Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus <i>Amanita</i>

Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS) fungi from the genus Amanita as well as an AS outgroup to study genome evolution following a single origin of symbiosis. Our aim was to identify the defining features of EM genomes, but our analyses suggest no clear differentiation of genome size, gene repertoire size, or transposable element content between EM and AS species. Phylogenetic inference of gene gains and losses suggests the transition to symbiosis was dominated by the loss of plant cell wall decomposition genes, a confirmation of previous findings. However, the same dynamic defines the AS species A. inopinata, suggesting loss is not strictly associated with origin of symbiosis. Gene expansions in the common ancestor of EM Amanita were modest, but lineage specific and large gene family expansions are found in two of the three EM extant species. Even closely related EM genomes appear to share few common features. The genetic toolkit required for symbiosis appears already encoded in the genomes of saprotrophic species, and this dynamic may explain the pervasive, recurrent evolution of ectomycorrhizal associations

The draft genome sequence of the ascomycete fungus Penicillium subrubescens reveals a highly enriched content of plant biomass related CAZymes compared to related fungi

Here we report the genome sequence of the ascomycete saprobic fungus Penicillium subrubescens FBCC1632/CBS132785 isolated from a Jerusalem artichoke field in Finland. The 39.75 Mb genome containing 14,188 gene models is highly similar for that reported for other Penicillitun species, but contains a significantly higher number of putative carbohydrate active enzyme (CAZyme) encoding genes. (C) 2017 Elsevier B.V. All rights reserved.Peer reviewe

Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi

Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle

Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2

We report here the first genome sequence of the white-rot fungus Obba rivulosa (Polyporales, Basidiomycota), a polypore known for its lignin-decomposing ability. The genome is based on the homokaryon 3A-2 originating in Finland. The genome is typical in size and carbohydrate active enzyme (CAZy) content for wood-decomposing basidiomycetes.Peer reviewe

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

The MYST-Containing Protein Chameau Is Required for Proper Sensory Organ Specification during Drosophila Thorax Morphogenesis

The adult thorax of Drosophila melanogaster is covered by a stereotyped pattern of mechanosensory bristles called macrochaetes. Here, we report that the MYST containing protein Chameau (Chm) contributes to the establishment of this pattern in the most dorsal part of the thorax. Chm mutant pupae present extra-dorsocentral (DC) and scutellar (SC) macrochaetes, but a normal number of the other macrochaetes. We provide evidences that chm restricts the singling out of sensory organ precursors from proneural clusters and genetically interacts with transcriptional regulators involved in the regulation of achaete and scute in the DC and SC proneural cluster. This function of chm likely relies on chromatin structure regulation since a protein with a mutation in the conserved catalytic site fails to rescue the formation of supernumerary DC and SC bristles in chm mutant flies. This is further supported by the finding that mutations in genes encoding chromatin modifiers and remodeling factors, including Polycomb group (PcG) and Trithorax group (TrxG) members, dominantly modulate the penetrance of chm extra bristle phenotype. These data support a critical role for chromatin structure modulation in the establishment of the stereotyped sensory bristle pattern in the fly thorax

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter-and intraspecies genomic variation. We further predicted 17,903 carbohydrateactive enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.Peer reviewe

Etude du rôle de l' histone acétyl-transférase chameau de drosophile dans le développement des organes sensitifs et le contrôle de la signalisation hormonale

Les histones acetyl transférase sont une classe de protéines jouant un rôle primordial dans la modification de l'état de la structure chromatinienne. Leur capacité à réaliser des modifications post-traductionnelles des queues N-terminales d'histone contribue à l'élaboration du « code histone ». Son interprétation permet d'influer sur le recrutement de co-facteurs, l'activité des complexes de remodelage et la possibilité pour certaines d'être maintenues à travers les divisions cellulaires, mettant en évidence un mécanisme primordial dans le contrôle de l'expression des gènes. Le gène chm code pour l'une de ces protéines de la famille MYST. Découvert dans le laboratoire, son étude a révélé sa capacité à maintenir la transcription de gènes Hox, à moduler l'activité transcriptionnelle de Fos/Jun par l'acétylation de l'histone H4 aux loci des gènes cibles dans la voie de signalisation Jun N-terminal Kinase (JNK) et enfin de contrôler l'origine de réplication. Aux phénotypes majeurs des mutants zygotiques pour chm ; qui sont : un défaut de fermeture du thorax adulte et la mort au stade pupe pharate ; s'ajoute : l'apparition de soies sensorielles extra-numéraire en position dorsocentral et scutellaire, des phénotypes reliés à un défaut des voies hormonales (hormone juvénile, peptide insulinique) : anomalies lors de la métamorphose, accroissement de la susceptibilité aux stress durant le stade adulte. Mes travaux de thèse m'ont permis d'identifier la place de Chm dans la voie de régulation de la formation de cluster prérequis à l'apparition de soies sensorielles.The histone acetyltransferase (HAT) Chameau (Chm) plays in various epigenetic mechanisms of transcription control : maintenance of Hox gene transcription ; modulation of Fos/Jun transcriptional activity by histone H4 acetylation at target gene loci; control of replication origins. Here, I will discuss about a neural function of Chm, which acts in few brain neurosecretory neurons to control the activity of neurohaemal organs. Genetic evidences for a neuroendocrine function of Chm are the following. On the one hand, chm inactivation causes phenotypes suggesting hormonal signaling defects : null mutation prevents abdominal differentiation and hatching – correlated to an juvenile hormone (JH) excess - chm late inactivation allows the emergence of adults that are highly susceptible to different types of stress (starvation, oxidative, infections) – related to a defect in insulin signaling. On the other hand, these two phenotype classes are rescued by providing back Chm in 6 neurons of the pars lateralis (CA-LPs, which innervate the CA) during development, and in 12 neurons of pars intercerabralis (IPCs, which produce insulin-like peptides and innervate the CC/CA complex) in adult. DNA chip experiments showed that chm mutation affects 6 functional classes of genes (defined by ‘biological process' Gene Ontology term) : (i) neurotransmission, synaptic activity; ii) hormones, JH and ecdysone; iii) nutritional control; iv) oxidative stress; v) life span; vi) immune defense. These classes match perfectly the phenotypes described above. Furthermore a significant fraction of these genes are similarly affected by the mutation of chm and by the inactivation of CA-LPs and IPCs neurons