The genome sequence of the Emperor moth, Saturnia pavonia (Linnaeus, 1758).

We present a genome assembly from an individual male Saturnia pavonia (the Emperor moth; Arthropoda; Insecta; Lepidoptera; Saturniidae). The genome sequence is 489.9 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.29 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,903 protein coding genes.

GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences.

The proportions of A:T and G:C nucleotide pairs are often unequal and can vary greatly between animal species and along chromosomes. The causes and consequences of this variation are incompletely understood. The recent release of high-quality genome sequences from the Darwin Tree of Life and other large-scale genome projects provides an opportunity for GC heterogeneity to be compared across a large number of insect species. Here we analyse GC content along chromosomes, and within protein-coding genes and codons, of 150 insect species from four holometabolous orders: Coleoptera, Diptera, Hymenoptera, and Lepidoptera. We find that protein-coding sequences have higher GC content than the genome average, and that Lepidoptera generally have higher GC content than the other three insect orders examined. GC content is higher in small chromosomes in most Lepidoptera species, but this pattern is less consistent in other orders. GC content also increases towards subtelomeric regions within protein-coding genes in Diptera, Coleoptera and Lepidoptera. Two species of Diptera, Bombylius major and B. discolor, have very atypical genomes with ubiquitous increase in AT content, especially at third codon positions. Despite dramatic AT-biased codon usage, we find no evidence that this has driven divergent protein evolution. We argue that the GC landscape of Lepidoptera, Diptera and Coleoptera genomes is influenced by GC-biased gene conversion, strongest in Lepidoptera, with some outlier taxa affected drastically by counteracting processes.

Evolution of the insect Hox gene cluster: Comparative analysis across 243 species.

The Hox gene cluster is an iconic example of evolutionary conservation between divergent animal lineages, providing evidence for ancient similarities in the genetic control of embryonic development. However, there are differences between taxa in gene order, gene number and genomic organisation implying conservation is not absolute. There are also examples of radical functional change of Hox genes; for example, the ftz, zen and bcd genes in insects play roles in segmentation, extraembryonic membrane formation and body polarity, rather than specification of anteroposterior position. There have been detailed descriptions of Hox genes and Hox gene clusters in several insect species, including important model systems, but a large-scale overview has been lacking. Here we extend these studies using the publicly-available complete genome sequences of 243 insect species from 13 orders. We show that the insect Hox cluster is characterised by large intergenic distances, consistently extreme in Odonata, Orthoptera, Hemiptera and Trichoptera, and always larger between the 'posterior' Hox genes. We find duplications of ftz and zen in many species and multiple independent cluster breaks, although certain modules of neighbouring genes are rarely broken apart suggesting some organisational constraints. As more high-quality genomes are obtained, a challenge will be to relate structural genomic changes to phenotypic change across insect phylogeny.

The genome sequence of the Sulphur Tubic, Esperia sulphurella (Fabricius, 1775).

We present a genome assembly from an individual male Esperia sulphurella (the Sulphur Tubic; Arthropoda; Insecta; Lepidoptera; Oecophoridae). The genome sequence is 453.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.2 kilobases in length.

The genome sequence of the Black-tipped Ermine, Yponomeuta plumbella (Denis & Schiffermüller, 1775).

We present a genome assembly from an individual male Yponomeuta plumbella (the Black-tipped Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence is 636.6 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 16.5 kilobases in length.

The genome sequence of the Feathered Bright, Incurvaria masculella (Denis & Schiffermüller, 1775).

We present a genome assembly from an individual male Incurvaria masculella (the Feathered Bright; Arthropoda; Insecta; Lepidoptera; Incurvariidae). The genome sequence is 552 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.

The genome sequence of the Miller, Acronicta leporina (Linnaeus, 1758).

We present a genome assembly from an individual female Acronicta leporina (the Miller; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 466 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.

Opsin Gene Duplication in Lepidoptera: Retrotransposition, Sex Linkage, and Gene Expression.

