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138 results for “Neurospora”
Genotypes for Neurospora nested association mapping population
<p>Genotype file that contains genotypes all the Neurospora association mapping population developed in Kronholm lab. See https://github.com/ikron/Neurospora_NAM_population</p> <p>The file is a tab-delimited text file in hapmap format and contains first contains the columns: rs alleles chrom pos strand assembly center protLSID assayLSID panel GCcode and then the subsequent columns are strains identifiers. The column 'rs' is the name of the SNP, column 'alleles' shows which two alternative bases occur, the column 'chrom' is the chromosome, column 'pos' is the coordinate, columns 'strand', 'center', 'protLSID', 'assayLSID', 'panel' and 'GCcode' contain all missing data. They are included for hapmap format compatibility. The column 'assembly' indicates the version of the Neurospora crassa reference genome that the coordinates are based on. And in this case it is NC12 for all SNPs.</p> <p>Missing data is indicated by 'N'</p>
Adaptation to starvation requires a flexible circadian clockwork in Neurospora crassa (RNAseq)
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Data from: Quantitative genetics of temperature performance curves of Neurospora crassa
Earth's temperature is increasing due to anthropogenic CO<sub>2</sub> emissions; and organisms need either to adapt to higher temperatures, migrate into colder areas, or face extinction. Temperature affects nearly all aspects of an organism's physiology via its influence on metabolic rate and protein structure, therefore genetic adaptation to increased temperature may be much harder to achieve compared to other abiotic stresses. There is still much to be learned about the evolutionary potential for adaptation to higher temperatures, therefore we studied the quantitative genetics of growth rates in different temperatures that make up the thermal performance curve of the fungal model system <i>Neurospora crassa</i>. We studied the amount of genetic variation for thermal performance curves and examined possible genetic constraints by estimating the <b>G</b>-matrix. We observed a substantial amount of genetic variation for growth in different temperatures, and most genetic variation was for performance curve elevation. Contrary to common theoretical assumptions, we did not find strong evidence for genetic trade-offs for growth between hotter and colder temperatures. We also simulated short term evolution of thermal performance curves of <i>N. crassa</i>, and suggest that they can have versatile responses to selection.
Fig. 4 in Neuropyrones A-E, five undescribed α-pyrone derivatives with tyrosinase inhibitory activity from the endophytic fungus Neurospora dictyophora WZ-497
Fig. 4. Ligand interaction map of the predicted binding mode of 3, and 3D molecular modeling interaction of the 3 in the binding site of the tyrosinase (PDB ID: 2Y9X).
Data from: Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta
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Data from: Quantitative genetics of temperature performance curves of Neurospora crassa
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Data from: Beyond animals and plants: dynamic maternal effects in the fungus Neurospora crassa
Maternal effects are widely documented in animals and plants, but not in fungi or other eukaryotes. A principal cause of maternal effects is asymmetrical parental investment in a zygote, creating greater maternal versus paternal influence on offspring phenotypes. Asymmetrical investments are not limited to animals and plants, but are also prevalent in fungi and groups including apicomplexans, dinoflagellates, and red algae. Evidence suggesting maternal effects among fungi is sparse and anecdotal. In an experiment designed to test for maternal effects across sexual reproduction in the model fungus Neurospora crassa, we measured offspring phenotypes from crosses of all possible pairs of 22 individuals. Crosses encompassed reciprocals of 11 mating-type "A" and 11 mating-type "a" wild strains. After controlling for the genetic and geographic distances between strains in any individual cross, we found strong evidence for maternal control of perithecia (sporocarp) production, as well as maternal effects on spore numbers and spore germination. However, both parents exert equal influence on the percentage of spores that are pigmented, and size of pigmented spores. We propose a model linking the stage-specific presence or absence of maternal effects to cellular developmental processes: effects appear to be mediated primarily through the maternal cytoplasm, and, after spore cell walls form, maternal influence on spore development is limited. Maternal effects in fungi, thus far largely ignored, are likely to shape species' evolution and ecologies. Moreover, the association of anisogamy and maternal effects in a fungus suggests maternal effects may also influence the biology of other anisogamous eukaryotes.
