- Results: There were major differences in gene expression with over 3400 genes upregulated in one or more of the light conditions compared to dark, and from 1909 to 2573 genes specifically upregulated in the dark compared to the individual light treatments. - Differences between light treatments were lower, ranging from only 79 differentially expressed genes in the red versus blue comparison to 585 between white light and red. - For those that did, analysis of the Gene Ontology (GO) terms showed that those related to metabolism were enriched in all three light treatments, while those related to growth and communication were more prevalent in the dark. - tritici could help to manage Septoria tritici blotch in the future.. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - This species has clearly delin- eated morphology between growth that occurs in the light versus the dark [1–6].. - Presumably this also would occur within plant hosts and may explain the spread of lesions in concentric circles seen in fungi such as many species in the genus Alternaria, some of which show maximum growth in culture under alternating cycles of light and dark [32].. - In Cercospora species that produce the light-activated phyto- toxin cercosporin, light induces production of the toxin, as that is when it is most effective [39, 40], and no cercos- porin is produced in the dark. - For example, in the plant pathogens Botryis. - However, in the rice pathogen Magnaporthe oryzae, light represses infection, and leads to much lower disease se- verity [45]. - oryzae showed greater disease severity, as it could infect in the light as well as in the dark, compared to wild type which only infects in the dark [45].. - Light is a very important environmental cue for some fungi in the Dothideomycetes, the class that contains Z. - For example, in the genus Cercos- pora, another genus in the same taxonomic order (Cap- nodiales), light represses asexual sporulation, and melanization is controlled by circadian rhythms [17, 44].. - The conidiation and growth of two species in the order Pleosporales, Alternaria alternata and Exserohilum turcicum, are also regulated by light [41, 61]. - Out of 13,522 total genes called in the reference gen- ome had greater than 10 reads in each replicate and more than 100 reads across all twelve repli- cates, and were used in analysis with DESeq2. - There were major differences in the numbers of differ- entially expressed genes (adjusted p value <. - All six comparisons between the treat- ments showed the expected concavity in the volcano plots, but the magnitudes of the adjusted p values were much greater in the three light versus dark comparisons, with the lowest magnitude of adjusted p values in white light versus blue light (Additional File 1C).. - This is just under a third (31%) of all genes present in the Z. - In the three light versus dark comparisons, 4019 unique genes were differentially expressed, which. - In the three light versus light comparisons, 804 unique genes were differentially expressed, which is only about 6% of the genes in the Z.. - The known light-signaling gene MVE1 was upregulated in the dark relative to white light and blue light (Fig. - All three of these SSPs are functionally unanno- tated, and had no fungal matches in the NCBI NR data- base. - Many other proteases had significant dif- ferences in transcript abundance between treatments, with approximately a third of the proteases upregulated, a third downregulated, and a third not differentially expressed in the light versus dark comparisons (Add- itional File 3D).. - Very few secreted lipase genes were differentially expressed in the various light versus dark comparisons (Additional File 3B). - The adjusted p value for this gene in the white versus dark and blue versus dark com- parisons was 0, with a log2 fold change of 8.7 and 8.9, respectively, and it had an adjusted p value of 1.1e − 214 and a log2 fold change of 6.7 in the red versus dark comparison. - Among all differentially expressed genes, approximately 3% of those in the light treatments relative to dark were located on dispensable chromosomes that are not present in all isolates of the pathogen [63]. - Very few genes on dispens- able chromosomes were differentially expressed when the three light treatments were compared to each other, ran- ging from 1 in the blue versus red light comparison to 57 between white light and red (Table 3).. - This includes KOG classes and GO terms in the frozen gene catalog created as part of the original annotation by the Joint Genome Institute [63], as well as EggNOG classifica- tions [76] generated with the analysis of additional RNA. - In the full genome, 55.3% of genes have annotations, and 32.8% have GO terms assigned. - Table 3 Numbers of differentially expressed genes on core (numbers 1 – 13) and dispensable (14 – 21) chromosomes in the six comparisons of RNA sequences from Zymoseptoria tritici cultures exposed to different wavelengths of light or kept in the dark Chromosome White versus dark Blue versus dark Red versus dark White versus blue White versus red Blue versus red Total genes. - 0006468), that was also enriched in the dark in all three of the light versus dark comparisons. - More enriched GO terms were identified when cultures were grown under blue or red light than in the wider- range, white-light condition.. - The variety of enriched GO terms was especially notable in the dark versus blue light comparison (Fig. - The dark treat- ment had more GO terms that were related to growth and development than did cultures grown in the light, where those GO terms occurred rarely. - This was very apparent in the blue light and red light versus dark com- parisons, where multiple GO terms for growth were enriched in the dark in each comparison. - 3 in red) as well as some that were related to transportation of sub- stances in the cell. - The KOG functional annotations had similar results to the GO annotations, showing that more genes related to the transport