The genome sequence of the seven-spotted ladybird, Coccinella septempunctata Linnaeus, 1758

We present a genome assembly from an individual female Coccinella septempunctata (the seven-spotted ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 399 megabases in span. The majority (99.96%) of the assembly is scaffolded into 9 chromosomal pseudomolecules, with the X sex chromosome assembled.


Background
The 7-spot ladybird, Coccinella septempunctata Linnaeus, 1758, is an iconic species of ladybird and one of the most common in the UK and across Europe. It is widespread and abundant throughout its native range of Europe, Asia and North Africa, although it's distribution trend in the UK is decreasing (Roy & Brown, 2018). It can be found across a wide range of habitats including gardens and agricultural land. Adults are large (5-8 mm), conspicuously marked species with vivid red elytra marked with 7 black spots. The head, pronotum and legs are black. The scarce 7-spot ladybird, Coccinella magnifica, is very similar, but can be distinguished by its larger black spots, and additional pair of white markings below the legs on the underside. The 7-spot ladybird is a predatory species, feeding on a wide range of aphid species both as a larva and as an adult. It overwinters as an adult in among foliage, dead plant material and leaf litter. The broad geographic success of this species may be underpinned by its ecological plasticity based on both genetic and phenotypic polymorphisms (Hodek et al., 2013). It has been repeatedly introduced to North America as a biological control agent against aphids in agricultural systems.

Genome sequence report
The genome was sequenced from one female C. septempunctata ( Figure 1) collected from Wytham Farm, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.779, longitude -0.317). A total of 76-fold coverage in Pacific Biosciences singlemolecule long reads and 89-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 78 missing/misjoins and removed 10 haplotypic duplications, reducing the assembly length by 2.60% and the scaffold number by 70.37%, and increasing the scaffold N50 by 49.73%.
The final assembly has a total length of 399 Mb in 24 sequence scaffolds with a scaffold N50 of 41.4 Mb ( Table 1). The majority, Figure 1. Image of the icCocSept1 specimen captured prior to preservation and processing. 99.96%, of the assembly sequence was assigned to 10 chromosomal-level scaffolds, representing 9 autosomes (numbered by sequence length), and the X sex chromosome (Figure 2- Figure 5; Table 2). There is a repeat that is shared between chromosomes X and 9 that could be slightly differently distributed between the two. The assembly has a BUSCO v5.1.2 (Manni et al., 2021) completeness of 97.5% (single 96.4%, duplicated 1.0%) using the endopterygota_odb10 reference set. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. Tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts. Fragment size analysis of 0.01-0.5 ng of DNA was then performed using an Agilent FemtoPulse. High molecular weight (HMW) DNA was again extracted using the Qiagen MagAttract HMW DNA extraction kit. HMW DNA was sheared into an average fragment size between 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. Sequencing was performed by the Scientific Operations core at the Wellcome Sanger Institute on Pacific Biosciences SEQUEL II and Illumina HiSeq X instruments. Hi-C data were generated using the Arima v2 Hi-C kit and sequenced on an Illumina NovaSeq 6000 instrument.

Genome assembly
Assembly was carried out with HiCanu (Nurk et al., 2020); 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 longranger 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   HiGlass (Kerpedjiev et al., 2018) and Pretext. The mitochondrial genome was assembled using MitoHiFi (Uliano-Silva et al., 2021). The genome was analysed and BUSCO scores generated within the Blob-ToolKit environment (Challis et al., 2020). The genome sequence is released openly for reuse. The C. septempunctata 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.The genome will be annotated and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1.