Rapid evolution in fungal reproductive genes as revealed by evolutionary analyses of expressed sequence tags in Neurospora
Ontology highlight
ABSTRACT:
ORGANISM(S): Neurospora intermedia
SUBMITTER: Nicklas Samils
PROVIDER: E-GEOD-37034 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Neurospora tetrasperma is a pseudohomothallic filamentous ascomycete with a large (~ 7 Mbp) region of suppressed recombination surrounding its mating-type (mat) locus. The suppressed recombination has lead to sequence divergence between the two mating-type chromosomes of wild-type heterokaryotic strains, while the remaining genome is largely homoallelic. In this study, we use microarray technology to manifest expression divergence linked to mating type in N. tetrasperma. N. tetrasperma and N. crassa, were grown on agar regimes inducing sexual growth (Synthetic Crossing medium) and vegetative growth (Vogel's Medium), respectively. [SC]: Neurospora tetrasperma mat-A FGSC#1270; mat-a FGSC#1271; Mat-A FGSC#9033; mat-a FGSC#9034; N. crassa mat-A FGSC#2489 and mat-a FGSC 4200: Synthetic Crossing medium was used as a nutrient regime before sampling and processing [Veg]: Neurospora tetrasperma mat-A FGSC#1270; mat-a FGSC#1271; Mat-A FGSC#9033; mat-a FGSC#9034; N. crassa mat-A FGSC#2489 and mat-a FGSC 4200: Vogel's Medium (Vegetative Medium) was used as a nutrient regime before sampling and processing
2011-01-26 | E-GEOD-26798 | biostudies-arrayexpress
Project description:Neurospora intermedia is a heterothallic filamentous ascomycete. In this study we use microarray technology to study the difference in gene expression between vegetative growth and early reproductive development.
2012-04-05 | GSE37034 | GEO
Project description:It is widely assumed that sex-determination loci have little impact upon dominant stage in the life history of filamentous fungi, asexual development. However, this hypothesis has not been thoroughly investigated. To investigate differences between mating types during asexual development, total RNA was sampled from otherwise largely isogenic Mat-A and Mat-a N. crassa strains at early, middle, and late clonal stages of development under a condition of constant light. Mating-type loci, pheromone precursor and receptor genes were assayed with real-time PCR. Mating loci were increasingly expressed during asexual development, and expression of pheromone precursors ccg-4 and mfa-1 and receptors pre-1 and pre-2 were detected in both mating types in all development stages. A circuit of microarray hybridizations of cDNA samples from all developmental stages was also performed. Gene expression for both mating types throughout vegetative development were characterized for developmental markers such as transcription factors, for genes related to conidiation, internal clock, cell division cycle, heat shock, and for light responsive genes. We observed significant differences in overall gene expression between the mating types across clonal development, especially at late development stages. The Mat-A genotype showed a higher expression level than Mat-a for many genes, and demonstrated greater transcriptional regulatory activity. Significant up-regulation of expression was observed for many late light responsive genes at late asexual development stages in both mating types. Further investigation of the impact of light and the roles of light response genes in asexual development in this fungus are warranted. Neurospora crassa mat A FGSC#2489 and mat-a FGSC 4200: Three developmental stages, 36hr, 60hr, 96 hr were sampled and compared
2011-06-06 | E-GEOD-26209 | biostudies-arrayexpress
Project description:Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development. Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences. Neurospora crassa mat A FGSC#2489 2 developmental stages and oligo(dT) primers.
2010-07-17 | E-GEOD-22972 | biostudies-arrayexpress
Project description:Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development. Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences. Neurospora crassa mat A FGSC#2489 Three developmental stages and two different primers used for reverse transcription: mycelium oligo(dT) M1 protoperithecia oligo(dT) PP1 perithecia oligo(dT) PT1 mycelium oligo(dT)+ Multi-Targeted Primer [MTP] (M2) protoperithecia oligo(dT)+ MTP (PP2) perithecia oligo(dT)+ MTP (PT2)
2010-07-03 | E-GEOD-22658 | biostudies-arrayexpress
Project description:A colony of fungus is comprised of long, branching filamentous cells called hyphae. Genetic mechanisms underlying the development of hyphae are poorly understood. We sectioned hyphae of a model fungus, Neurospora crassa (pink bread mold), into six parts depending on the age of the cells; 1 hour, 3 hour, 9 hour, 15 hour, 21 hour and 27 hour old, respectively. This data submission reflects an RNAseq analysis of mRNA extracted from the 1 hour time-point. 1 mycelial mRNA profile of 1 hour growth (hyphal tip) from Neurospora crassa strain FGSC 2489, Data was generated using Illumina GAIIx.
