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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2

To investigate the evolutionary history of the recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China, a total of 70 genomes of virus strains from China and elsewhere with sampling dates between 24 December 2019 and 3 February 2020 were analyzed. To explore the potential intermediate animal host of the SARS-CoV-2 virus, we reanalyzed virome data sets from pangolins and representative SARS-related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood-mapping, and comparative analyses of the genomes. Additionally, based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10 -3 substitutions per site per year, respectively. Our results also revealed that the BetaCoV/bat/Yunnan/RaTG13/2013 virus was more similar to the SARS-CoV-2 virus than the coronavirus obtained from the two pangolin samples (SRR10168377 and SRR10168378). We also identified a unique peptide (PRRA) insertion in the human SARS-CoV-2 virus, which may be involved in the proteolytic cleavage of the spike protein by cellular proteases, and thus could impact host range and transmissibility. Interestingly, the coronavirus carried by pangolins did not have the RRAR motif. Therefore, we concluded that the human SARS-CoV-2 virus, which is responsible for the recent outbreak of COVID-19, did not come directly from pangolins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Integration of ultra-low coverage whole-genome sequences for reconstructing the evolutionary history of Galapagos giant tortoises

Genomic data from contemporary and historical samples often need to be coupled for evolutionary reconstructions of multitaxon complexes. However, the genetic data recovered from historical samples may result only in ultra-low coverage whole-genome sequences (ulcWGS; <0.15× depth), leading to inaccurate evolutionary inferences given a preponderance of missing data. Using the Galapagos giant tortoise radiation as a study system (Chelonoidis spp., composed of 13 extant and four extinct lineages), we assembled a novel methodological pipeline that removes potential noise introduced by the missing data and enhances the evolutionary signal from ulcWGS samples. We leveraged existing tools for phylogenomic placement (EPA-ng), population genomic structure (smartsnp) and admixture (Admixfrog, NGSadmix) to demonstrate that the evolutionary history of samples can be uncovered with sequencing depths as low as 0.008–0.139×. Importantly, these approaches do not use genotype imputation of the ulcWGS samples, which would require extensive reference datasets. Our application to two cases of extinct lineages of Galapagos giant tortoises, with and without references from the same lineage, demonstrates the general value of the approach. We confirm where the extinct lineages from San Cristóbal and Santa Fe islands fit into the Galapagos giant tortoise radiation, and that these lineages were evolutionarily distinct entities.

ancient DNA↗
DOE OSTI2024

Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis

The colonization of land and the diversification of terrestrial plants is intimately linked to the evolutionary history of their symbiotic fungal partners. Extant representatives of these fungal lineages include mutualistic plant symbionts, the arbuscular mycorrhizal (AM) fungi in Glomeromycota and fine root endophytes in Endogonales (Mucoromycota), as well as fungi with saprotrophic, pathogenic and endophytic lifestyles. These fungal groups separate into three monophyletic lineages but their evolutionary relationships remain enigmatic confounding ancestral reconstructions. Their taxonomic ranks are currently fluid. In this study, we recognize these three monophyletic linages as phyla, and use a balanced taxon sampling and broad taxonomic representation for phylogenomic analysis that rejects a hard polytomy and resolves Glomeromycota as sister to a clade composed of Mucoromycota and Mortierellomycota. Low copy numbers of genes associated with plant cell wall degradation could not be assigned to the transition to a plant symbiotic lifestyle but appears to be an ancestral phylogenetic signal. Both plant symbiotic lineages, Glomeromycota and Endogonales, lack numerous thiamine metabolism genes but the lack of fatty acid synthesis genes is specific to AM fungi. Many genes previously thought to be missing specifically in Glomeromycota are either missing in all analyzed phyla, or in some cases, are actually present in some of the analyzed AM fungal lineages, e.g. the high affinity phosphorus transporter Pho89. Based on a broad taxon sampling of fungal genomes we present a well-supported phylogeny for AM fungi and their sister lineages. We show that among these lineages, two independent evolutionary transitions to mutualistic plant symbiosis happened in a genomic background profoundly different from that known from the emergence of ectomycorrhizal fungi in Dikarya. These results call for further reevaluation of genomic signatures associated with plant symbiosis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evolutionary History of Plant Metabolism

Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO 2 and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.

