The genome sequence of a leaf beetle, Chrysomela saliceti (Weise, 1884) (Coleoptera: Chrysomelidae)

TL;DR

This paper presents the genome sequence of the leaf beetle Chrysomela saliceti, including detailed assembly and gene annotation as part of a larger biodiversity project.

Contribution

The study provides a high-quality genome assembly and gene annotation for Chrysomela saliceti, contributing to the Darwin Tree of Life project.

Findings

The genome assembly includes two haplotypes totaling 738.63 and 703.32 megabases.

14,722 protein-coding genes were identified through Ensembl annotation.

The mitochondrial genome was assembled with a length of 21.9 kilobases.

Abstract

We present a genome assembly from an individual male
Chrysomela saliceti (leaf beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The assembly contains two haplotypes with total lengths of 738.63 megabases and 703.32 megabases. Most of haplotype 1 (98.68%) is scaffolded into 17 chromosomal pseudomolecules, including the X sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 21.9 kilobases. Gene annotation of this assembly on Ensembl identified 14 722 protein-coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

Figures

Photograph of the Chrysomela saliceti (icChrSali1) specimen used for genome sequencing.

Frequency distribution of k-mers generated using GenomeScope2.The plot shows observed and modelled k-mer spectra, providing estimates of genome size, heterozygosity, and repeat content based on unassembled sequencing reads.

Hi-C contact map of the Chrysomela saliceti genome assembly.Assembled chromosomes are shown in order of size and labelled along the axes, with a megabase scale shown below. The plot was generated using PretextSnapshot.

Evaluation of k-mer completeness using MerquryFK.This plot illustrates the recovery of k-mers from the original read data in the final assemblies. The horizontal axis represents k-mer multiplicity, and the vertical axis shows the number of k-mers. The black curve represents k-mers that appear in the reads but are not assembled. The green curve corresponds to k-mers shared by both haplotypes, and the red and blue curves show k-mers found only in one of the haplotypes.

Assembly metrics for icChrSali1.hap1.1.The BlobToolKit snail plot provides an overview of assembly metrics and BUSCO gene completeness. The circumference represents the length of the whole genome sequence, and the main plot is divided into 1 000 bins around the circumference. The outermost blue tracks display the distribution of GC, AT, and N percentages across the bins. Scaffolds are arranged clockwise from longest to shortest and are depicted in dark grey. The longest scaffold is indicated by the red arc, and the deeper orange and pale orange arcs represent the N50 and N90 lengths. A light grey spiral at the centre shows the cumulative scaffold count on a logarithmic scale. A summary of complete, fragmented, duplicated, and missing BUSCO genes in the set is presented at the top right. An interactive version of this figure can be accessed on the BlobToolKit viewer.

BlobToolKit GC-coverage plot for icChrSali1.hap1.1.Blob plot showing sequence coverage (vertical axis) and GC content (horizontal axis). The circles represent scaffolds, with the size proportional to scaffold length and the colour representing phylum membership. The histograms along the axes display the total length of sequences distributed across different levels of coverage and GC content. An interactive version of this figure is available on the BlobToolKit viewer.

Tables

Table 1.. Specimen and sequencing data for BioProject PRJEB79783.

Platform	PacBio HiFi	Hi-C
ToLID	icChrSali1	icChrSali1
Specimen ID	NHMUK014560511	NHMUK014560511
BioSample (source individual)	SAMEA114806286	SAMEA114806286
BioSample (tissue)	SAMEA114806422	SAMEA114806422
Tissue	whole organism	whole organism
Instrument	Revio	Illumina NovaSeq X
Run accessions	ERR13650041	ERR13654251
Read count total	1.72 million	767.45 million
Base count total	19.08 Gb	115.88 Gb

Table 2.. Genome assembly statistics.

