Abstract
We present a genome assembly from an individual female Apeira syringaria (the Lilac Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 544.4 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 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,426 protein coding genes.
Keywords: Apeira syringaria, Lilac Beauty, genome sequence, chromosomal, Lepidoptera
Species taxonomy
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Geometroidea; Geometridae; Ennominae; Apeira; Apeira syringaria (Linnaeus, 1758) (NCBI:txid934915).
Background
The Lilac Beauty, Apeira syringaria (Linnaeus, 1758) is a moth in the family Geometridae, from the ‘thorn’ subfamily, Ennominae. Adult moths of this species have an unusual resting posture, with the forewings slightly raised, and the leading edge slightly folded ( Waring et al., 2017), increasing their resemblance to a crumpled dead leaf. Males are smaller and more brightly coloured than females ( South, 1961).
Apeira syringaria has a local distribution in Britain and Ireland, occurring mostly in south and central areas. It was not recorded from Scotland in the early part of the twentieth century ( South, 1961), but has extended its distribution there in recent decades ( Randle et al., 2019). At monitored sites, the abundance of this species has declined greatly since 1970 ( Randle et al., 2019). Internationally, the distribution of A. syringaria extends across Europe and temperate Asia ( GBIF Secretariat, 2022).
The main larval foodplants include honeysuckle ( Lonicera spp.), privet ( Ligustrum spp.), ash ( Fraxinus spp.) and lilac ( Syringa vulgaris) among other trees and shrubs ( Henwood et al., 2020).
A genome sequence for Apeira syringaria will contribute to a growing data set of resources for understanding Lepidopteran biology. The genome of Apeira syringaria was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland. Here we present a chromosomally complete genome sequence for Apeira syringaria, based on one female specimen from Wytham Woods, Oxfordshire, UK.
Genome sequence report
The genome was sequenced from one female Apeira syringaria ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude –1.34). A total of 49-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.
Figure 1. Photograph of the Apeira syringaria (ilApeSyri1) specimen used for genome sequencing.
The final assembly has a total length of 544.4 Mb in 51 sequence scaffolds with a scaffold N50 of 21.0 Mb ( Table 1). Most (99.96%) of the assembly sequence was assigned to 30 chromosomal-level scaffolds, representing 29 autosomes, and the Z sex chromosome. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 2– Figure 5; Table 2). The assembly has a BUSCO v5.3.2 ( Manni et al., 2021) completeness of 98.4% (single 97.7%, duplicated 0.7%), using the lepidoptera_odb10 reference set. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.
Figure 2. Genome assembly of Apeira syringaria, ilApeSyri1.1: metrics.
The BlobToolKit Snailplot shows N50 metrics and BUSCO gene completeness. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 544,443,574 bp assembly. The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (37,666,467 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (20,999,187 and 10,846,250 bp), respectively. The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated and missing BUSCO genes in the lepidoptera_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilApeSyri1.1/dataset/CAKOGW01/snail.
Figure 5. Genome assembly of Apeira syringaria, ilApeSyri1.1: Hi-C contact map.
Hi-C contact map of the ilApeSyri1.1 assembly, visualised using HiGlass. Chromosomes are shown in order of size from left to right and top to bottom. An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=BdknbMWvQoywaKY2jyxqZA.
Table 1. Genome data for Apeira syringaria, ilApeSyri1.1.
