The goals of the Earth Biogenome Project-to sequence the genomes of all eukaryotic life on earth-are as daunting as they are ambitious. The Darwin Tree of Life Project was founded to demonstrate the ...credibility of these goals and to deliver at-scale genome sequences of unprecedented quality for a biogeographic region: the archipelago of islands that constitute Britain and Ireland. The Darwin Tree of Life Project is a collaboration between biodiversity organizations (museums, botanical gardens, and biodiversity institutes) and genomics institutes. Together, we have built a workflow that collects specimens from the field, robustly identifies them, performs sequencing, generates high-quality, curated assemblies, and releases these openly for the global community to use to build future science and conservation efforts.
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•Large-scale molecular phylogenetic synthesis of the third largest class of fungi.•Based on a cumulative supermatrix approach of >1100 species representing all orders.•Up to ca. 8kb ...from four nuclear and one mitochondrial genes were included per species.•Comprehensive revision of classification including 74 taxonomic conclusions.•A new module “Hypha” of the Mesquite software is introduced.
The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, ‘Candelariomycetidae’). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module (“Hypha”) of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.
New scientific discoveries: Plants and fungi Cheek, Martin; Nic Lughadha, Eimear; Kirk, Paul ...
Plants, people, planet,
September 2020, 2020-09-00, 20200901, 2020-09-01, Letnik:
2, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Research and publication of the planet's remaining plant and fungal species as yet unknown to science is essential if we are to address the United Nations Sustainable Development Goal (SDG) 15 “Life ...on Land” which includes the protection of terrestrial ecosystems and halting of biodiversity loss. If species are not known to science, they cannot be assessed on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species and so the possibility to protect them from extinction is reduced. Furthermore, until species are known to science they cannot be fully scientifically evaluated for their potential as new foods, medicines, and products which would help address SDGs 1,2,3, and 8.
Societal Impact Statement
Research and publication of the planet's remaining plant and fungal species as yet unknown to science is essential if we are to address the United Nations Sustainable Development Goal (SDG) 15 “Life on Land” which includes the protection of terrestrial ecosystems and halting of biodiversity loss. If species are not known to science, they cannot be assessed on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species and so the possibility to protect them from extinction is reduced. Furthermore, until species are known to science they cannot be fully scientifically evaluated for their potential as new foods, medicines, and products which would help address SDGs 1,2,3, and 8.
Summary
Scientific discovery, including naming new taxa, is important because without a scientific name, a species is invisible to science and the possibilities of researching its ecology, applications and threats, and conserving it, are greatly reduced. We review new scientific discoveries in the plant and fungal kingdoms, based largely on new names of taxa published in 2019 and indexed in the International Plant Names Index and Index Fungorum. Numbers of new species in both kingdoms were similar with 1942 new species of plant published and 1882 species of fungi. However, while >50% of plant species have likely been discovered, >90% of fungi remain unknown. This gulf likely explains the greater number of higher order taxa for fungi published in 2019: three classes, 18 orders, 48 families and 214 genera versus one new family and 87 new genera for plants. We compare the kingdoms in terms of rates of scientific discovery, globally and in different taxonomic groups and geographic areas, and with regard to the use of DNA in discovery. We review species new to science, especially those of interest to humanity as new products, and also by life‐form. We consider where future such discoveries can be expected. We recommend an urgent increase in investment in scientific discovery of plant and fungal species, while they still survive. Priorities include more investment in training taxonomists, in building and equipping collections‐based research centers for them, especially in species‐rich, income‐poor countries where the bulk of species as yet unknown to science are thought to occur.
Adaptive radiations play key roles in the generation of biodiversity and biological novelty, and therefore understanding the factors that drive them remains one of the most important challenges of ...evolutionary biology. Although both intrinsic innovations and extrinsic ecological opportunities contribute to diversification bursts, few studies have looked at the synergistic effect of such factors. Here we investigate the Teloschistales (Ascomycota), a group of >1,000 lichenized species with variation in species richness and phenotypic traits that hinted at a potential adaptive radiation. We found evidence for a dramatic increase in diversification rate for one of four families within this order—Teloschistaceae—which occurred ∼100 Mya (Late Cretaceous) and was associated with a switch from bark to rock and from shady to sun-exposed habitats. This adaptation to sunny habitats is likely to have been enabled by a contemporaneous key novel phenotypic innovation: the production in both vegetative structure (thallus) and fruiting body (apothecia) of anthraquinones, secondary metabolites known to protect against UV light. We found that the two ecological factors (sun exposure and rock substrate) and the phenotypic innovation (anthraquinones in the thallus) were all significant when testing for state-dependent shifts in diversification rates, and together they seem likely to be responsible for the success of the Teloschistaceae, one of the largest lichen-forming fungal lineages. Our results support the idea that adaptive radiations are driven not by a single factor or key innovation, but require a serendipitous combination of both intrinsic biotic and extrinsic abiotic and ecological factors.
