A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project.

Biodiversity genomics research requires reliable organismal identification, which can be difficult based on morphology alone. DNA-based identification using DNA barcoding can provide confirmation of species identity and resolve taxonomic issues but is rarely used in studies generating reference genomes. Here, we describe the development and implementation of DNA barcoding for the Darwin Tree of Life Project (DToL), which aims to sequence and assemble high quality reference genomes for all eukaryotic species in Britain and Ireland. We present a standardised framework for DNA barcode sequencing and data interpretation that is then adapted for diverse organismal groups. DNA barcoding data from over 12,000 DToL specimens has identified up to 20% of samples requiring additional verification, with 2% of seed plants and 3.5% of animal specimens subsequently having their names changed. We also make recommendations for future developments using new sequencing approaches and streamlined bioinformatic approaches.

Identifying species based solely on their morphology can be difficult. DNA-based identification using DNA barcoding can aid species identification, but can be challenging to implement in biodiversity projects sampling diverse organismal groups. Here, we describe the development and implementation of DNA barcoding for the Darwin Tree of Life Project (DToL), which aims to sequence and assemble high quality reference genomes for all eukaryotic species in Britain and Ireland. We discuss how a standardised approach has been adapted by each partner to suit different organismal groups, show the efficacy of this approach for confirming species identities and resolving taxonomic issues, and make recommendations for future developments.

The genome sequence of the cephid sawfly, Cephus spinipes (Panzer, 1800).

We present a genome assembly from an individual male cephid sawfly, Cephus spinipes (Arthropoda; Insecta; Hymenoptera; Cephidae). The genome sequence has a total length of 238.60 megabases. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.43 kilobases in length.

The genome sequence of the Rivulet moth, Perizoma affinitatum (Stephens, 1831).

We present a genome assembly from an individual male Perizoma affinitatum (the Rivulet moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 357.7 megabases in span. Most of the assembly is scaffolded into 25 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.9 kilobases in length.

The genome sequence of the European pine marten, Martes martes (Linnaeus, 1758).

We present a genome assembly from an individual male Martes martes (the European pine marten; Chordata; Mammalia; Carnivora; Mustelidae). The genome sequence is 2,484.6 megabases in span. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.57 kilobases in length.

The genome sequence of an ichneumonid wasp, Oxytorus armatus Thomson, 1883.

We present a genome assembly from an individual male Oxytorus armatus (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 367.8 megabases in span. Most of the assembly is scaffolded into 13 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 56.22 kilobases in length.

The genome sequence of the White-pinion Spotted, Lomographa bimaculata (Fabricius, 1775).

We present a genome assembly from an individual male Lomographa bimaculata (the White-pinion Spotted; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 554.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.66 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,749 protein coding genes.

The genome sequence of the Banded Burying beetle, Nicrophorus investigator Zetterstedt, 1824.

We present a genome assembly from a female Nicrophorus investigator (Banded Burying beetle; Arthropoda; Insecta; Coleoptera; Silphidae). The genome sequence is 202.3 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 23.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,046 protein coding genes.

Prevalence and Molecular Analysis of Encephalomyocarditis Virus-2 in the Hazel Dormouse.

The hazel dormouse (Muscardinus avellanarius) population in the UK continues to decline due to habitat loss, despite reintroductions of captive-bred individuals being conducted nationally for over 30 years. Disease surveillance of captive-bred and wild dormice is performed to identify novel and existing disease threats which could impact populations. In this study, we firstly investigated cause of death in seven hazel dormice found dead in England, through next-generation sequencing identifying a virus closely related to a wood mouse encephalomyocarditis virus-2 (EMCV-2). Subsequently, lung tissue samples from 35 out of 44 hazel dormice tested positive for EMCV-2 RNA using a reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and Sanger sequencing methods developed in this study. Formalin-fixed tissues available for nine hazel dormice which tested positive for EMCV-2 RNA were examined microscopically. Three cases showed moderate interstitial pneumonia with minimal to mild lymphoplasmacytic myocarditis, but no evidence of encephalitis. However, the presence of possible alternative causes of death in these cases means that the lesions cannot be definitively attributed to EMCV-2. Here, we report the first detection of EMCV-2 in hazel dormice and conclude that EMCV-2 is likely to be endemic in the hazel dormouse population in England and may be associated with clinical disease.

A sampling strategy for genome sequencing the British terrestrial arthropod fauna.

The Darwin Tree of Life (DToL) project aims to sequence and assemble high-quality genomes from all eukaryote species in Britain and Ireland, with the first phase of the project concentrating on family-level coverage plus species of particular ecological, biomedical or evolutionary interest. We summarise the processes involved in (1) assessing the UK arthropod fauna and the status of individual species on UK lists; (2) prioritising and collecting species for initial genome sequencing; (3) handling methods to ensure that high-quality genomic DNA is preserved; and (4) compiling standard operating procedures for processing specimens for genome sequencing, identification verification and voucher specimen curation. We briefly explore some lessons learned from the pilot phase of DToL and the impact of the Covid-19 pandemic.

The genome sequence of an ichneumonid wasp, Campoletis raptor (Zetterstedt, 1838).

We present a genome assembly from an individual female Campoletis raptor (an ichneumonid wasp; Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 218.6 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.53 kilobases in length.

The genome sequence of the Lunar-spotted Pinion, Cosmia pyralina (Denis & Schiffermüller, 1775).

We present a genome assembly from an individual male Cosmia pyralina (the Lunar-spotted Pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 803.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,901 protein coding genes.

The genome sequence of a chalcid wasp, Gastracanthus pulcherrimus (Westwood, 1833).

We present a genome assembly from an individual female Gastracanthus pulcherrimus (a chalcid wasp; Arthropoda; Insecta; Hymenoptera; Pteromalidae). The genome sequence is 1,010.0 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.4 kilobases in length.

Somatic mutation rates scale with lifespan across mammals.

The rates and patterns of somatic mutation in normal tissues are largely unknown outside of humans1-7. Comparative analyses can shed light on the diversity of mutagenesis across species, and on long-standing hypotheses about the evolution of somatic mutation rates and their role in cancer and ageing. Here we performed whole-genome sequencing of 208 intestinal crypts from 56 individuals to study the landscape of somatic mutation across 16 mammalian species. We found that somatic mutagenesis was dominated by seemingly endogenous mutational processes in all species, including 5-methylcytosine deamination and oxidative damage. With some differences, mutational signatures in other species resembled those described in humans8, although the relative contribution of each signature varied across species. Notably, the somatic mutation rate per year varied greatly across species and exhibited a strong inverse relationship with species lifespan, with no other life-history trait studied showing a comparable association. Despite widely different life histories among the species we examined-including variation of around 30-fold in lifespan and around 40,000-fold in body mass-the somatic mutation burden at the end of lifespan varied only by a factor of around 3. These data unveil common mutational processes across mammals, and suggest that somatic mutation rates are evolutionarily constrained and may be a contributing factor in ageing.