Data from: Neurospora and the dead-end hypothesis: genomic consequences of selfing in the model genus.
It is becoming increasingly evident that adoption of different reproductive strategies, such as sexual selfing and asexuality, greatly impacts genome evolution. In this study, we test theoretical predictions on genomic maladaptation of selfing lineages using empirical data from the model fungus Neurospora. We sequenced the genomes of four species representing distinct transitions to selfing within the history of the genus, as well as the transcriptome of one of these, and compared with available data from three outcrossing species. Our results provide evidence for a relaxation of purifying selection in protein-coding genes and for a reduced efficiency of transposable element silencing by Repeat Induced Point mutation. A reduction in adaptive evolution was also identified in the form of reduced codon usage bias in highly expressed genes of selfing Neurospora, but this result may be confounded by mutational bias. Potentially counteracting these negative effects, the nucleotide substitution rate and the spread of transposons is reduced in selfing species. We suggest that differences in substitution rate relate to the absence of the asexual pathway producing conidia in selfing Neurospora. Our results support the dead-end theory and show that Neurospora genomes bear signatures of both sexual and asexual reproductive mode.
Data from: Regular bottlenecks and restrictions to somatic fusion prevent the accumulation of mitochondrial defects in Neurospora
The replication and segregation of the multi-copy mitochondrial DNA (mtDNA) are not under strict control of the nuclear DNA. Within-cell selection may thus favour variants with an intracellular selective advantage but a detrimental effect on cell fitness. High relatedness among the mtDNA variants of an individual is predicted to disfavour such deleterious selfish genetic elements, but experimental evidence for this hypothesis is scarce. We studied the effect of mtDNA relatedness on the opportunities for suppressive mtDNA variants in the fungus Neurospora carrying the mitochondrial mutator plasmid pKALILO (pKAL). During growth, this plasmid integrates into the mitochondrial genome, generating suppressive mtDNA variants. These mtDNA variants gradually replace the wild-type mtDNA, ultimately culminating in growth arrest and death. We show that regular sequestration of mtDNA variation is required for effective selection against suppressive mtDNA variants. First, bottlenecks in the number of mtDNA copies from which a 'Kalilo' culture started significantly increased the maximum lifespan and variation in life span among cultures. Second, restrictions to somatic fusion among fungal individuals, either by using anastomosis-deficient mutants or by generating allotype diversity, prevented the accumulation of suppressive mtDNA variants. We discuss the implications of these results for the somatic accumulation of mitochondrial defects during ageing.
Data from: Multilevel selection in the filamentous ascomycete Neurospora tetrasperma
The history of life has been driven by evolutionary transitions in individuality, i.e., the aggregation of autonomous individuals to form a new, higher-level individual. The fungus Neurospora tetrasperma has recently undergone an evolutionary transition in individuality from homokaryosis (one single type of nuclei in the same cytoplasm) to heterokaryosis (two genetically divergent and free-ranging nuclear types). In this species, selection can act at different levels: while nuclei can compete in their replication and transmission into short-lived asexual spores, at the level of the heterokaryotic individual cooperation between nuclear types is required to produce the long-lived sexual spores. Conflicts can arise between these two levels of selection if the coevolution between nuclear types is disrupted. Here, we investigated the extent of multilevel selection in three strains of N. tetrasperma. We assessed the ratio between nuclear types under different conditions, and measured fitness traits of homo- and heterokaryotic mycelia with varying nuclear ratios. We show that the two nuclei have complementary traits, consistent with division of labor and cooperation. In one strain, for which a recent chromosomal introgression was detected, we observed the occurrence of selfish nuclei, enjoying better replication and transmission than sister nuclei at the same time as being detrimental to the heterokaryon. We hypothesize that introgression has disrupted the coevolution between nuclear types in this strain.