Color vision in insects is determined by signaling cascades, central to which are opsin proteins, resulting in sensitivity to light at different wavelengths. In certain insect groups, lineage-specific evolution of opsin genes, in terms of copy number, shifts in expression patterns, and functional amino acid substitutions, has resulted in changes in color vision with subsequent behavioral and niche adaptations. Lepidoptera are a fascinating model to address whether evolutionary change in opsin content and sequence evolution are associated with changes in vision phenotype. Until recently, the lack of high-quality genome data representing broad sampling across the lepidopteran phylogeny has greatly limited our ability to accurately address this question. Here, we annotate opsin genes in 219 lepidopteran genomes representing 33 families, reconstruct their evolutionary history, and analyze shifts in selective pressures and expression between genes and species. We discover 44 duplication events in opsin genes across ∼300 million years of lepidopteran evolution. While many duplication events are species or family specific, we find retention of an ancient long-wavelength-sensitive (LW) opsin duplication derived by retrotransposition within the speciose superfamily Noctuoidea (in the families Nolidae, Erebidae, and Noctuidae). This conserved LW retrogene shows life stage-specific expression suggesting visual sensitivities or other sensory functions specific to the early larval stage. This study provides a comprehensive order-wide view of opsin evolution across Lepidoptera, showcasing high rates of opsin duplications and changes in expression patterns.

The genome sequence of the Leopard Moth, Zeuzera pyrina (Linnaeus, 1761).

We present a genome assembly from an individual male Zeuzera pyrina (the Leopard Moth, Arthropoda; Insecta; Lepidoptera; Cossidae). The genome sequence is 687 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,738 protein coding genes.

The genome sequence of the Lesser Broad-bordered Yellow Underwing, Noctua janthe (Borkhausen, 1792).

We present a genome assembly from an individual male Noctua janthe (the Lesser Broad-bordered Yellow Underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 532.8 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 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,653 protein coding genes.

The genome sequence of the Light Brocade, Lacanobia w-latinum (Hufnagel, 1766).

We present a genome assembly from an individual male Lacanobia w-latinum (the Light Brocade; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 903.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,592 protein coding genes.

The genome sequence of the Round-winged Muslin, Thumatha senex (Hübner, 1804).

We present a genome assembly from an individual female Thumatha senex (the Round-winged Muslin; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 810.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.5 kilobases in length.

The genome sequence of the Rustic Shoulder-knot, Apamea sordens (Hufnagel, 1766).

We present a genome assembly from an individual male Apamea sordens (the Rustic Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 614 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.3 kilobases in length.

The genome sequence of the Feathered Gothic, Tholera decimalis (Poda, 1761).

We present a genome assembly from an individual female Tholera decimalis (the Feathered Gothic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 1,334.1 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 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,771 protein coding genes.

The genome sequence of the Buff Ermine, Spilarctia lutea (Hufnagel, 1766).

We present a genome assembly from an individual female Spilarctia lutea (the Buff Ermine; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 584.8 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the assembled Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,304 protein coding genes.

The genome sequence of the Northern Deep-brown Dart, Aporophyla lueneburgensis (Freyer, 1848).

We present a genome assembly from an individual female Aporophyla lueneburgensis (the Northern Deep-brown Dart; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 978.3 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 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,580 protein coding genes.

The genome sequence of the Spruce Carpet Moth, Thera britannica (Turner, 1925).

We present a genome assembly from an individual male Thera britannica (the Spruce Carpet Moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 381 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.9 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,457 protein coding genes.

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 the Burnished Brass, Diachrysia chrysitis (Linnaeus, 1758).

We present a genome assembly from an individual male Diachrysia chrysitis (the Burnished Brass; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 386 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,320 protein coding genes.

The genome sequence of the Oak-tree Pug, Eupithecia dodoneata (Guenée, 1858).

We present a genome assembly from an individual male Eupithecia dodoneata (the Oak-tree Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 353.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.