Assembly name	icChrSali1.hap1.1	icChrSali1.hap2.1
Assembly accession	GCA_965121785.1	GCA_965122525.1
Assembly level	chromosome	scaffold
Span (Mb)	738.63	703.32
Number of chromosomes	17	scaffold-level
Number of contigs	709	798
Contig N50	2.15 Mb	2.04 Mb
Number of scaffolds	122	242
Scaffold N50	45.39 Mb	43.77 Mb
Longest scaffold length (Mb)	66.92	-
Sex chromosomes	X	-
Organelles	Mitochondrion: 21.9 kb	-

Table 3.. Chromosomal pseudomolecules in the haplotype 1 genome assembly of Chrysomela saliceti icChrSali1.

INSDC accession	Molecule	Length (Mb)	GC%
OZ222417.1	1	66.92	35.50
OZ222418.1	2	64.84	35.50
OZ222419.1	3	50.83	35.50
OZ222420.1	4	46.81	35.50
OZ222421.1	5	46.69	35.50
OZ222422.1	6	45.39	36
OZ222423.1	7	43.49	35.50
OZ222424.1	8	40.56	35.50
OZ222425.1	9	38.56	35.50
OZ222426.1	10	37.08	35.50
OZ222427.1	11	36.81	35.50
OZ222428.1	12	34.91	36
OZ222429.1	13	33.28	36
OZ222430.1	14	31.33	36
OZ222431.1	15	30.44	36
OZ222432.1	16	30.37	36.50
OZ222433.1	X	50.58	36.50

Table 4.. Earth Biogenome Project summary metrics for the Chrysomela saliceti assembly.

Measure	Value	Benchmark
EBP summary (haplotype 1)	6.C.Q60	6.C.Q40
Contig N50 length	2.15 Mb	≥ 1 Mb
Scaffold N50 length	45.39 Mb	= chromosome N50
Consensus quality (QV)	Haplotype 1: 60.6; haplotype 2: 60.3; combined: 60.5	≥ 40
k-mer completeness	Haplotype 1: 82.53%; Haplotype 2: 78.73%; combined: 99.01%	≥ 95%
BUSCO	C:99.0% [S:98.2%; D:0.8%]; F:0.2%; M:0.8%; n:2 124	S > 90%; D < 5%
Percentage of assembly assigned to chromosomes	98.68%	≥ 90%

Full text

Species taxonomy

Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Chrysomeloidea; Chrysomelidae; Chrysomelinae; Chrysomelini; Chrysomela; Chrysomela saliceti (Weise, 1884) (NCBI:txid1587176)

Background

We present a chromosome-level genome sequence for Chrysomela saliceti. The assembly was produced using the Tree of Life pipeline from a specimen collected from the WWT London Wetland Centre, Barnes, London, England, UK ( Figure 1). This assembly was generated as part of the Darwin Tree of Life Project, which aims to generate high-quality reference genomes for all named eukaryotic species in Britain and Ireland to support research, conservation, and the sustainable use of biodiversity ( Darwin Tree of Life Project Consortium, 2022).

Photograph of the Chrysomela saliceti (icChrSali1) specimen used for genome sequencing.

Methods

Sample acquisition and DNA barcoding

The specimen used for genome sequencing was an adult male Chrysomela saliceti (specimen ID NHMUK014560511, ToLID icChrSali1; Figure 1), collected from WWT London Wetland Centre, Barnes, London, England, UK (latitude 51.48, longitude –0.24) on 2022-05-02. The specimen was collected and identified by Michael Geiser (Natural History Museum). Details of the sampling and metadata procedures, which followed recommended standards, are described in Lawniczak et al. (2022).

The initial identification was verified by an additional DNA barcoding process according to the framework developed by Twyford et al. (2024). A small sample was dissected from the specimen and stored in ethanol, while the remaining parts were shipped on dry ice to the Wellcome Sanger Institute (WSI) (see the protocol). The tissue was lysed, the COI marker region was amplified by PCR, and amplicons were sequenced and compared to the BOLD database, confirming the species identification ( Crowley et al., 2023). Following whole genome sequence generation, the relevant DNA barcode region was also used alongside the initial barcoding data for sample tracking at the WSI ( Twyford et al., 2024). The standard operating procedures for Darwin Tree of Life barcoding are available on protocols.io.

