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LIQ254RAFAR_X.fa - extracted marker genes for newly sequenced Ramalina farinacea used for UNITE and TBAS identification tbas21_archiveZ33LHEX2_.tar.gz - results of TBAS phylogenetic placement Z33LHEX2.mep.gz - Metadata Enhanced PhyloXML (MEP) file of TBAS run. The MEP is a phyloXML file that includes the tree, alignments and metadata for the run UNITE serial BLAST search - output to screen.html - results of the UNITE massblaster analysis using LIQ254RAFAR_ITS.fa as the query, which was pulled from the whole genome sequence using ITSx, This work was funded by the Natural Environment Research Council (NERC) studentship NE/S007415/1 and the Emily Holmes Scholarship fund to T.L.

Anthraquinone_aa_sequences_and_tree - FASTA files containing aligned amino acid and nucleotide sequences for putative anthraquinone PKSI genes from 45 whole genome Lecanoromycetes lichen dataset used to generate gene tree. Also contain ML gene tree generated by RAxML-ng Orthogroup_trimmed_alignments - FASTA files containing trimAl trimmed alignments for single copy orthologues used to reconstruct ML and coalescent-based phylogenomic trees. Phylogenetic_trees - gene and species trees used for whole genome phylogenetic analysis HMM_seed_alignment_and_tree - CLUSTAL file containing multiple sequence alignemnt for anthraquinone PT domains with the PT domain Pfam seed alignment. Also includes ML tree generated by IQTree, This work was supported by the Natural Environment Research Council (NERC) studentship NE/S007415/1 to T.L and the Evolution and Education Trust (EET) and Pragnell Fund to E.G.

The vision of the Earth BioGenome Project1 is to complete reference genomes for all of the planet’s ~2M described eukaryotic species in the coming decade. To contribute to this global endeavour, the Darwin Tree of Life Project (DToL2) was launched in 2019 with the aim of generating complete genomes for the ~70k described eukaryotic species that can be found in Britain and Ireland. One of the early tasks of the DToL project was to determine, define, and standardise the important metadata that must accompany every sample contributing to this ambitious project. This ensures high-quality contextual information is available for the associated data, enabling a richer set of information upon which to search and filter datasets as well as enabling interoperability between datasets used for downstream analysis. Here we describe some of the key factors we considered in the process of determining, defining, and documenting the metadata required for DToL project samples. The manifest and Standard Operating Procedure that are referred to throughout this paper are likely to be useful for other projects, and we encourage re-use while maintaining the standards and rules set out here.

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.

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.

Fungi are more important to our lives than is assumed by the general public. They can comprise both devastating pathogens and plant-associated mutualists in nature, and several species have also become important workhorses of biotechnology. Fungal diversity research has in a short time transcended from a low-tech research area to a methodintensive high-tech discipline. With the advent of the new genomic and post-genomic methodologies, large quantities of new fungal data are currently becoming available each year. Whilst these new data and methodologies may help modern fungal diversity researchers to explore and discover the yet hidden diversity within a context of biological processes and organismal diversity, they need to be reconciled with the traditional approaches. Such a synthesis is actually difficult to accomplish given the current discouraging situation of fungal biology education, especially in the areas of biodiversity and taxonomic research. The number of fungal diversity researchers and taxonomists in academic institutions is decreasing, as are opportunities for mycological education in international curricula. How can we educate and stimulate students to pursue a career in fungal diversity research and taxonomy and avoid the situation whereby only those few institutions with strong financial support are able to conduct excellent research? Our short answer is that we need a combination of increased specialization and increased collaboration, i.e. that scientists with specialized expertise (e.g., in data generation, compilation, interpretation, and communication) consistently work together to generate and delivernew fungal knowledge in a more integrative manner e closing the gap between both traditional and modern approaches and academic and non-academic environments. Here we discuss how this perspective could be implemented in the training of the ‘next generation fungal diversity researcher’.

Fungi are more important to our lives than is assumed by the general public. They can comprise both devastating pathogens and plant-associated mutualists in nature, and several species have also become important workhorses of biotechnology. Fungal diversity research has in a short time transcended from a low-tech research area to a method-intensive high-tech discipline. With the advent of the new genomic and post-genomic methodologies, large quantities of new fungal data are currently becoming available each year. Whilst these new data and methodologies may help modern fungal diversity researchers to explore and discover the yet hidden diversity within a context of biological processes and organismal diversity, they need to be reconciled with the traditional approaches. Such a synthesis is actually difficult to accomplish given the current discouraging situation of fungal biology education, especially in the areas of biodiversity and taxonomic research. The number of fungal diversity researchers and taxonomists in academic institutions is decreasing, as are opportunities for mycological education in international curricula. How can we educate and stimulate students to pursue a career in fungal diversity research and taxonomy and avoid the situation whereby only those few institutions with strong financial support are able to conduct excellent research? Our short answer is that we need a combination of increased specialization and increased collaboration, i.e. that scientists with specialized expertise (e.g., in data generation, compilation, interpretation, and communication) consistently work together to generate and deliver new fungal knowledge in a more integrative manner – closing the gap between both traditional and modern approaches and academic and non-academic environments. Here we discuss how this perspective could be implemented in the training of the ‘next generation fungal diversity researcher’.