Plant Sciences↗
DOE OSTI2022

Biomineralization: Integrating mechanism and evolutionary history

Calcium carbonate (CaCO 3 ) biomineralizing organisms have played major roles in the history of life and the global carbon cycle during the past 541 Ma. Both marine diversification and mass extinctions reflect physiological responses to environmental changes through time. An integrated understanding of carbonate biomineralization is necessary to illuminate this evolutionary record and to understand how modern organisms will respond to 21st century global change. Biomineralization evolved independently but convergently across phyla, suggesting a unity of mechanism that transcends biological differences. In this review, we combine CaCO 3 skeleton formation mechanisms with constraints from evolutionary history, omics, and a meta-analysis of isotopic data to develop a plausible model for CaCO 3 biomineralization applicable to all phyla. The model provides a framework for understanding the environmental sensitivity of marine calcifiers, past mass extinctions, and resilience in 21st century acidifying oceans. Thus, it frames questions about the past, present, and future of CaCO 3 biomineralizing organisms.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily

Abstract Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

The genomic and epigenomic evolutionary history of papillary renal cell carcinomas

Intratumor heterogeneity (ITH) and tumor evolution have been well described for clear cell renal cell carcinomas (ccRCC), but they are less studied for other kidney cancer subtypes. Here we investigate ITH and clonal evolution of papillary renal cell carcinoma (pRCC) and rarer kidney cancer subtypes, integrating whole-genome sequencing and DNA methylation data. In 29 tumors, up to 10 samples from the center to the periphery of each tumor, and metastatic samples in 2 cases, enable phylogenetic analysis of spatial features of clonal expansion, which shows congruent patterns of genomic and epigenomic evolution. In contrast to previous studies of ccRCC, in pRCC, driver gene mutations and most arm-level somatic copy number alterations (SCNAs) are clonal. These findings suggest that a single biopsy would be sufficient to identify the important genetic drivers and that targeting large-scale SCNAs may improve pRCC treatment, which is currently poor. While type 1 pRCC displays near absence of structural variants (SVs), the more aggressive type 2 pRCC and the rarer subtypes have numerous SVs, which should be pursued for prognostic significance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A haplotype‐resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks

Summary White oak ( Quercus alba ) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype‐resolved chromosome‐scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data. Despite strongly conserved chromosome synteny and genome size across Quercus , certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species – as are the chromosomal locations of R gene clusters – but, gene number within clusters is more labile. We found that Q. alba has high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus. The white oak genome represents a major new resource for studying genome diversity and evolution in Quercus . Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution in Quercus .

Larson, Drew A. [Department of Biology Indiana Uni↗
DOE OSTI2024

Multisubstrate specificity shaped the complex evolution of the aminotransferase family across the tree of life

Aminotransferases (ATs) are an ancient enzyme family that play central roles in core nitrogen metabolism, essential to all organisms. However, many of the AT enzyme functions remain poorly defined, limiting our fundamental understanding of the nitrogen metabolic networks that exist in different organisms. Here, we traced the deep evolutionary history of the AT family by analyzing AT enzymes from 90 species spanning the tree of life (ToL). We found that each organism has maintained a relatively small and constant number of ATs. Mapping the distribution of ATs across the ToL uncovered that many essential AT reactions are carried out by taxon-specific AT enzymes due to wide-spread nonorthologous gene displacements. This complex evolutionary history explains the difficulty of homology-based AT functional prediction. Biochemical characterization of diverse aromatic ATs further revealed their broad substrate specificity, unlike other core metabolic enzymes that evolved to catalyze specific reactions today. Interestingly, however, we found that these AT enzymes that diverged over billion years share common signatures of multisubstrate specificity by employing different nonconserved active site residues. These findings illustrate that AT family enzymes had leveraged their inherent substrate promiscuity to maintain a small yet distinct set of multifunctional AT enzymes in different taxa. This evolutionary history of versatile ATs likely contributed to the establishment of robust and diverse nitrogen metabolic networks that exist throughout the ToL. The study provides a critical foundation to systematically determine diverse AT functions and underlying nitrogen metabolic networks across the ToL.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Novel Gloeobacterales spp. from Diverse Environments across the Globe

