The evolutionary trajectory of the mating-type (mat) genes in Neurospora relates to reproductive behavior of taxa

<p>Abstract</p> <p>Background</p> <p>Comparative sequencing studies among a wide range of taxonomic groups, including fungi, have led to the discovery that reproductive genes evolve more rapidly than other genes. However, for fungal reproductive genes the question has remained whether the rapid evolution is a result of stochastic or deterministic processes. The mating-type (<it>mat</it>) genes constitute the master regulators of sexual reproduction in filamentous ascomycetes and here we present a study of the molecular evolution of the four <it>mat</it>-genes (<it>mat a-1</it>, <it>mat A-1</it>, <it>mat A-2 </it>and <it>mat A-3</it>) of 20 <it>Neurospora </it>taxa.</p> <p>Results</p> <p>We estimated nonsynonymous and synonymous substitution rates of genes to infer their evolutionary rate, and confirmed that the <it>mat</it>-genes evolve rapidly. Furthermore, the evolutionary trajectories are related to the reproductive modes of the taxa; likelihood methods revealed that positive selection acting on specific codons drives the diversity in heterothallic taxa, while among homothallic taxa the rapid evolution is due to a lack of selective constraint. The latter finding is supported by presence of stop codons and frame shift mutations disrupting the open reading frames of <it>mat a-1</it>, <it>mat A-2 </it>and <it>mat A-3 </it>in homothallic taxa. Lower selective constraints of <it>mat</it>-genes was found among homothallic than heterothallic taxa, and comparisons with non-reproductive genes argue that this disparity is not a nonspecific, genome-wide phenomenon.</p> <p>Conclusion</p> <p>Our data show that the <it>mat</it>-genes evolve rapidly in <it>Neurospora</it>. The rapid divergence is due to either adaptive evolution or lack of selective constraints, depending on the reproductive mode of the taxa. This is the first instance of positive selection acting on reproductive genes in the fungal kingdom, and illustrates how the evolutionary trajectory of reproductive genes can change after a switch in reproductive behaviour of an organism.</p

Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies

A large portion of nuclear DNA is composed of transposable element (TE) sequences, whose transposition is controlled by diverse host defense strategies in order to maintain genomic integrity. One such strategy is the fungal-specific Repeat-Induced Point mutation (RIP) that hyper-mutates repetitive DNA sequences. While RIP is found across Fungi, it has been shown to vary in efficiency. The filamentous ascomycete Neurospora crassa has been a pioneer in the study of RIP, but data on TEs and RIP from other species in the genus is limited. In this study, we investigated 18 nearly gapless genome assemblies of ten Neurospora species, which diverged from a common ancestor about 7 MYA, to determine and compare genome-wide TE distribution and their associated RIP patterns. Four of these assemblies, generated by PacBio technology, represent new genomic datasets. We showed that the TE contents between 8.7-18.9% covary with genome sizes that range between 37.8-43.9 Mb. Degraded copies of Long Terminal Repeat (LTR) retrotransposons were abundant among the identified TEs, and these are distributed across the genome at varying frequencies. In all investigated Neurospora genomes, TE sequences had signs of numerous C-to-T substitutions, suggesting that RIP occurred in all species, and accordingly, RIP signatures correlated with TE-dense regions in all genomes. In conclusion, essentially gapless genome assemblies allowed us to identify TEs in Neurospora genomes, and reveal that TEs contribute to genome size variation in this group. Our study suggests that TEs and RIP are highly correlated in each examined Neurospora species, and hence, the pattern of interaction is conserved over the investigated evolutionary timescale. Finally, with our results, we verify that RIP signatures can be used to facilitate the identification of TE-rich region in the genome. The comprehensive genomic dataset of Neurospora is a rich resource for further in-depth analyses of fungal genomes by the community

The Plot Thickens: Haploid and Triploid-Like Thalli, Hybridization, and Biased Mating Type Ratios in Letharia

The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in Letharia. Here, we infer the genome organization and reproduction in Letharia by analyzing genomic data from a pure culture and from thalli, and performing a PCR survey of the MAT locus in natural populations. We found that the read count variation in the four Letharia specimens, including the pure culture derived from a single sexual spore of L. lupina, is consistent with haploidy. By contrast, the L. lupina read counts from a thallus' metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America for L. vulpina and L. lupina, suggesting widespread sexual reproduction, but highly skewed in Europe for L. vulpina, consistent with predominant asexuality. Taken together, we propose that Letharia fungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are hybrids between L. lupina and an unknown Letharia lineage, reconciling classic systematic and genetic studies with recent genomic observations