Nucleic acid extraction

Protocols for high molecular weight (HMW) DNA extraction developed at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory are available on protocols.io ( Howard et al., 2025). The icChrSali1 sample was weighed and triaged to determine the appropriate extraction protocol. Tissue from the whole organism was homogenised by powermashing using a PowerMasher II tissue disruptor.

HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol. DNA was sheared into an average fragment size of 12–20 kb following the Megaruptor®3 for LI PacBio protocol. Sheared DNA was purified by automated SPRI (solid-phase reversible immobilisation). The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system. For this sample, the final post-shearing DNA had a Qubit concentration of 31.9 ng/μL and a yield of 1 499.30 ng, with a fragment size of 16.1 kb.

PacBio HiFi library preparation and sequencing

Library preparation and sequencing were performed at the WSI Scientific Operations core. Libraries were prepared using the SMRTbell Prep Kit 3.0 (Pacific Biosciences, California, USA), following the manufacturer’s instructions. The kit includes reagents for end repair/A-tailing, adapter ligation, post-ligation SMRTbell bead clean-up, and nuclease treatment. Size selection and clean-up were performed using diluted AMPure PB beads (Pacific Biosciences). DNA concentration was quantified using a Qubit Fluorometer v4.0 (ThermoFisher Scientific) and the Qubit 1X dsDNA HS assay kit. Final library fragment size was assessed with the Agilent Femto Pulse Automated Pulsed Field CE Instrument (Agilent Technologies) using the gDNA 55 kb BAC analysis kit.

The sample was sequenced on a Revio instrument (Pacific Biosciences). The prepared library was normalised to 2 nM, and 15 μL was used for making complexes. Primers were annealed and polymerases bound to generate circularised complexes, following the manufacturer’s instructions. Complexes were purified using 1.2X SMRTbell beads, then diluted to the Revio loading concentration (200–300 pM) and spiked with a Revio sequencing internal control. The sample was sequenced on a Revio 25M SMRT cell. The SMRT Link software (Pacific Biosciences), a web-based workflow manager, was used to configure and monitor the run and to carry out primary and secondary data analysis.

Hi-C

** Sample preparation and crosslinking **

The Hi-C sample was prepared from 20–50 mg of frozen tissue from the icChrSali1 sample using the Arima-HiC v2 kit (Arima Genomics). Following the manufacturer’s instructions, tissue was fixed and DNA crosslinked using TC buffer to a final formaldehyde concentration of 2%. The tissue was homogenised using the Diagnocine Power Masher-II. Crosslinked DNA was digested with a restriction enzyme master mix, biotinylated, and ligated. Clean-up was performed with SPRISelect beads before library preparation. DNA concentration was measured with the Qubit Fluorometer (Thermo Fisher Scientific) and Qubit HS Assay Kit. The biotinylation percentage was estimated using the Arima-HiC v2 QC beads.

** Hi-C library preparation and sequencing **

Biotinylated DNA constructs were fragmented using a Covaris E220 sonicator and size selected to 400–600 bp using SPRISelect beads. DNA was enriched with Arima-HiC v2 kit Enrichment beads. End repair, A-tailing, and adapter ligation were carried out with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs), following a modified protocol where library preparation occurs while DNA remains bound to the Enrichment beads. Library amplification was performed using KAPA HiFi HotStart mix and a custom Unique Dual Index (UDI) barcode set (Integrated DNA Technologies). Depending on sample concentration and biotinylation percentage determined at the crosslinking stage, libraries were amplified with 10–16 PCR cycles. Post-PCR clean-up was performed with SPRISelect beads. Libraries were quantified using the AccuClear Ultra High Sensitivity dsDNA Standards Assay Kit (Biotium) and a FLUOstar Omega plate reader (BMG Labtech).

Prior to sequencing, libraries were normalised to 10 ng/μL. Normalised libraries were quantified again and equimolar and/or weighted 2.8 nM pools were created. Pool concentrations were checked using the Agilent 4200 TapeStation (Agilent) with High Sensitivity D500 reagents before sequencing. Sequencing was performed using paired-end 150 bp reads on the Illumina NovaSeq X.

