Abstract
We present a genome assembly from an individual female Archips xylosteana (the Variegated Golden Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 650.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,861 protein coding genes.
Keywords: Archips xylosteana, variegated golden tortrix, genome sequence, chromosomal, Lepidoptera
Species taxonomy
Eukaryota; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Apoditrysia; Tortricoidea; Tortricidae; Tortricinae; Archipini; Archips; Archips xylosteana (Linnaeus, 1758) (NCBI:txid1100919).
Background
The Variegated Golden Tortrix, Archips xylosteana (Linnaeus, 1758), from the family Tortricidae is native across most of Europe, eastern and central Asia, and northern Africa ( Hoebeke et al., 2008). Archips xylosteana was inadvertently introduced into North America from Eurasia ( Gilligan et al., 2020; Hoebeke et al., 2008). In Eurasia, this species is univoltine, and adult flight times vary between June to August ( Hoebeke et al., 2008). Adult forewings vary in colour from yellowish- to pinkish-brown, mottled with dark reddish-brown markings ( Hoebeke et al., 2008). The hind wings are light greyish-brown ( Hoebeke et al., 2008). In general, Archips species can be morphologically very similar and benefit from identification that combines both molecular genetic variation and morphology ( Gilligan et al., 2020; Kruse & Sperling, 2002). Female A. xylosteana lay egg masses on tree branches or trunks ( Hoebeke et al., 2008). Eggs overwinter ( Hoebeke et al., 2008; Szabóky & Csóka, 2010). Early larval instars feed on leaves and buds ( Hoebeke et al., 2008); later instars produce a leaf roll ( Szabóky & Csóka, 2010). Pupation occurs in leaf rolls ( Hoebeke et al., 2008).
Tortricidae is a large family that includes major pests, biological control agents and model Lepidoptera for the study of genetics, insect pheromones, and evolution ( Regier et al., 2012; Roe et al., 2009). Archips xylosteana is a polyphagous minor pest of fruit trees ( Hoebeke et al., 2008). As part of wider efforts to study Tortricidae, Archips xylosteana has been investigated to determine the presence and prevalence of naturally occurring microsporidian pathogens (e.g., Nosema spp., Pilarska et al., 2017), and their pheromone blend composition ( Safonkin & Triseleva, 2008).
Genome sequence report
The genome was sequenced from one female Archips xylosteana ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, –1.34). A total of 41-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 7 missing joins or mis-joins, increasing the scaffold N50 by 3.31%.
Figure 1. Photograph of the Archips xylosteana (ilArcXylo1) specimen used for genome sequencing.
The final assembly has a total length of 650.6 Mb in 113 sequence scaffolds with a scaffold N50 of 22.4 Mb ( Table 1). The snailplot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3. The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla. Most (99.57%) of the assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 29 autosomes and the W and Z sex chromosomes. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 5; Table 2). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.
Figure 2. Genome assembly of Archips xylosteana, ilArcXylo1.1: 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 650,610,935 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 (51,300,854 bp, shown in red). . Orange and pale-orange arcs show the N50 and N90 scaffold lengths (22,404,545 and 12,542,217 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/Archips%20xylosteana/dataset/CANOAX01/snail.
Figure 3. Genome assembly of Archips xylosteana, ilArcXylo1.1: 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/Archips%20xylosteana/dataset/CANOAX01/blob.
Figure 4. Genome assembly of Archips xylosteana, ilArcXylo1.1: 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/Archips%20xylosteana/dataset/CANOAX01/cumulative.
Figure 5. Genome assembly of Archips xylosteana, ilArcXylo1.1: Hi-C contact map of the ilArcXylo1.1 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=Kb-HksSUTSudYmUTC5iP3A.
Table 1. Genome data for Archips xylosteana, ilArcXylo1.1.