Abstract
Fungi
are integral to well-functioning ecosystems, and their broader impact on Earth systems is widely acknowledged. Fossil evidence from the Rhynie Chert (Scotland, UK) shows that
Fungi
...were already diverse in terrestrial ecosystems over 407-million-years-ago, yet evidence for the occurrence of
Dikarya (
the subkingdom of
Fungi
that includes the phyla
Ascomycota
and
Basidiomycota
) in this site is scant. Here we describe a particularly well-preserved asexual fungus from the Rhynie Chert which we examined using brightfield and confocal microscopy. We document
Potteromyces asteroxylicola
gen. et sp. nov. that we attribute to
Ascomycota incertae sedis (Dikarya)
. The fungus forms a stroma-like structure with conidiophores arising in tufts outside the cuticle on aerial axes and leaf-like appendages of the lycopsid plant
Asteroxylon mackiei
. It causes a reaction in the plant that gives rise to dome-shaped surface projections. This suite of features in the fungus together with the plant reaction tissues provides evidence of it being a plant pathogenic fungus. The fungus evidently belongs to an extinct lineage of ascomycetes that could serve as a minimum node age calibration point for the
Ascomycota
as a whole, or even the
Dikarya
crown group, along with some other
Ascomycota
previously documented in the Rhynie Chert.
Seed banks were first established to conserve crop genetic diversity, but seed banking has more recently been extended to wild plants, particularly crop wild relatives (CWRs) (e.g., by the Millennium ...Seed Bank (MSB), Royal Botanic Gardens Kew). CWRs have been recognised as potential reservoirs of beneficial traits for our domesticated crops, and with mounting evidence of the importance of the microbiome to organismal health, it follows that the microbial communities of wild relatives could also be a valuable resource for crop resilience to environmental and pathogenic threats. Endophytic fungi reside asymptomatically inside all plant tissues and have been found to confer advantages to their plant host. Preserving the natural microbial diversity of plants could therefore represent an important secondary conservation role of seed banks. At the same time, species that are reported as endophytes may also be latent pathogens. We explored the potential of the MSB as an incidental fungal endophyte bank by assessing diversity of fungi inside stored seeds. Using banana CWRs in the genus
as a case-study, we sequenced an extended ITS-LSU fragment in order to delimit operational taxonomic units (OTUs) and used a similarity and phylogenetics approach for classification. Fungi were successfully detected inside just under one third of the seeds, with a few genera accounting for most of the OTUs-primarily
,
, and
-while a large variety of rare OTUs from across the Ascomycota were isolated only once.
species were notably abundant-of significance in light of Fusarium wilt, a disease threatening global banana crops-and so were targeted for additional sequencing with the marker
in order to delimit species and place them in a phylogeny of the genus. Endophyte community composition, diversity and abundance was significantly different across habitats, and we explored the relationship between community differences and seed germination/viability. Our results show that there is a previously neglected invisible fungal dimension to seed banking that could well have implications for the seed collection and storage procedures, and that collections such as the MSB are indeed a novel source of potentially useful fungal strains.
We present a genome assembly from an individual Lactarius evosmus (Fruity Milkcap; Basidiomycota; Agaricomycetes; Russulales; Russulaceae). The genome sequence is 57.2 megabases in span. Most of the ...assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 61.51 kilobases in length.
Urban areas may contain a wide range of potential habitats and environmental gradients and, given the many benefits to human health and well-being, there is a growing interest in maximizing their ...biodiversity potential. However, the ecological patterns and processes in urban areas are poorly understood. Using a widely applicable ecological survey method, we sampled epiphytic lichen communities, important bioindicators of atmospheric pollution, on host Quercus trees in urban parks of London, UK, to test if common patterns relating to lichen diversity are mirrored in urban green spaces. We found lichen diversity to be dependent on host species identity, and negatively related to local tree crowding. In addition, we found a strong negative effect of tree size on lichen diversity, leaving large trees as unexploited niches. A novel network analysis revealed the presence of only pioneer communities, showing the lichen communities are being held in successional stasis, likely due to the heritage effects of SO2 emissions and current nitrogen pollution and particulate emissions. Our study highlights that jointly assessing species richness, community structure and the successional stage can be key to understanding diversity patterns in urban ecosystems. Subsequently, this may help best determine the optimum conditions that will facilitate biodiversity increase within cities.
The enormity of the breadth and depth of specimens held within the world's biological collections offers unparalleled opportunities to capture genomic data from across the entire range of known ...biological diversity. Such a task would take many lifetimes to complete if we could rely only on fresh samples. High‐throughput sequencing provides a technical solution to the long‐term problems of recalcitrant and degraded DNA typical of museum specimens, suggesting that we may be on the verge of a major collections‐based revolution. Although the potential is great, the feasibility of using preserved collections for large‐scale, taxonomically comprehensive phylogenomic studies remains unknown. In the present study, we demonstrate the continued relevance of fungarium collections in the genomic era by analyzing a genomic dataset composed of 39 genomes representing 26 family‐level clades, including 14 newly generated draft genomes derived from short‐read shotgun sequencing of preserved specimens, frozen and freeze‐dried material, representing most of the known families of Agaricales. We predicted homologues of 210 putative single copy genes in the newly generated draft genome assemblies, of which 208 were used for phylogenetic reconstruction. Our analyses resulted in a robust and, for the first time, fully supported phylogeny of the Agaricales, enabling the recognition of seven suborders and providing a resource for testing hypotheses of the evolution of mushrooms. Our analysis of optimal combinations of ranked genes using an information theory‐based method provides guidance on gene selection for future studies, enabling efficient application of high‐throughput sequencing techniques toward unlocking the potential of collections‐based research in the genomic era.
We present a genome assembly from an individual
(the chicken of the woods fungus; Basidiomycota; Agaricomycetes; Polyporales; Laetiporaceae). The genome sequence is 37.4 megabases in span. The ...complete assembly is scaffolded into 14 chromosomal pseudomolecules.
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