In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies

Morphological characters and nuclear ribosomal DNA (rDNA) phylogenies have so far been the basis of the current classifications of arbuscular mycorrhizal (AM) fungi. Improved understanding of the evolutionary history of AM fungi requires extensive ortholog sampling and analyses of genome and transcriptome data from a wide range of taxa. To circumvent the need for axenic culturing of AM fungi we gathered and combined genomic data from single nuclei to generate de novo genome assemblies covering seven families of AM fungi. We successfully sequenced the genomes of 15 AM fungal species for which genome data was not previously available. Comparative analysis of the previously published Rhizophagus irregularis DAOM197198 assembly confirm that our novel workflow generates genome assemblies suitable for phylogenomic analysis. Predicted genes of our assemblies, together with published protein sequences of AM fungi and their sister clades, were used for phylogenomic analyses. We evaluated the phylogenetic placement of Glomeromycota in relation to its sister phyla (Mucoromycota and Mortierellomycota), and found no support to reject a polytomy. Finally, we explored the phylogenetic relationships within Glomeromycota. Our results support family level classification from previous phylogenetic studies, and the polyphyly of the order Glomerales with Claroideoglomeraceae as the sister group to Glomeraceae and Diversisporales

The Mating-Type Chromosome in the Filamentous Ascomycete Neurospora tetrasperma Represents a Model for Early Evolution of Sex Chromosomes

We combined gene divergence data, classical genetics, and phylogenetics to study the evolution of the mating-type chromosome in the filamentous ascomycete Neurospora tetrasperma. In this species, a large non-recombining region of the mating-type chromosome is associated with a unique fungal life cycle where self-fertility is enforced by maintenance of a constant state of heterokaryosis. Sequence divergence between alleles of 35 genes from the two single mating-type component strains (i.e. the homokaryotic mat A or mat a-strains), derived from one N. tetrasperma heterokaryon (mat A+mat a), was analyzed. By this approach we were able to identify the boundaries and size of the non-recombining region, and reveal insight into the history of recombination cessation. The non-recombining region covers almost 7 Mbp, over 75% of the chromosome, and we hypothesize that the evolution of the mating-type chromosome in this lineage involved two successive events. The first event was contemporaneous with the split of N. tetrasperma from a common ancestor with its outcrossing relative N. crassa and suppressed recombination over at least 6.6 Mbp, and the second was confined to a smaller region in which recombination ceased more recently. In spite of the early origin of the first “evolutionary stratum”, genealogies of five genes from strains belonging to an additional N. tetrasperma lineage indicate independent initiations of suppressed recombination in different phylogenetic lineages. This study highlights the shared features between the sex chromosomes found in the animal and plant kingdoms and the fungal mating-type chromosome, despite fungi having no separate sexes. As is often found in sex chromosomes of plants and animals, recombination suppression of the mating-type chromosome of N. tetrasperma involved more than one evolutionary event, covers the majority of the mating-type chromosome and is flanked by distal regions with obligate crossovers

Localization and broadband follow-up of the gravitational-wave transient GW150914

A gravitational-wave (GW) transient was identified in data recorded by the Advanced Laser Interferometer Gravitational-wave Observatory (LIGO) detectors on 2015 September 14. The event, initially designated G184098 and later given the name GW150914, is described in detail elsewhere. By prior arrangement, preliminary estimates of the time, significance, and sky location of the event were shared with 63 teams of observers covering radio, optical, near-infrared, X-ray, and gamma-ray wavelengths with ground- and space-based facilities. In this Letter we describe the low-latency analysis of the GW data and present the sky localization of the first observed compact binary merger. We summarize the follow-up observations reported by 25 teams via private Gamma-ray Coordinates Network circulars, giving an overview of the participating facilities, the GW sky localization coverage, the timeline, and depth of the observations. As this event turned out to be a binary black hole merger, there is little expectation of a detectable electromagnetic (EM) signature. Nevertheless, this first broadband campaign to search for a counterpart of an Advanced LIGO source represents a milestone and highlights the broad capabilities of the transient astronomy community and the observing strategies that have been developed to pursue neutron star binary merger events. Detailed investigations of the EM data and results of the EM follow-up campaign are being disseminated in papers by the individual teams