| Project accession data | ||
|---|---|---|
| Assembly identifier | ilArcXylo1.1 | |
| Species | Archips xylosteana | |
| Specimen | ilArcXylo1 | |
| NCBI taxonomy ID | 1100919 | |
| BioProject | PRJEB56130 | |
| BioSample ID | SAMEA7701541 | |
| Isolate information | ilArcXylo1, female: whole organism (DNA sequencing)
ilArcXylo2: whole organism (Hi-C data) |
|
| Assembly metrics * | Benchmark | |
| Consensus quality (QV) | 65.6 | ≥ 50 |
| k-mer completeness | 100% | ≥ 95% |
| BUSCO ** | C:98.4%[S:97.8%,D:0.5%],
F:0.4%,M:1.2%,n:5,286 |
C ≥ 95% |
| Percentage of assembly
mapped to chromosomes |
99.57% | ≥ 95% |
| Sex chromosomes | W and Z sex chromosomes |
localised homologous
pairs |
| Organelles | Mitochondrial genome assembled | complete single alleles |
| Raw data accessions | ||
| PacificBiosciences SEQUEL II | ERR10287579 | |
| Hi-C Illumina | ERR10297859 | |
| Genome assembly | ||
| Assembly accession | GCA_947563465.1 | |
| Accession of alternate haplotype | GCA_947563285.1 | |
| Span (Mb) | 650.6 | |
| Number of contigs | 136 | |
| Contig N50 length (Mb) | 20.4 | |
| Number of scaffolds | 113 | |
| Scaffold N50 length (Mb) | 22.4 | |
| Longest scaffold (Mb) | 51.3 | |
| Genome annotation | ||
| Number of protein-coding
genes |
19,861 | |
| Number of gene transcripts | 20,029 | |
* 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/Archips%20xylosteana/dataset/CANOAX01/busco.
Table 2. Chromosomal pseudomolecules in the genome assembly of Archips xylosteana, ilArcXylo1.
| INSDC accession | Chromosome | Length (Mb) | GC% |
|---|---|---|---|
| OX387344.1 | 1 | 26.11 | 38.0 |
| OX387345.1 | 2 | 25.59 | 38.5 |
| OX387346.1 | 3 | 24.61 | 38.0 |
| OX387347.1 | 4 | 24.42 | 38.0 |
| OX387348.1 | 5 | 24.1 | 38.5 |
| OX387349.1 | 6 | 23.98 | 38.0 |
| OX387350.1 | 7 | 23.89 | 38.0 |
| OX387351.1 | 8 | 23.65 | 38.0 |
| OX387352.1 | 9 | 23.41 | 38.0 |
| OX387353.1 | 10 | 23.09 | 38.5 |
| OX387355.1 | 11 | 22.57 | 38.0 |
| OX387356.1 | 12 | 22.4 | 38.0 |
| OX387357.1 | 13 | 21.46 | 38.5 |
| OX387358.1 | 14 | 20.98 | 38.5 |
| OX387359.1 | 15 | 20.37 | 38.5 |
| OX387360.1 | 16 | 20.3 | 38.5 |
| OX387361.1 | 17 | 19.84 | 38.5 |
| OX387362.1 | 18 | 19.67 | 38.5 |
| OX387363.1 | 19 | 19.23 | 38.5 |
| OX387364.1 | 20 | 18.63 | 38.5 |
| OX387365.1 | 21 | 17.65 | 39.0 |
| OX387366.1 | 22 | 16.5 | 38.5 |
| OX387367.1 | 23 | 15.91 | 38.5 |
| OX387368.1 | 24 | 13.94 | 39.0 |
| OX387369.1 | 25 | 13.47 | 39.0 |
| OX387370.1 | 26 | 12.54 | 39.5 |
| OX387371.1 | 27 | 12.38 | 39.5 |
| OX387372.1 | 28 | 11.73 | 38.5 |
| OX387373.1 | 29 | 11.34 | 39.0 |
| OX387354.1 | W | 3.79 | 39.0 |
| OX387343.1 | Z | 51.3 | 37.5 |
| OX387374.1 | MT | 0.02 | 19.0 |
The estimated Quality Value (QV) of the final assembly is 65.6 with k-mer completeness of 100%, and the assembly has a BUSCO v5.3.2 completeness of 98.4% (single = 97.8%, duplicated = 0.5%), using the lepidoptera_odb10 reference set ( n = 5,286).
Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/1100919.
Genome annotation report
The Archips xylosteana genome assembly (GCA_947563465.1) was annotated using the Ensembl rapid annotation pipeline ( Table 1; https://rapid.ensembl.org/Archips_xylosteana_GCA_947563465.1/Info/Index). The resulting annotation includes 20,029 transcribed mRNAs from 19,861 protein-coding genes.