Genome assembly

Prior to assembly of the PacBio HiFi reads, a database of k-mer counts ( k = 31) was generated from the filtered reads using FastK. GenomeScope2 ( Ranallo-Benavidez et al., 2020) was used to analyse the k-mer frequency distributions, providing estimates of genome size, heterozygosity, and repeat content.

The HiFi reads were assembled using Hifiasm in Hi-C phasing mode ( Cheng et al., 2021; Cheng et al., 2022), producing two haplotypes. Hi-C reads ( Rao et al., 2014) were mapped to the primary contigs using bwa-mem2 ( Vasimuddin et al., 2019). Contigs were further scaffolded with Hi-C data in YaHS ( Zhou et al., 2023), using the --break option for handling potential misassemblies. The scaffolded assemblies were evaluated using Gfastats ( Formenti et al., 2022), BUSCO ( Manni et al., 2021) and MERQURY.FK ( Rhie et al., 2020).

The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2023), which runs MitoFinder ( Allio et al., 2020) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.

Assembly curation

The assembly was decontaminated using the Assembly Screen for Cobionts and Contaminants ( ASCC) pipeline. TreeVal was used to generate the flat files and maps for use in curation. Manual curation was conducted primarily in PretextView and HiGlass ( Kerpedjiev et al., 2018). Scaffolds were visually inspected and corrected as described by Howe et al. (2021). Manual corrections included 49 breaks and 128 joins. These changes reduced the scaffold count by 28.1% and increased the scaffold N50 by 17.7%. The curation process is documented at https://gitlab.com/wtsi-grit/rapid-curation. PretextSnapshot was used to generate a Hi-C contact map of the final assembly.

Assembly quality assessment

The Merqury.FK tool ( Rhie et al., 2020) was run in a Singularity container ( Kurtzer et al., 2017) to evaluate k-mer completeness and assembly quality for both haplotypes using the k-mer databases ( k = 31) computed prior to genome assembly. The analysis outputs included assembly QV scores and completeness statistics.

The genome was analysed using the BlobToolKit pipeline, a Nextflow implementation of the earlier Snakemake version ( Challis et al., 2020). The pipeline aligns PacBio reads using minimap2 ( Li, 2018) and SAMtools ( Danecek et al., 2021) to generate coverage tracks. It runs BUSCO ( Manni et al., 2021) using lineages identified from the NCBI Taxonomy ( Schoch et al., 2020). For the three domain-level lineages, BUSCO genes are aligned to the UniProt Reference Proteomes database ( Bateman et al., 2023) using DIAMOND blastp ( Buchfink et al., 2021). The genome is divided into chunks based on the density of BUSCO genes from the closest taxonomic lineage, and each chunk is aligned to the UniProt Reference Proteomes database with DIAMOND blastx. Sequences without hits are chunked using seqtk and aligned to the NT database with blastn ( Altschul et al., 1990). The BlobToolKit suite consolidates all outputs into a blobdir for visualisation. The BlobToolKit pipeline was developed using nf-core tooling ( Ewels et al., 2020) and MultiQC ( Ewels et al., 2016), with containerisation through Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017).

Genome sequence report

Sequence data

PacBio sequencing of the Chrysomela saliceti specimen generated 19.08 Gb (gigabases) from 1.72 million reads, which were used to assemble the genome. GenomeScope2.0 analysis estimated the haploid genome size at 726.46 Mb, with a heterozygosity of 0.89% and repeat content of 49.89% ( Figure 2). These estimates guided expectations for the assembly. Based on the estimated genome size, the sequencing data provided approximately 26× coverage. Hi-C sequencing produced 115.88 Gb from 767.45 million reads, which were used to scaffold the assembly. Table 1 summarises the specimen and sequencing details.

Frequency distribution of k-mers generated using GenomeScope2.The plot shows observed and modelled k-mer spectra, providing estimates of genome size, heterozygosity, and repeat content based on unassembled sequencing reads.

Assembly statistics

The genome was assembled into two haplotypes using Hi-C phasing. Haplotype 1 was curated to chromosome level, while haplotype 2 was assembled to scaffold level. The final assembly has a total length of 738.63 Mb in 122 scaffolds, with 587 gaps, and a scaffold N50 of 45.39 Mb ( Table 2).