Growth And The Growth Hormone-Insulin Like Growth Factor 1 Axis In Children With Chronic Inflammation:Current Evidence, Gaps In Knowledge And Future Directions

Growth failure is frequently encountered in children with chronic inflammatory conditions like juvenile idiopathic arthritis, inflammatory bowel disease and cystic fibrosis. Delayed puberty and attenuated pubertal growth spurt is often seen during adolescence. The underlying inflammatory state mediated by pro-inflammatory cytokines, prolonged use of glucocorticoid and suboptimal nutrition contribute to growth failure and pubertal abnormalities. These factors can impair growth by their effects on the growth hormone-insulin like growth factor axis and also directly at the level of the growth plate via alterations in chondrogenesis and local growth factor signaling. Recent studies on the impact of cytokines and glucocorticoid on the growth plate studies further advanced our understanding of growth failure in chronic disease and provided a biological rationale of growth promotion. Targeting cytokines using biologic therapy may lead to improvement of growth in some of these children but approximately one third continue to grow slowly. There is increasing evidence that the use of relatively high dose recombinant human growth hormone may lead to partial catch up growth in chronic inflammatory conditions, although long term follow-up data is currently limited. In this review, we comprehensively review the growth abnormalities in children with juvenile idiopathic arthritis, inflammatory bowel disease and cystic fibrosis, systemic abnormalities of the growth hormone-insulin like growth factor axis and growth plate perturbations. We also systematically reviewed all the current published studies of recombinant human growth hormone in these conditions and discuss the role of recombinant human insulin like growth factor-1

Ecology of Daldinia spp. with special emphasis on Daldinia loculata

This thesis comprises studies on the xerophytic ascomycete genus Daldinia. By studying ecological, morphological and molecular characters of herbarium specimens, five distinct Daldinia species were identified from northern Europe: D. concentrica, D. fissa, D. grandis, D. loculata and D. petriniae. The last two mentioned have previously been referred to as D. concentrica in the literature. The distinct stromatal host-specificity of the three species: D. concentrica, D. loculata and D. petriniae was studied in an inoculation experiment. The results indicate that the observed substrate-specificity is not a result of enhanced wood-decaying capability in the substrate on which stromata are usually found. Reproducible PCR-based molecular markers were developed for the postfire species D. loculata by using available sequence data of nuclear genes from species closely related to D. loculata. Each marker spans over one or several introns and showed relatively high intraspecific variability. The genetic variation of D. loculata was studied both within and among forest sites. In a local population structure study of D. loculata in burned birches, we found that it can establish endophytically in sound-looking wood of living trees, most probably by sexual ascospores. In birches killed by forest fire, each haploid genet occupied an extensive volume of wood. Multilocus genotyping of vegetative mycelia and offspring of the attached stromata indicated multiple matings of the relatively large vegetative mycelia in wood by several other, very small, genets. The genetic structure of six Fennoscandian and one Kamchatkan D. loculata subpopulation was studied in order to reveal any differentiation on a continental scale. Low levels of genetic differentiation among the Eurasian subpopulations of D. loculata were found, and the differentiation did not increase with distance; the Kamchatkan subpopulation, sampled more than 7000 km from the Fennoscandian subpopulations, was only moderately differentiated from the others. These results suggest that D. loculata consists of a large, coherent Eurasian population of latent mycelia in unburned forests, established by ascospores dispersed from scattered burned forest sites. A tentative life cycle of D. loculata is present

TIVOLI I DEN NYA STADEN - Folkliga kulturvärden i en förändrad stadsbild

This essay examines how ideas that guide current city planning affects traveling fairs and the so called tivoli tradition and its representatives in Sweden. The analysed material includes qualitative interviews with tivoli representatives and one person working with city planning. But also live digital events and a central dokument in city planning in Gothenburg called ”Vision Älvstaden”. Using the logical perspektive, a subtheory to political discourse theory, in combination with other relevant concepts related to space and tradition, we shed light on how current processes related to city planning often come in conflict with the tivoli and traveling fair line of business. By examining articulations we also show how the two parties construct different meanings in relation to the use of space in the Swedish cities. Although this is the case we also show how their goals and wills sometimes align with each other and that a large part of the issue actually lies in the city planners having to take into account a lot of other perspectives. Perspectives such as environmental factors, the will of different actors, and the question of how to make room for all types of cultural expressions and traditions at the same time. This makes it hard for the tradition to make itself visible and to be included in the planning processes