Methods
Sample acquisition and nucleic acid extraction
A female Archips xylosteana (specimen ID Ox000680, ToLID ilArcXylo1) was collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude –1.34) on 2020-07-20, using a light trap. The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice. The specimen used for Hi-C sequencing (specimen ID Ox001601, ToLID ilArcXylo2) was collected from the same location by Liam Crowley (University of Oxford) on 2021-11-15, and was then preserved on dry ice.
The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) includes a sequence of core procedures: sample preparation; sample homogenisation; DNA extraction; HMW DNA fragmentation; and fragmented DNA clean-up. The ilArcXylo1 sample was weighed and dissected on dry ice as per the protocol at https://dx.doi.org/10.17504/protocols.io.x54v9prmqg3e/v1. For sample homogenisation, thorax tissue was cryogenically disrupted using the Sample Homogenisation: Covaris cryoPREP® Automated Dry Pulverizer protocol ( https://dx.doi.org/10.17504/protocols.io.eq2lyjp5qlx9/v1). HMW DNA was extracted by means of the Automated MagAttract protocol ( https://dx.doi.org/10.17504/protocols.io.kxygx3y4dg8j/v1). HMW DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 30, following the HMW DNA Fragmentation: Diagenode Megaruptor®3 for PacBio HiFi protocol ( https://dx.doi.org/10.17504/protocols.io.8epv5x2zjg1b/v1). Sheared DNA was purified by solid-phase reversible immobilisation (SPRI), following the protocol at https://dx.doi.org/10.17504/protocols.io.kxygx3y1dg8j/v1. In brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA. 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.
Protocols developed by the Tree of Life laboratory are publicly available on protocols.io: https://dx.doi.org/10.17504/protocols.io.8epv5xxy6g1b/v1.
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 the Pacific Biosciences SEQUEL II instrument. Hi-C data were also generated from whole organism tissue of ilArcXylo2 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.
Genome assembly, curation and evaluation
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 and corrected 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., 2023), which runs MitoFinder ( Allio et al., 2020) or MITOS ( Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
A Hi-C map for the final assembly was produced using bwa-mem2 ( Vasimuddin et al., 2019) in the Cooler file format ( Abdennur & Mirny, 2020). To assess the assembly metrics, the k-mer completeness and QV consensus quality values were calculated in Merqury ( Rhie et al., 2020). This work was done using Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a) and “sanger-tol/genomenote” ( Surana et al., 2023b). The genome was analysed within the BlobToolKit environment ( Challis et al., 2020) and BUSCO scores ( Manni et al., 2021; Simão et al., 2015) were calculated.
Table 3 contains a list of relevant software tool versions and sources.
Table 3. Software tools: versions and sources.
| Software tool | Version | Source |
|---|---|---|
| BlobToolKit | 4.1.7 | https://github.com/blobtoolkit/blobtoolkit |
| BUSCO | 5.3.2 | https://gitlab.com/ezlab/busco |
| Hifiasm | 0.16.1-r375 | https://github.com/chhylp123/hifiasm |
| HiGlass | 1.11.6 | https://github.com/higlass/higlass |
| Merqury | MerquryFK | https://github.com/thegenemyers/MERQURY.FK |
| MitoHiFi | 2 | https://github.com/marcelauliano/MitoHiFi |
| PretextView | 0.2 | https://github.com/wtsi-hpag/PretextView |
| purge_dups | 1.2.3 | https://github.com/dfguan/purge_dups |
| sanger-tol/genomenote | v1.0 | https://github.com/sanger-tol/genomenote |
| sanger-tol/readmapping | 1.1.0 | https://github.com/sanger-tol/readmapping/tree/1.1.0 |
| YaHS | yahs-1.1.91eebc2 | https://github.com/c-zhou/yahs |
Genome annotation
The BRAKER2 pipeline ( Brůna et al., 2021) was used in the default protein mode to generate annotation for the Archips xylosteana assembly (GCA_947563465.1) in Ensembl Rapid Release.
Wellcome Sanger Institute – Legal and Governance
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’, which can be found in full on the Darwin Tree of Life website here. 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.
Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use. The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible. The overarching areas of consideration are:
• Ethical review of provenance and sourcing of the material
• Legality of collection, transfer and use (national and international)
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) and the Darwin Tree of Life Discretionary Award (218328).
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: Archips xylosteana (variegated golden tortrix). Accession number PRJEB56130; https://identifiers.org/ena.embl/PRJEB56130 ( Wellcome Sanger Institute, 2022). The genome sequence is released openly for reuse. The Archips xylosteana 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.7125292.
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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