| Project accession data | ||
|---|---|---|
| Assembly identifier | ilApeSyri1.1 | |
| Species | Apeira syringaria | |
| Specimen | ilApeSyri1 | |
| NCBI taxonomy ID | 934915 | |
| BioProject | PRJEB50739 | |
| BioSample ID | SAMEA7520685 | |
| Isolate information | ilApeSyri1; female, head and thorax (PacBio and Hi-C) | |
| Assembly metrics * | Benchmark | |
| Consensus quality (QV) | 64.8 | ≥ 50 |
| k-mer completeness | 100% | ≥ 95% |
| BUSCO ** | C:98.4%[S:97.7%,D:0.7%],
F:0.5%,M:1.0%,n:5,286 |
C ≥ 95% |
| Percentage of assembly mapped to chromosomes | 99.96% | ≥ 95% |
| Sex chromosomes | Z chromosome | localised homologous pairs |
| Organelles | Mitochondrial genome assembled | complete single alleles |
| Raw data accessions | ||
| PacificBiosciences SEQUEL II | ERR8575375 | |
| Hi-C Illumina | ERR8571657 | |
| Genome assembly | ||
| Assembly accession | GCA_934044485.1 | |
| Accession of alternate haplotype | GCA_934045895.1 | |
| Span (Mb) | 544.4 | |
| Number of contigs | 51 | |
| Contig N50 length (Mb) | 21.0 | |
| Number of scaffolds | 51 | |
| Scaffold N50 length (Mb) | 21.0 | |
| Longest scaffold (Mb) | 37.7 | |
| Genome annotation | ||
| Number of protein-coding genes | 18,426 | |
| Number of non-coding genes | 18,577 | |
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from ( Rhie et al., 2021).
** BUSCO scores based on the lepidoptera_odb10 BUSCO set using v5.3.2. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/ilApeSyri1.1/dataset/CAKOGW01/busco.
Figure 3. Genome assembly of Apeira syringaria, ilApeSyri1.1: GC coverage.
BlobToolKit GC-coverage plot. Scaffolds are coloured by phylum. Circles are sized in proportion to scaffold length. Histograms show the distribution of scaffold length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilApeSyri1.1/dataset/CAKOGW01/blob.
Figure 4. Genome assembly of Apeira syringaria, ilApeSyri1.1: cumulative sequence.
BlobToolKit cumulative sequence plot. The grey line shows cumulative length for all scaffolds. Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilApeSyri1.1/dataset/CAKOGW01/cumulative.
Table 2. Chromosomal pseudomolecules in the genome assembly of Apeira syringaria, ilApeSyri1.
| INSDC accession | Chromosome | Size (Mb) | GC% |
|---|---|---|---|
| OW203654.1 | 1 | 37.67 | 37.1 |
| OW203656.1 | 2 | 35.28 | 36.7 |
| OW203657.1 | 3 | 28.52 | 36.7 |
| OW203658.1 | 4 | 26.6 | 37.2 |
| OW203659.1 | 5 | 25.94 | 37 |
| OW203660.1 | 6 | 24.87 | 36.7 |
| OW203661.1 | 7 | 22.17 | 37 |
| OW203662.1 | 8 | 21.85 | 37.2 |
| OW203663.1 | 9 | 21 | 36.9 |
| OW203664.1 | 10 | 20.5 | 37.2 |
| OW203665.1 | 11 | 20.36 | 37 |
| OW203666.1 | 12 | 18.76 | 37.2 |
| OW203667.1 | 13 | 18.56 | 37.2 |
| OW203668.1 | 14 | 18.19 | 37.2 |
| OW203669.1 | 15 | 13.3 | 37.7 |
| OW203670.1 | 16 | 12.4 | 37.2 |
| OW203671.1 | 17 | 12.31 | 37.3 |
| OW203672.1 | 18 | 12.2 | 37.7 |
| OW203673.1 | 19 | 11.85 | 38 |
| OW203674.1 | 20 | 11.81 | 37.9 |
| OW203675.1 | 21 | 11.58 | 37.8 |
| OW203676.1 | 22 | 11.43 | 37.5 |
| OW203677.1 | 23 | 11.03 | 37.6 |
| OW203678.1 | 24 | 10.85 | 37.9 |
| OW203679.1 | 25 | 10.3 | 37.7 |
| OW203680.1 | 26 | 10.27 | 38.2 |
| OW203681.1 | 27 | 9.64 | 39.3 |
| OW203682.1 | 28 | 9.55 | 38.3 |
| OW203683.1 | 29 | 2.78 | 42.8 |
| OW203655.1 | Z | 36.04 | 36.7 |
| OW203684.1 | MT | 0.02 | 19.7 |
| - | unplaced | 6.82 | 41 |
Genome annotation report
The Apeira syringaria genome assembly GCA_934044485.1 (ilApeSyri1.1) was annotated using the Ensembl rapid annotation pipeline ( Table 1; Ensembl accession number GCA_934044485.1). The resulting annotation includes 18,426 protein-coding and 18,577 non-coding genes.