and metabolism of major substances are upregulated in the light rather than the dark. - “defense mechanisms” also had more genes upregulated in the light than in the dark. - The opposite trend oc- curred with some KOG classes related to growth, which had more genes upregulated in the dark. - These differences did not appear in the light versus light comparisons. - Despite these changes in transcription of genes involved in growth and development and previous studies [57, 58], there were no obvious differences in the morphologies of cultures grown in the dark versus any of the light conditions (Fig. - tritici alters its transcriptome in the dark compared to when it is growing in the light and between different wavelengths of light. - The proportions of unannotated genes among those that were differentially expressed in the light and dark treatments were moderately higher than their rep- resentations in the genome in general. - crassa in the class Sordariomycetes. - Light responses of fungi in the class Dothideomycetes to which Z. - The differentially expressed genes with no functional annotations could indicate that novel path- ways are involved in the responses of Dothideomycetes to light. - This hypothesis could be tested in the future by. - Light affected expression of genes on all 21 chromo- somes in the Z. - One interesting result was that genes with annotations relating to oxidative stress, metabolism and transportation were upregulated primarily in the light, while the fungus would be growing on its host during the day, while genes with annotations relating to growth and general cell maintenance were more common pri- marily in the dark, and therefore would be expressed at night. - tritici, in Tricho- derma atroviride, transport-related genes were repressed in the wild type when grown under constant light and were expressed in a wc1 knockout mutant [85]. - One of the two putative Z. - In contrast, many genes with light-related biological functions in other organisms were not differentially expressed in the Z. - Similarly, while Mg1LysM is not actively responsible for blocking a defense response, it is not clear why it would be expressed in the light rather than constitutively unless it has another role related to growth or pathogenicity.. - tritici varied in whether they were up or down regulated in the light. - Another gene that is known to be directly involved in the synthesis of mel- anin, the polyketide synthase PKS1 [74], was downregu- lated in white light only. - Other genes in the secondary metabolism pathways also are differentially expressed and tend to be upregu- lated in the light. - Nearly half of them were upregulated in the light, and the remaining half were divided be- tween being downregulated and not differentially expressed (Fig. - This correlates with the findings from the enriched GO terms, where metabolism and secondary metabolism GO classes were expressed more in the light than in the dark (Fig. - A better understanding of how these genes are expressed in the host under vari- ous light conditions is essential for a complete picture of gene expression during infection.. - fungus could provide the basis for development of im- proved disease management strategies in the future.. - CateGOrizer was used to map the biological processes of each enriched GO term to a parent term in the stand- ard GO_slim [103]. - Treatments of white, blue and red light, and dark are indicated in the diagonal by W, B, R and D, respectively. - All genes that were differentially expressed in the six possible comparisons between the dark and three light treatments. - The datasets generated and/or analysed during the current study are available in the SRA repository, under accession number SRP151591.. - https://doi.org/10.. - Isolation of new White collar mutants of Neurospora crassa and studies on their behavior in the blue light-induced formation of protoperithecia. - https://doi.org/10.1128/mcb . - https://doi.. - https://doi.org/10.1074/jbc . - The blue-light photoreceptor Sfwc-1 gene regulates the phototropic response and fruiting-body development in the homothallic ascomycete Sordaria fimicola. - https://doi.org/. - org/10.1007/s . - The fast-evolving phy-2 gene modulates sexual development in response to light in the model fungus Neurospora crassa. - Tailor-made CRISPR/Cas system for highly efficient targeted gene replacement in the rice blast fungus. - Light-driven diurnal zonation in the filamentous fungus Fusarium solani. - https://doi.org . - https://doi.org/10.5423/PPJ . - Factors determining the severity of epidemics of Mycosphaerella graminicola (Septoria tritici) on winter wheat in the UK. - https://doi.org/10.1111/j tb02674.x.. - Risk assessment studies on succinate dehydrogenase inhibitors, the new weapons in the battle to control Septoria leaf blotch in wheat. - The ZtvelB gene is required for vegetative growth and sporulation in the wheat pathogen Zymoseptoria tritici.. - https://doi.org/10.3389/fmicb . - Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. - https://doi.org/10.1111/j x.. - https://doi.org/10.1073/pnas . - MgHog1 regulates dimorphism and pathogenicity in the fungal wheat pathogen Mycosphaerella graminicola. - Quantitative trait locus mapping of melanization in the plant pathogenic fungus Zymoseptoria tritici. - https://doi.org/10.1534/. - https://doi.org/10.1093/nar/gkv1248.. - In silico prediction and characterization of secondary metabolite biosynthetic gene clusters in the wheat pathogen Zymoseptoria tritici. - https://doi.org/10.1186/s y.. - https://doi.org/10.1093/nar/gku1221.. - Light regulation of asexual development in the rice blast fungus, Magnaporthe oryzae. - https://doi.org/10.1021/bi00167a001.. - https://doi.org/10.1104/pp . - An aspartic proteinase gene family in the filamentous fungus Botrytis cinerea contains members with novel features. - https://doi.org/10.1104/pp.. - https://doi.org/10.1093/. - https://doi.org/10.1109/TCBB
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