Photosynthetic Cyanobacteria and their descendants are the only known organisms capable of oxygenic photosynthesis. Their metabolism permanently changed the Earth’s surface and the evolutionary trajectory of life, but little is known about their evolutionary history. Genomes of the Gloeobacterales, an order of deeply divergent photosynthetic Cyanobacteria, may hold clues about the evolutionary process. However, there are only three published genomes within this order, and it is difficult to make broad inferences based on such little data. Here, I describe five species within the Gloeobacterales retrieved from publicly available databases and examine their photosynthetic gene content and the environments in which Gloeobacterales genomes and 16S rRNA gene sequences are found. The Gloeobacterales contain reduced photosystems and inhabit cold, wet-rock, and low-light environments. They are likely present in low abundances due to their low growth rate. Future searches for Gloeobacterales should target these environments, and samples should be deeply sequenced to capture the low-abundance taxa. Publicly available databases contain undescribed taxa within the Gloeobacterales. However, searching through all available data with current methods is computationally expensive. Therefore, new methods must be developed to search for these and other evolutionarily important taxa. Once identified, these novel photosynthetic Cyanobacteria will help illuminate the origin and evolution of oxygenic photosynthesis. Early branching photosynthetic Cyanobacteria such as the Gloeobacterales may provide clues into the evolutionary history of oxygenic photosynthesis, but there are few genomes or cultured taxa from this order. Five new metagenome-assembled genomes suggest that members of the Gloeobacterales all contain reduced photosystems and lack genes associated with thylakoids and circadian rhythms. Their distribution suggests that they may thrive in environments that are marginal for other species, including wet-rock and cold environments. These traits may aid in the discovery and cultivation of novel species in this clade.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost lineages and horizontal gene transfer

Photosynthesis—both oxygenic and more ancient anoxygenic forms—has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O 2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic “Granick hypothesis” for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.

58 GEOSCIENCES↗
DOE OSTI2023

Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies

Within-host HIV evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is re-activation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in bifurcating trees. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an Ancestral Recombination Graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time-signals or population bottlenecks. Further, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an Approximate Bayesian Computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally-sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past

Abstract Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Connecting galaxy evolution in clusters with their radial profiles and phase space distribution: results from the IllustrisTNG hydrodynamical simulations

ABSTRACT We study the population of galaxies around galaxy clusters in the hydrodynamic simulation suite IllustrisTNG 300-1 to study the signatures of their evolutionary history on observable properties. We measure the radial number density profile, phase space distribution, and splashback radius for galaxies of different masses and colours over the redshift range z = 0−1. The three primary physical effects which shape the galaxy distribution within clusters are the galaxy quenching, angular momentum distribution, and dynamical friction. We find three distinct populations of galaxies by applying a Gaussian mixture model to their distribution in colour and mass. They have distinct evolutionary histories and leave distinct signatures on their distribution around cluster haloes. We find that low-mass red galaxies show the most concentrated distribution in clusters and the largest splashback radius, while high-mass red galaxies show a less concentrated distribution and a smaller splashback radius. Blue galaxies, which mostly quench into the low-mass red population, have the shallowest distribution within the clusters, with those on radial orbits quenched rapidly before reaching pericentre. Comparison with the distribution of galaxies from the Dark Energy Survey survey around Sunyaev–Zeldovich clusters from the Atacama Cosmology Telescope and South Pole Telescope surveys shows evidence for differences in galaxy evolution between simulations and data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

RF-Net 2: fast inference of virus reassortment and hybridization networks

Abstract Motivation A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g. hybridization, reassortment, recombination) evolution. The standard approach to inference of hybridization networks is to (i) reconstruct rooted gene trees and (ii) leverage gene tree discordance for network inference. Recently, we introduced a method called RF-Net for accurate inference of virus reassortment and hybridization networks from input gene trees in the presence of errors commonly found in phylogenetic trees. While RF-Net demonstrated the ability to accurately infer networks with up to four reticulations from erroneous input gene trees, its application was limited by the number of reticulations it could handle in a reasonable amount of time. This limitation is particularly restrictive in the inference of the evolutionary history of segmented RNA viruses such as influenza A virus (IAV), where reassortment is one of the major mechanisms shaping the evolution of these pathogens. Results Here, we expand the functionality of RF-Net that makes it significantly more applicable in practice. Crucially, we introduce a fast extension to RF-Net, called Fast-RF-Net, that can handle large numbers of reticulations without sacrificing accuracy. In addition, we develop automatic stopping criteria to select the appropriate number of reticulations heuristically and implement a feature for RF-Net to output error-corrected input gene trees. We then conduct a comprehensive study of the original method and its novel extensions and confirm their efficacy in practice using extensive simulation and empirical IAV evolutionary analyses. Availability and implementation RF-Net 2 is available at https://github.com/flu-crew/rf-net-2. Supplementary information Supplementary data are available at Bioinformatics online.