Data from: Introgression maintains the genetic integrity of the sex-determining chromosome of the fungus Neurospora tetrasperma
Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora tetrasperma, it has been proposed that this molecular degeneration is counteracted by the introgression of non-degenerated DNA from closely related species. In this study, we used comparative and population genomic analyses of variation among 92 genomes from eight phylogenetically and reproductively isolated lineages of N. tetrasperma, and its three closest relatives, to investigate the factors shaping the evolutionary history of the genomes. We found that suppressed recombination extends across at least 6 Mbp (~63%) of the mating-type (mat) chromosome in N. tetrasperma, and is associated with decreased genetic diversity, which is likely the result primarily of selection at linked sites. Furthermore, analyses of molecular evolution revealed an increased mutational load in this region, relative to recombining regions. However, comparative genomic and phylogenetic analyses indicate that the mat chromosomes are temporarily regenerated via introgression from sister species; six out of eight lineages show introgression into one of their mat chromosomes, with at least three other Neurospora species acting as donors. The introgressed tracts have been driven to fixation in lineages, suggesting that they confer an adaptive advantage in natural populations, and our analyses support the presence of selective sweeps in at least one of the lineages. Thus, these data strongly support the previously hypothesized role of introgression as a mechanism for the maintenance of mating-type determining chromosomal regions.
Data from: Effects of acclimation time and epigenetic mechanisms on growth of Neurospora in fluctuating environments
Reaction norms or tolerance curves have often been used to predict how organisms deal with fluctuating environments. A potential drawback is that reaction norms measured in different constant environments may not capture all aspects of organismal responses to fluctuating environments. We examined growth of the filamentous fungus Neurospora crassa in fluctuating temperatures and tested if growth in fluctuating temperatures can be explained simply by growth in different constant temperatures or if more complex models are needed. In addition, as previous studies on fluctuating environments have revealed that past temperatures that organisms have experienced can affect their response to current temperature, we tested the roles of different epigenetic mechanisms in response to fluctuating environments using different mutants. We found that growth of Neurospora can be predicted in fluctuating temperatures to some extent if acclimation times are taken into account in the model. Interestingly, while fluctuating environments have been linked with epigenetic responses we found only some evidence of involvement of epigenetic mechanisms on tolerating fluctuating temperatures. Mutants which lacked H3K4 or H3K36 methylation had slightly impaired response to temperature fluctuations, in addition the H3K4 methylation mutant and a mutant in the RNA interference pathway had altered acclimation times.
Fig. 3 in Neuropyrones A-E, five undescribed α-pyrone derivatives with tyrosinase inhibitory activity from the endophytic fungus Neurospora dictyophora WZ-497
Fig. 3. The inhibitory effects of 1–5 on tyrosinase.
Fig. 2. Key 1 H– 1 H in Neuropyrones A-E, five undescribed α-pyrone derivatives with tyrosinase inhibitory activity from the endophytic fungus Neurospora dictyophora WZ-497
Fig. 2. Key 1 H– 1 H COSY and HMBC correlations of neuropyrones A–E (1–5).
Fig. 1 in Neuropyrones A-E, five undescribed α-pyrone derivatives with tyrosinase inhibitory activity from the endophytic fungus Neurospora dictyophora WZ-497
Fig. 1. Chemical structures of neuropyrones A–E (1–5).
Data from: Introgression maintains the genetic integrity of the sex-determining chromosome of the fungus Neurospora tetrasperma
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Data from: Neurospora and the dead-end hypothesis: genomic consequences of selfing in the model genus.
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Data from: Regular bottlenecks and restrictions to somatic fusion prevent the accumulation of mitochondrial defects in Neurospora
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Data from: Multilevel selection in the filamentous ascomycete Neurospora tetrasperma
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Data from: Evidence of the accumulation of allele-specific non-synonymous substitutions in the young region of recombination suppression within the mating-type chromosomes of Neurospora tetrasperma
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