2013-08-28 | E-GEOD-50205 | biostudies-arrayexpress
Project description:Fungal fruiting body size and form are influenced by the ecology of the species, including diverse environmental stimuli. Accordingly, nutritional resources available to the fungus during development can be vital to successful production of fruiting bodies. To investigate the effect of nutrition, perithecial development of N. crassa was induced on two different media, a sparsely nutritive Synthetic Crossing Medium (SCM) and a natural Carrot Agar (CA). Protoperithecia were collected before crossing, and perithecia were collected at 2, 24, 48, 72, 96, 120, and at full maturity 144 hours after crossing. No differences in fruiting body morphology were observed between the two media at any time point. A circuit of microarray hybridizations comparing cDNA from all neighboring stages was performed. For a majority of differentially expressed genes, expression was higher in SCM than in CA, and expression of core metabolic genes was particularly affected. Effects of nutrition were highest in magnitude before crossing, lowering in magnitude during early perithecial development. Interestingly, metabolic effects of the media were also large in magnitude during late perithecial development, at which stage the lower expression in CA presumably reflected the continued intake of diverse complex initial compounds, diminishing the need for expression of anabolic pathways. However, for genes with key regulatory roles in sexual development, including pheromone precursor ccg-4 and poi2, expression patterns were similar between treatments. When possible, a common nutritional environment is ideal for comparing transcriptional profiles between different fungi. Nevertheless, the observed consistency of the developmental program across media, despite considerable metabolic differentiation is reassuring. This result facilitates comparative studies that will require different nutritional resources for sexual development in different fungi. Neurospora crassa mat A FGSC#2489 and mat-a FGSC 4200: Eight perithecial developmental stages, 0hr, 2 hr, 24 hr, 48 hr, 72 hr, 96 hr, 120 hr, and 144 hr were sampled and compared
2012-05-31 | E-GEOD-34436 | biostudies-arrayexpress
Project description:To determine the genes directly and indirectly under the control of the Grainy-head homolog (GHH) transcription factor in Neurospora crassa Three different sample types (Aerial Hyphae & Conidia; Mycelia; or Whole Colonies) of both wild-type (FGSC #2489) and grainy-head homolog (FGSC #13563) strains of Neurospora crassa were subjected to transcriptome analyses to determine the genes differentially expressed in the ghh background compared to wild type.
2012-03-01 | E-GEOD-35017 | biostudies-arrayexpress
Project description:Cytosine methylation of DNA is an important epigenetic gene silencing mechanism in plants, fungi, and animals. In the filamentous fungus Neurospora crassa, nearly all known DNA methylations occur in transposon relics and repetitive sequences, and DNA methylation does not depend on the canonical RNAi pathway. disiRNAs are Dicer-independent small non-coding RNAs that arise from gene-rich part of the Neurospora genome. Here we describe a new type of DNA methylation that is associated with the disiRNA loci. Unlike the known DNA methylation in Neurospora, disiRNA loci DNA methylation (DLDM) is highly dynamic and is regulated by an on/off mechanism. Surprisingly, some of the DLDM is independent of the known DNA methyltransferase. At least in disi47, disiRNA production appears to rely on pol II directed transcription. Importantly, DLDM is triggered by convergent transcription and enriched in promoter regions. Together, our results establish a new mechanism that triggers DNA methylation. Two small RNA library were generated from Neurospora wild type (FGSC4200) and wc-2 KO mutant
2013-08-01 | E-GEOD-47666 | biostudies-arrayexpress
Project description:Abstract BACKGROUND: Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in Saccharomyces cerevisiae and Schizosaccharomyces pombe; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus Podospora anserina serves as a model for understanding the basic features of mating-type control. Its mat+ and mat- mating types are determined by dissimilar allelic sequences. The mat- sequence contains three genes, designated FMR1, SMR1 and SMR2, while the mat+ sequence contains one gene, FPR1. FMR1 and FPR1 are the major regulators of fertilization, and this study presents a genome-wide view of their target genes and analyzes their target gene regulation. METHODOLOGY/PRINCIPAL FINDINGS: The transcriptomic profiles of the mat+ and mat- strains revealed 157 differentially transcribed genes, and transcriptomic analysis of fmr1(-) and fpr1(-) mutant strains was used to determine the regulatory actions exerted by FMR1 and FPR1 on these differentially transcribed genes. All possible combinations of transcription repression and/or activation by FMR1 and/or FPR1 were observed. Furthermore, 10 additional mating-type target genes were identified that were up- or down-regulated to the same level in mat+ and mat- strains. Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential for the sexual cycle. Interspecies comparisons of mating-type target genes revealed significant numbers of orthologous pairs, although transcriptional profiles were not conserved between species. CONCLUSIONS/SIGNIFICANCE: This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus. Mating-type transcription factors have many more target genes than are found in yeasts and exert a much greater diversity of regulatory actions on target genes, most of which are not directly related to mating.
2011-12-22 | GSE27297 | GEO