The genome sequence of the Wainscot Smudge, Ypsolopha scabrella (Linnaeus, 1761)

TL;DR

This paper provides the genome sequence of the Wainscot Smudge moth, including chromosomal scaffolding and gene annotations.

Contribution

The study presents a high-quality genome assembly and gene annotation for Ypsolopha scabrella.

Findings

The genome assembly spans 853.6 megabases and is scaffolded into 31 chromosomal pseudomolecules.

The mitochondrial genome is 16.7 kilobases long.

Gene annotation identified 20,594 protein-coding genes.

Abstract

We present a genome assembly from an individual male
Ypsolopha scabrella (the Wainscot Smudge; Arthropoda; Insecta; Lepidoptera; Ypsolophidae). The genome sequence is 853.6 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 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,594 protein coding genes.

Figures

Photograph of the Ypsolopha scabrella (ilYpsScab1) specimen used for genome sequencing.

Genome assembly of Ypsolopha scabrella, ilYpsScab1.1: 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 853,595,150 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 (52,420,632 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (29,858,840 and 19,866,168 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/ilYpsScab1.1/dataset/CAJUZF01.1/snail.

Genome assembly of Ypsolopha scabrella, ilYpsScab1.1: 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/ilYpsScab1.1/dataset/CAJUZF01.1/blob.

Genome assembly of Ypsolopha scabrella, ilYpsScab1.1: 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/ilYpsScab1.1/dataset/CAJUZF01.1/cumulative.

Genome assembly of Ypsolopha scabrella, ilYpsScab1.1: Hi-C contact map of the ilYpsScab1.1 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=MEkHt8scQR6xmc-6DNy3Gg.

Tables

Table 1.. Genome data for Ypsolopha scabrella, ilYpsScab1.1.

Project accession data
Assembly identifier	ilYpsScab1.1
Species	Ypsolopha scabrella
Specimen	ilYpsScab1
NCBI taxonomy ID	1870435
BioProject	PRJEB45184
BioSample ID	SAMEA7701504
Isolate information	ilYpsScab1, male: whole organism (DNA sequencing) ilYpsScab2, female: whole organism (Hi-C scaffolding)
Assembly metrics *		Benchmark
Consensus quality (QV)	58.8	≥ 50
k-mer completeness	99.99%	≥ 95%
BUSCO **	C:98.1%[S:96.4%,D:1.6%], F:0.5%,M:1.5%,n:5,286	C ≥ 95%
Percentage of assembly mapped to chromosomes	99.97%	≥ 95%
Sex chromosomes	Z chromosome	localised homologous pairs
Organelles	Mitochondrial genome assembled	complete single alleles
Raw data accessions
PacificBiosciences SEQUEL II	ERR6454731, ERR6454732
10X Genomics Illumina	ERR6054910, ERR6054912, ERR6054909, ERR6054911
Hi-C Illumina	ERR6054913
Genome assembly
Assembly accession	GCA_910592155.1
Accession of alternate haplotype	GCA_910591985.1
Span (Mb)	853.6
Number of contigs	91
Contig N50 length (Mb)	26.5
Number of scaffolds	40
Scaffold N50 length (Mb)	29.9
Longest scaffold (Mb)	52.4
Genome annotation
Number of protein-coding genes	20,594
Number of gene transcripts	20,761

Table 2.. Chromosomal pseudomolecules in the genome assembly of Ypsolopha scabrella, ilYpsScab1.

INSDC accession	Chromosome name	Length (MB)	GC Percent
OU342961.1	1	33.96	36.5
OU342962.1	2	32.86	36.5
OU342963.1	3	32.56	36.5
OU342964.1	4	31.86	36
OU342965.1	5	31.59	36.5
OU342966.1	6	31.45	36.5
OU342967.1	7	31.33	36.5
OU342968.1	8	31.04	36
OU342969.1	9	31.02	36
OU342970.1	10	30.74	36.5
OU342971.1	11	29.93	36.5
OU342972.1	12	29.86	37
OU342973.1	13	29.63	36.5
OU342974.1	14	29.51	36.5
OU342975.1	15	28.82	36.5
OU342976.1	16	27.76	36
OU342977.1	17	26.93	36.5
OU342978.1	18	26.87	36.5
OU342979.1	19	26.54	36.5
OU342980.1	20	25.07	36.5
OU342981.1	21	24.93	37
OU342982.1	22	24.6	36.5
OU342983.1	23	21.95	36.5
OU342984.1	24	21.05	36.5
OU342985.1	25	20.85	36.5
OU342986.1	26	19.87	37.5
OU342987.1	27	19.5	37
OU342988.1	28	16.98	37
OU342989.1	29	16.64	37
OU342990.1	30	15.21	38.5
OU342960.1	Z	52.42	36
OU342991.1	MT	0.2

Table 3.. Software tools: versions and sources.

