicle transport, and immune system, and kinase binding was the molecular function overrepresented in IgAN. B cell signaling, chemokine signal transduction, and Fcγ receptor-mediated phagocytosis were the canonical pathways overrepresented. In vitro experiments confirmed that spleen tyrosine kinase (SYK), reported as upregulated in the IgAN transcriptome, was also upregulated in glomeruli from an independent set of patients with IgAN and that treatment with patient-derived IgA1 increased the expression of SYK in mesangial cells. In conclusion, transcriptomic profiling of the IgAN glomerulus provides insights in the intraglomerular pathophysiology of IgAN before it reaches profound kidney dysfunction. SYK may have a pathogenetic role in IgAN.

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Exon-level estimates improve the detection of differentially expressed genes in RNA-seq studies

RNA Biology ◽

10.1080/15476286.2020.1868151 ◽

2021 ◽

pp. 1-8

Author(s):

Arfa Mehmood ◽

Asta Laiho ◽

Laura L. Elo

Keyword(s):

Differentially Expressed Genes ◽

Differentially Expressed ◽

Rna Seq ◽

Exon Level

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OP0021 IDENTIFICATION OF DIFFERENTIALLY EXPRESSED GENES IN EARLY RHEUMATOID ARTHRITIS PATIENTS RESPONDING TO TOCILIZUMAB

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2021-eular.3668 ◽

2021 ◽

Vol 80 (Suppl 1) ◽

pp. 12.2-12

Author(s):

I. Muller ◽

M. Verhoeven ◽

H. Gosselt ◽

M. Lin ◽

T. De Jong ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Gene Expression ◽

T Cells ◽

Gene Ontology ◽

Regulatory T Cells ◽

Early Rheumatoid Arthritis ◽

Whole Blood ◽

Differentially Expressed ◽

Rna Seq ◽

Double Blind

Background:Tocilizumab (TCZ) is a monoclonal antibody that binds to the interleukin 6 receptor (IL-6R), inhibiting IL-6R signal transduction to downstream inflammatory mediators. TCZ has shown to be effective as monotherapy in early rheumatoid arthritis (RA) patients (1). However, approximately one third of patients inadequately respond to therapy and the biological mechanisms underlying lack of efficacy for TCZ remain elusive (1). Here we report gene expression differences, in both whole blood and peripheral blood mononuclear cells (PBMC) RNA samples between early RA patients, categorized by clinical TCZ response (reaching DAS28 < 3.2 at 6 months). These findings could lead to identification of predictive biomarkers for TCZ response and improve RA treatment strategies.Objectives:To identify potential baseline gene expression markers for TCZ response in early RA patients using an RNA-sequencing approach.Methods:Two cohorts of RA patients were included and blood was collected at baseline, before initiating TCZ treatment (8 mg/kg every 4 weeks, intravenously). DAS28-ESR scores were calculated at baseline and clinical response to TCZ was defined as DAS28 < 3.2 at 6 months of treatment. In the first cohort (n=21 patients, previously treated with DMARDs), RNA-sequencing (RNA-seq) was performed on baseline whole blood PAXgene RNA (Illumina TruSeq mRNA Stranded) and differential gene expression (DGE) profiles were measured between responders (n=14) and non-responders (n=7). For external replication, in a second cohort (n=95 therapy-naïve patients receiving TCZ monotherapy), RNA-seq was conducted on baseline PBMC RNA (SMARTer Stranded Total RNA-Seq Kit, Takara Bio) from the 2-year, multicenter, double-blind, placebo-controlled, randomized U-Act-Early trial (ClinicalTrials.gov identifier: NCT01034137) and DGE was analyzed between 84 responders and 11 non-responders.Results:Whole blood DGE analysis showed two significantly higher expressed genes in TCZ non-responders (False Discovery Rate, FDR < 0.05): urotensin 2 (UTS2) and caveolin-1 (CAV1). Subsequent analysis of U-Act-Early PBMC DGE showed nine differentially expressed genes (FDR < 0.05) of which expression in clinical TCZ non-responders was significantly higher for eight genes (MTCOP12, ZNF774, UTS2, SLC4A1, FECH, IFIT1B, AHSP, and SPTB) and significantly lower for one gene (TND2P28M). Both analyses were corrected for baseline DAS28-ESR, age and gender. Expression of UTS2, with a proposed function in regulatory T-cells (2), was significantly higher in TCZ non-responders in both cohorts. Furthermore, gene ontology enrichment analysis revealed no distinct gene ontology or IL-6 related pathway(s) that were significantly different between TCZ-responders and non-responders.Conclusion:Several genes are differentially expressed at baseline between responders and non-responders to TCZ therapy at 6 months. Most notably, UTS2 expression is significantly higher in TCZ non-responders in both whole blood as well as PBMC cohorts. UTS2 could be a promising target for further analyses as a potential predictive biomarker for TCZ response in RA patients in combination with clinical parameters (3).References:[1]Bijlsma JWJ, Welsing PMJ, Woodworth TG, et al. Early rheumatoid arthritis treated with tocilizumab, methotrexate, or their combination (U-Act-Early): a multicentre, randomised, double-blind, double-dummy, strategy trial. Lancet. 2016;388(10042):343-55.[2]Bhairavabhotla R, Kim YC, Glass DD, et al. Transcriptome profiling of human FoxP3+ regulatory T cells. Human Immunology. 2016;77(2):201-13.[3]Gosselt HR, Verhoeven MMA, Bulatovic-Calasan M, et al. Complex machine-learning algorithms and multivariable logistic regression on par in the prediction of insufficient clinical response to methotrexate in rheumatoid arthritis. Journal of Personalized Medicine. 2021;11(1).Disclosure of Interests:None declared