Most of the assembly sequence (98.68%) was assigned to 17 chromosomal-level scaffolds, representing 16 autosomes and the X sex chromosome. These chromosome-level scaffolds, confirmed by Hi-C data, are named according to size ( Figure 3; Table 3). Chromosome X was identified by BUSCO gene painting with ancestral elements and by copy number in the diploid assembly. No Chromosome Y could be identified.

Hi-C contact map of the Chrysomela saliceti genome assembly.Assembled chromosomes are shown in order of size and labelled along the axes, with a megabase scale shown below. The plot was generated using PretextSnapshot.

Table 3.: Chromosomal pseudomolecules in the haplotype 1 genome assembly of Chrysomela saliceti icChrSali1.

The mitochondrial genome was also assembled (length 21.9 kb, OZ222434.1). This sequence is included as a contig in the multifasta file of the genome submission and as a standalone record.

For haplotype 1, the estimated QV is 60.6, and for haplotype 2, 60.3. When the two haplotypes are combined, the assembly achieves an estimated QV of 60.5. The k-mer completeness is 82.53% for haplotype 1, 78.73% for haplotype 2, and 99.01% for the combined haplotypes ( Figure 4).

Evaluation of k-mer completeness using MerquryFK.This plot illustrates the recovery of k-mers from the original read data in the final assemblies. The horizontal axis represents k-mer multiplicity, and the vertical axis shows the number of k-mers. The black curve represents k-mers that appear in the reads but are not assembled. The green curve corresponds to k-mers shared by both haplotypes, and the red and blue curves show k-mers found only in one of the haplotypes.

BUSCO analysis using the endopterygota_odb10 reference set ( n = 2 124) identified 99.0% of the expected gene set (single = 98.2%, duplicated = 0.8%) for haplotype 1. The snail plot in Figure 5 summarises the scaffold length distribution and other assembly statistics for haplotype 1. The blob plot in Figure 6 shows the distribution of scaffolds by GC proportion and coverage for haplotype 1.

Assembly metrics for icChrSali1.hap1.1.The BlobToolKit snail plot provides an overview of assembly metrics and BUSCO gene completeness. The circumference represents the length of the whole genome sequence, and the main plot is divided into 1 000 bins around the circumference. The outermost blue tracks display the distribution of GC, AT, and N percentages across the bins. Scaffolds are arranged clockwise from longest to shortest and are depicted in dark grey. The longest scaffold is indicated by the red arc, and the deeper orange and pale orange arcs represent the N50 and N90 lengths. A light grey spiral at the centre shows the cumulative scaffold count on a logarithmic scale. A summary of complete, fragmented, duplicated, and missing BUSCO genes in the set is presented at the top right. An interactive version of this figure can be accessed on the BlobToolKit viewer.

BlobToolKit GC-coverage plot for icChrSali1.hap1.1.Blob plot showing sequence coverage (vertical axis) and GC content (horizontal axis). The circles represent scaffolds, with the size proportional to scaffold length and the colour representing phylum membership. The histograms along the axes display the total length of sequences distributed across different levels of coverage and GC content. An interactive version of this figure is available on the BlobToolKit viewer.

Table 4 lists the assembly metric benchmarks adapted from Rhie et al. (2021) and the Earth BioGenome Project Report on Assembly Standards September 2024. The EBP metric, calculated for the haplotype 1, is 6.C.Q60, meeting the recommended reference standard.

Table 4.: Earth Biogenome Project summary metrics for the Chrysomela saliceti assembly.

Genome annotation report

The Chrysomela saliceti genome assembly (GCA_965121785.1) was annotated by Ensembl at the European Bioinformatics Institute (EBI), using the Ensembl non-vertebrate genome annotation method. This annotation includes 27 910 transcribed mRNAs from 14 722 protein-coding and 4 217 non-coding genes. The average transcript length is 15 492.29 bp, with an average of 1.47 coding transcripts per gene and 4.84 exons per transcript. For further information about the annotation, please refer to the annotation page on Ensembl.

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. 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 materialLegality 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.