Software tool	Version	Source
BlobToolKit	4.0.7	https://github.com/blobtoolkit/blobtoolkit
BUSCO	5.3.2	https://gitlab.com/ezlab/busco
FreeBayes	1.3.1-17-gaa2ace8	https://github.com/freebayes/freebayes
gEVAL	N/A	https://geval.org.uk/
Hifiasm	0.15.1-r328	https://github.com/chhylp123/hifiasm
HiGlass	1.11.6	https://github.com/higlass/higlass
Long Ranger ALIGN	2.2.2	https://support.10xgenomics.com/genome-exome/software/pipelines/latest/advanced/other-pipelines
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
SALSA	2.2	https://github.com/salsa-rs/salsa
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

Full text

Species taxonomy

Eukaryota; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Yponomeutoidea; Ypsolophidae; Ypsolopha; Ypsolopha scabrella (Linnaeus, 1761) (NCBI:txid1870435).

Background

Ypsolopha scabrella (Wainscot Smudge) is a common micro-moth in the family Ypsolophidae. The species has a southerly distribution in Britain and is found throughout Europe apart from Portugal and Greece ( GBIF Secretariat, 2022).

Y. scabrella has one generation a year and flies between June and October. It readily comes to light and is found in woodland, scrub and gardens ( Sterling et al., 2012). The small (wingspan 15–21 mm) adult moth rests with its wings curled around its body. The forewing colour is whitish, with pale and dark brown streaks. There are three tufts of raised, darkened scales along the back ( Emmet, 1996). The egg is usually laid on hawthorn or apple, but occasionally on cotoneaster where it overwinters. The larvae feed in a rather insignificant web and pupate during June and July in a boat-shaped cocoon on the ground ( Langmaid et al., 2018).

A genome sequence from Y. scabrella will be useful for comparative studies across the Lepidoptera. The genome of Y. scabrella 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 Y. scabrella based on a male specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report

The genome was sequenced from one male Ypsolopha scabrella ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, –1.34). A total of 36-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 40-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 35 missing joins or misjoins, reducing the scaffold number by 38.46%, and increasing the scaffold N50 by 1.37%.

Photograph of the Ypsolopha scabrella (ilYpsScab1) specimen used for genome sequencing.

The final assembly has a total length of 853.6 Mb in 40 sequence scaffolds with a scaffold N50 of 29.9 Mb ( Table 1). Most (99.97%) of the assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 30 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). 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.

Table 1.: Genome data for Ypsolopha scabrella, ilYpsScab1.1.

Genome assembly of Ypsolopha scabrella, ilYpsScab1.1: 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 853,595,150 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 (52,420,632 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (29,858,840 and 19,866,168 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/ilYpsScab1.1/dataset/CAJUZF01.1/snail.

Genome assembly of Ypsolopha scabrella, ilYpsScab1.1: 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/ilYpsScab1.1/dataset/CAJUZF01.1/blob.

Genome assembly of Ypsolopha scabrella, ilYpsScab1.1: 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/ilYpsScab1.1/dataset/CAJUZF01.1/cumulative.

Genome assembly of Ypsolopha scabrella, ilYpsScab1.1: Hi-C contact map of the ilYpsScab1.1 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=MEkHt8scQR6xmc-6DNy3Gg.

The estimated Quality Value (QV) of the final assembly is 58.8 with k-mer completeness of 99.99%, and the assembly has a BUSCO v5.3.2 completeness of 98.1% (single = 96.4%, duplicated = 1.6%), using the lepidoptera_odb10 reference set ( n = 5,286).

Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/1870435.

Genome annotation report

The Ypsolopha scabrella genome assembly (GCA_910592155.1) was annotated using the Ensembl rapid annotation pipeline ( Table 1; https://rapid.ensembl.org/Ypsolopha_scabrella_GCA_910592155.1/Info/Index). The resulting annotation includes 20,761 transcribed mRNAs from 20,594 protein-coding and $NCG non-coding genes.

Methods

Sample acquisition and nucleic acid extraction

Two Ypsolopha scabrella specimens were collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude –1.34) on 2020-07-20 using a light trap. The specimens were collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice. The specimen used for genome sequencing was specimen ID Ox000642, ToLID ilYpsScab1, while the specimen used for Hi-C scaffolding was specimen ID Ox000643, ToLID ilYpsScab2.

DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The ilYpsScab1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Tissue from the whole organism 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. Low molecular weight DNA was removed from a 20 ng aliquot of extracted DNA using the 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing. 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 and 10X Genomics read cloud DNA sequencing libraries were constructed according to the manufacturers’ instructions. DNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (10X) instruments. Hi-C data were also generated from whole organism tissue of ilYpsScab2 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). One round of polishing was performed by aligning 10X Genomics read data to the assembly with Long Ranger ALIGN, calling variants with FreeBayes ( Garrison & Marth, 2012). The assembly was then scaffolded with Hi-C data ( Rao et al., 2014) using SALSA2 ( Ghurye et al., 2019). The assembly was checked for contamination and corrected using the gEVAL system ( Chow et al., 2016) as described previously ( Howe et al., 2021). Manual curation was performed using gEVAL, 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.

Genome annotation

The BRAKER2 pipeline ( Brůna et al., 2021) was used in the default protein mode to generate annotation for the Ypsolopha scabrella assembly (GCA_910592155.1) 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.