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HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles

Viruses ◽

10.3390/v13020244 ◽

2021 ◽

Vol 13 (2) ◽

pp. 244 ◽

Cited By ~ 1

Author(s):

Antonio Victor Campos Coelho ◽

Rossella Gratton ◽

João Paulo Britto de Melo ◽

José Leandro Andrade-Santos ◽

Rafael Lima Guimarães ◽

...

Keyword(s):

Gene Expression ◽

T Cells ◽

Differentially Expressed Genes ◽

Cd4 T Cells ◽

Expression Profiles ◽

Meta Analysis ◽

Differentially Expressed ◽

Rna Seq ◽

Infected Cells ◽

Hiv 1

HIV-1 infection elicits a complex dynamic of the expression various host genes. High throughput sequencing added an expressive amount of information regarding HIV-1 infections and pathogenesis. RNA sequencing (RNA-Seq) is currently the tool of choice to investigate gene expression in a several range of experimental setting. This study aims at performing a meta-analysis of RNA-Seq expression profiles in samples of HIV-1 infected CD4+ T cells compared to uninfected cells to assess consistently differentially expressed genes in the context of HIV-1 infection. We selected two studies (22 samples: 15 experimentally infected and 7 mock-infected). We found 208 differentially expressed genes in infected cells when compared to uninfected/mock-infected cells. This result had moderate overlap when compared to previous studies of HIV-1 infection transcriptomics, but we identified 64 genes already known to interact with HIV-1 according to the HIV-1 Human Interaction Database. A gene ontology (GO) analysis revealed enrichment of several pathways involved in immune response, cell adhesion, cell migration, inflammation, apoptosis, Wnt, Notch and ERK/MAPK signaling.

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Phytophthora infestans Sporangia Produced in Culture and on Tomato Leaflet Lesions Show Marked Differences in Indirect Germination Rates, Aggressiveness, and Global Transcription Profiles

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-09-18-0255-ta ◽

2019 ◽

Vol 32 (5) ◽

pp. 515-526 ◽

Cited By ~ 5

Author(s):

William E. Fry ◽

Sean P. Patev ◽

Kevin L. Myers ◽

Kan Bao ◽

Zhangjun Fei

Keyword(s):

Phytophthora Infestans ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

Rna Seq ◽

Moist Chamber ◽

Field Isolates ◽

Rxlr Effectors ◽

Transcription Profiles ◽

Independent Field ◽

Pure Cultures

Sporangia of Phytophthora infestans from pure cultures on agar plates are typically used in lab studies, whereas sporangia from leaflet lesions drive natural infections and epidemics. Multiple assays were performed to determine if sporangia from these two sources are equivalent. Sporangia from plate cultures showed much lower rates of indirect germination and produced much less disease in field and moist-chamber tests. This difference in aggressiveness was observed whether the sporangia had been previously incubated at 4°C (to induce indirect germination) or at 21°C (to prevent indirect germination). Furthermore, lesions caused by sporangia from plates produced much less sporulation. RNA-Seq analysis revealed that thousands of the >17,000 P. infestans genes with a RPKM (reads per kilobase of exon model per million mapped reads) >1 were differentially expressed in sporangia obtained from plate cultures of two independent field isolates compared with sporangia of those isolates from leaflet lesions. Among the significant differentially expressed genes (DEGs), putative RxLR effectors were overrepresented, with almost half of the 355 effectors with RPKM >1 being up- or downregulated. DEGs of both isolates include nine flagellar-associated genes, and all were down-regulated in plate sporangia. Ten elicitin genes were also detected as DEGs in both isolates, and nine (including INF1) were up-regulated in plate sporangia. These results corroborate previous observations that sporangia produced from plates and leaflets sometimes yield different experimental results and suggest hypotheses for potential mechanisms. We caution that use of plate sporangia in assays may not always produce results reflective of natural infections and epidemics.

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