Markin, Alexey (ORCID:0000000332809050)↗
DOE OSTI2020

Evidence for non–methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales

Recent discoveries of mcr and mcr–like genes in genomes from diverse archaeal lineages suggest that methane metabolism is an ancient pathway with a complicated evolutionary history. One conventional view is that methanogenesis is an ancestral metabolism of the class Thermoplasmata. Through comparative genomic analysis of 12 Thermoplasmata metagenome–assembled genomes (MAGs) basal to the Methanomassiliicoccales, we show that these microorganisms do not encode the genes required for methanogenesis. Further analysis of 770 Ca. Thermoplasmatota genomes/MAGs found no evidence of mcrA homologues outside of the Methanomassiliicoccales. Together, these results suggest that methanogenesis was laterally acquired by an ancestor of the Methanomassiliicoccales. The 12 analysed MAGs include representatives from four orders basal to the Methanomassiliicoccales, including a high–quality MAG that likely represents a new order, Ca. Lunaplasma lacustris ord. nov. sp. nov. These MAGs are predicted to use diverse energy conservation pathways, including heterotrophy, sulfur and hydrogen metabolism, denitrification, and fermentation. Two lineages are widespread among anoxic, sedimentary environments, whereas Ca. Lunaplasma lacustris has thus far only been detected in alpine caves and subarctic lake sediments. Furthermore, these findings advance our understanding of the metabolic potential, ecology, and global distribution of the Thermoplasmata and provide insight into the evolutionary history of methanogenesis within the Ca. Thermoplasmatota.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cell wall biology of the moss Physcomitrium patens

Abstract The moss Physcomitrium (previously Physcomitrella) patens is a non-vascular plant belonging to the bryophytes that has been used as a model species to study the evolution of plant cell wall structure and biosynthesis. Here, we present an updated review of the cell wall biology of P. patens. Immunocytochemical and structural studies have shown that the cell walls of P. patens mainly contain cellulose, hemicelluloses (xyloglucan, xylan, glucomannan, and arabinoglucan), pectin, and glycoproteins, and their abundance varies among different cell types and at different plant developmental stages. Genetic and biochemical analyses have revealed that a number of genes involved in cell wall biosynthesis are functionally conserved between P. patens and vascular plants, indicating that the common ancestor of mosses and vascular plants had already acquired most of the biosynthetic machinery to make various cell wall polymers. Although P. patens does not synthesize lignin, homologs of the phenylpropanoid biosynthetic pathway genes exist in P. patens and they play an essential role in the production of caffeate derivatives for cuticle formation. Further genetic and biochemical dissection of cell wall biosynthetic genes in P. patens promises to provide additional insights into the evolutionary history of plant cell wall structure and biosynthesis.

Plant Sciences↗
DOE OSTI2025

Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota)

Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in Discinaceae. We recognized 10 genera across two tribes: tribe Discineae (Discina, Maublancomyces, Neogyromitra, Piscidiscina, and Pseudodiscina) and tribe Gyromitreae (Gyromitra, Hydnotrya, Paragyromitra, Pseudorhizina, and Pseudoverpa); Piscidiscina was newly erected and 26 new combinations were formalized. Paradiscina melaleuca and Marcelleina donadinii formed their own family-level clade sister to Morchellaceae, which merits further taxonomic study. Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (Hydnotrya spp.), whereas the other Discinaceae genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic-either MAT1-1 or MAT1-2-but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in Gyromitra esculenta strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (Gyromitra and Piscidiscina) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of Geomoriaceae and Helvellaceae-two closely related families with no publicly available genomes-these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.

Dirks, Alden C↗