Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 Genome

The DNA sequences of chromosomes I and II of Rhodobacter sphaeroides strain 2.4.1 have been revised, and the annotation of the entire genomic sequence, including both chromosomes and the five plasmids, has been updated. Errors in the originally published sequence have been corrected, and ∼11% of the coding regions in the original sequence have been affected by the revised annotation

High phenotypic and genotypic plasticity among strains of the mushroom-forming fungus Schizophyllum commune

Schizophyllum commune is a mushroom-forming fungus notable for its distinctive fruiting bodies with split gills. It is used as a model organism to study mushroom development, lignocellulose degradation and mating type loci. It is a hypervariable species with considerable genetic and phenotypic diversity between the strains. In this study, we systematically phenotyped 16 dikaryotic strains for aspects of mushroom development and 18 monokaryotic strains for lignocellulose degradation. There was considerable heterogeneity among the strains regarding these phenotypes. The majority of the strains developed mushrooms with varying morphologies, although some strains only grew vegetatively under the tested conditions. Growth on various carbon sources showed strain-specific profiles. The genomes of seven monokaryotic strains were sequenced and analyzed together with six previously published genome sequences. Moreover, the related species Schizophyllum fasciatum was sequenced. Although there was considerable genetic variation between the genome assemblies, the genes related to mushroom formation and lignocellulose degradation were well conserved. These sequenced genomes, in combination with the high phenotypic diversity, will provide a solid basis for functional genomics analyses of the strains of S. commune

O poder e a luta pela propriedade da terra no vale do rio Iconha/Piúma: o caso Thomaz Dutton Junior (1870-1906)

Ao chegar ao povoado de Piúma, região sul capixaba, por volta dos anos iniciais da década de 1870, Thomaz Dutton Junior, inglês de nascimento e mais tarde naturalizado brasileiro, desejava fazer parte da boa sociedade e ter direito a todas as prerrogativas que o grupo proporcionaria. No território de Piúma, adquiriu boa parte da massa falida de João Baptista Rodocanachi, um comerciante grego de grosso trato que explorava madeiras de lei e as comercializava para construção civil e naval. Na fazenda Monte Bello, após instalar colonos ingleses, Thomaz Dutton se envolveu em querelas jurídico-fundiárias com mandões do lugar com quem tinha relações interdependentes, sobretudo com Alexandrino Pires Martins e José Gonçalves Costa Beiriz, que ocultavam, ao fim e ao cabo, um complexo jogo por disputas políticas locais, por prestígio, por boa reputação e poder. No seio dessas disputas estava a propriedade da terra, símbolo de poder e mando, que o levou à insolvência. Este estudo investiga a trajetória de Thomaz Dutton, pautando-se na teoria da Configuração de Norbert Elias associada à teoria do Poder Simbólico de Pierre Bourdier. Objetiva compreender a maneira como as práticas do poder são materializadas nas relações sociais, identificando a aprendizagem extraída de relações interdependentes bem como os valores construídos a partir delas. Parte de análises de fontes documentais, como relatórios presidenciais provinciais, requerimentos, atas, cartas e artigos de jornais corpus documental, dominante nesta investigação , buscando vestígios no conteúdo dos discursos ali inseridos para poder descortinar as tramas do tecido social com lentes de objetivas aumentadas. Desse modo, torna possível trazer à tona a história local do território do vale do Iconha/Piúma no espaço de tempo entre 1870 e 1906 e assim expor suas particularidades e singularidades, inserindo-a no contexto da história regional capixaba e nacional. Destarte, usando o alicerce teórico-metodológico já apresentado, destaca as particularidades e feitos do passado da sociedade piumense que ainda estavam fora do campo de experiência e precisavam ser conhecidas para fazer parte da História do Espírito Santo

Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants

As decomposers, fungi are key players in recycling plant material in global carbon cycles. We hypothesized that genomes of early diverging fungi may have inherited pectinases from an ancestral species that had been able to extract nutrients from pectin-containing land plants and their algal allies (Streptophytes). We aimed to infer, based on pectinase gene expansions and on the organismal phylogeny, the geological timing of the plant–fungus association. We analyzed 40 fungal genomes, three of which, including Gonapodya prolifera, were sequenced for this study. In the organismal phylogeny from 136 housekeeping loci, Rozella diverged first from all other fungi. Gonapodya prolifera was included among the flagellated, predominantly aquatic fungal species in Chytridiomycota. Sister to Chytridiomycota were the predominantly terrestrial fungi including zygomycota I and zygomycota II, along with the ascomycetes and basidiomycetes that comprise Dikarya. The Gonapodya genome has 27 genes representing five of the seven classes of pectin-specific enzymes known from fungi. Most of these share a common ancestry with pectinases from Dikarya. Indicating functional and sequence similarity, Gonapodya, like many Dikarya, can use pectin as a carbon source for growth in pure culture. Shared pectinases of Dikarya and Gonapodya provide evidence that even ancient aquatic fungi had adapted to extract nutrients from the plants in the green lineage. This implies that 750 million years, the estimated maximum age of origin of the pectin-containing streptophytes represents a maximum age for the divergence of Chytridiomycota from the lineage including Dikarya.Keywords: fungal phylogeny, carbohydrate active enzymes, streptophytes, geological time, Gonapodya, evolution, pectinasesKeywords: fungal phylogeny, carbohydrate active enzymes, streptophytes, geological time, Gonapodya, evolution, pectinase

The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8 Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identified 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebi to colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is confirmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were identified although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic.Keywords: Ion homeostasis, Aqua(glycero)porins, Solute accumulation, Electron microscopy, Xerophile, Halophil

Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus

White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.Peer reviewe

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild. Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.Peer reviewe

IMA genome-F18 The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1

SUPPLEMENTARY INFORMATION : Additional file 1. Table 1. Summary of genomes analysed during this study that were correctly identified.AVAILABILITY OF DATA AND MATERIAL : Genome data for the Penicillium genomes are publicly available in the NCBI genome database (https:// www. ncbi. nlm. nih. gov/ datas ets/ genome). The datasets generated from Trichoderma atroviride during the current study are available in the NCBI repository, https:// www. ncbi. nlm. nih. gov/ biopr oject/ 923860. For the Penicillium species from dry cured meat the genome assembly and annotations are available from JGI Fungal genome portal MycoCosm under JGI Projects: 1,289,827 (ITEM 15300), 1,289,819 (ITEM 18316), 1,289,903 (ITEM 18327), and have been deposited to GenBank under BioProjects: PRJNA970850 (ITEM 15300), PRJNA971651 (ITEM 18316), PRJNA970851 (ITEM 18327). Genome assembly and annotations are available from JGI Fungal genome portal MycoCosm under JGI Project Id 1,289,847 and has been deposited to GenBank under BioProject n.PRJNA971650 (BioSample n. SAMN35051277; Project Accession n. SRP442271). The genomic sequences of T. carnegiei have been deposited at DDJ/EMBL/GenBank under the accession JANYMD000000000. This paper describes the first version. The genomes of the Pewenomyces species have been deposited in the NCBI genome database.Sequencing fungal genomes has now become very common and the list of genomes in this manuscript reflects this. Particularly relevant is that the first announcement is a re-identification of Penicillium genomes available on NCBI. The fact that more than 100 of these genomes have been deposited without the correct species names speak volumes to the fact that we must continue training fungal taxonomists and the importance of the International Mycological Association (after which this journal is named). When we started the genome series in 2013, one of the essential aspects was the need to have a phylogenetic tree as part of the manuscript. This came about as the result of a discussion with colleagues in NCBI who were trying to deal with the very many incorrectly identified bacterial genomes (at the time) which had been submitted to NCBI. We are now in the same position with fungal genomes. Sequencing a fungal genome is all too easy but providing a correct species name and ensuring that the fungus has in fact been correctly identified seems to be more difficult. We know that there are thousands of fungi which have not yet been described. The availability of sequence data has made identification of fungi easier but also serves to highlight the need to have a fungal taxonomist in the project to make sure that mistakes are not made.Trichoderma atroviride SC1 genome sequencing was funded by the Ministerstvo Školství, Mládeže a Tělovýchovy and by the Internal Grant of Mendel University in Brno. The work on Penicillium species from dry cured meat is supported by the Office of Science of the U.S. Department of Energy. US Department of Energy Joint Genome Institute are supported by the Office of Science of the US Department of Energy. Funding for the project on the T. carnegiei and the Pewenomyces species genomes was provided by Department of Science and Innovation (DSI)-National Research Foundation (NRF) Centre of Excellence in Plant Health Biotechnology (CPHB), South Africa and the DST-NRF SARChI chair in Fungal Genomics.https://imafungus.biomedcentral.comam2024BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyPlant Production and Soil ScienceSDG-15:Life on lan