Methods
Sample acquisition and nucleic acid extraction
A female Apeira syringaria specimen (ilApeSyri1) was collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire) (latitude 51.77, longitude –1.34) on 13 June 2020. The specimen was taken from woodland habitat by Douglas Boyes (University of Oxford) using a light trap. The specimen was identified by Douglas Boyes using field ID and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The ilApeSyri1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Head and thorax tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle. High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit. HMW DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 30. Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample. The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.
Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. DNA sequencing was performed by the Scientific Operations core at the WSI on a Pacific Biosciences SEQUEL II (HiFi) instruments. Hi-C data were also generated from tissue of ilApeSyri1 using the Arima v2 kit and sequenced on the HiSeq X Ten instrument.
Genome assembly
Assembly was carried out with Hifiasm ( Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups ( Guan et al., 2020). The assembly was then scaffolded with Hi-C data ( Rao et al., 2014) using YaHS ( Zhou et al., 2023). The assembly was checked for contamination as described previously ( Howe et al., 2021). Manual curation was performed using HiGlass ( Kerpedjiev et al., 2018) and Pretext ( Harry, 2022). The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2022), which performed annotation using MitoFinder ( Allio et al., 2020). The genome was analysed and BUSCO scores generated within the BlobToolKit environment ( Challis et al., 2020). Table 3 contains a list of all software tool versions used, where appropriate.
Table 3. Software tools and versions used.
| Software tool | Version | Source |
|---|---|---|
| BlobToolKit | 4.0.7 | Challis et al., 2020 |
| Hifiasm | 0.16.1-r375 | Cheng et al., 2021 |
| HiGlass | 1.11.6 | Kerpedjiev et al., 2018 |
| MitoHiFi | 2 | Uliano-Silva et al., 2022 |
| PretextView | 0.2 | Harry, 2022 |
| purge_dups | 1.2.3 | Guan et al., 2020 |
| YaHS | yahs-1.1.91eebc2 | Zhou et al., 2023 |
Genome annotation
The BRAKER2 pipeline ( Brůna et al., 2021) was used in the default protein mode to generate annotation for the Apeira syringaria assembly (GCA_934044485.1) in Ensembl Rapid Release.
Ethics and compliance issues
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner. The submission of materials by a Darwin Tree of Life Partner is subject to the Darwin Tree of Life Project Sampling Code of Practice. By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project. All efforts are undertaken to minimise the suffering of animals used for sequencing. Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.
Funding Statement
This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (206194, <a href=https://doi.org/10.35802/206194>https://doi.org/10.35802/206194</a>) and the Darwin Tree of Life Discretionary Award (218328, <a href=https://doi.org/10.35802/218328>https://doi.org/10.35802/218328</a>).
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
[version 1; peer review: 2 approved]
Data availability
European Nucleotide Archive: Apeira syringaria (lilac beauty). Accession number PRJEB50739; https://identifiers.org/ena.embl/PRJEB50739 ( Wellcome Sanger Institute, 2022)
The genome sequence is released openly for reuse. The Apeira syringaria genome sequencing initiative is part of the Darwin Tree of Life (DToL) project. All raw sequence data and the assembly have been deposited in INSDC databases. Raw data and assembly accession identifiers are reported in Table 1.
Author information
Members of the University of Oxford and Wytham Woods Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.4789928.
Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.4893703.
Members of the Wellcome Sanger Institute Tree of Life programme are listed here: https://doi.org/10.5281/zenodo.4783585.
Members of Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective are listed here: https://doi.org/10.5281/zenodo.4790455.
Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.
Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.
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