The genome sequence of the bishop’s mitre shieldbug, Aelia acuminata (Linnaeus, 1758)

We present a genome assembly from an individual male Aelia acuminata (the bishop’s mitre shieldbug; Arthropoda; Insecta; Hemiptera; Pentatomidae). The genome sequence is 1,170 megabases in span. The majority of the assembly (99.78%) is scaffolded into 8 chromosomal pseudomolecules, with the X and Y sex chromosome assembled.


Background
The Bishop's mitre shieldbug, Aelia acuminata, is a common mid-sized (8-9 mm) shieldbug. The vernacular name derives from the characteristically pointed head and pronotum forming a shape reminiscent of its namesake. It is common in grassland habitats across Europe, North Africa, the Middle East and Northern Asia. In the UK it is common and widespread across the south, and can be found in most dry grassland habitats. It feeds on the seeds of a range of grasses in the Poaceae family and may be a minor pest in cereal fields (Vaccino et al., 2017). It is univoltine, with adults mating and laying eggs in the spring and early summer. Nymphs develop through five instars throughout the summer months and reach adulthood by August. Aelia acuminata overwinters as an imago, with the increased photoperiod a key factor in termination of diapause in the spring (Hodek, 1971).

Genome sequence report
The genome was sequenced from one male A. acuminata ( Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.771, longitude -1.338). A total of 31-fold coverage in Pacific Biosciences single-molecule long reads and 24-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 241 missing/misjoins and removed 25 haplotypic duplications, reducing the assembly size by 0.73% and the scaffold number by 67.21% and increasing the scaffold N50 by 132.84%.
The final assembly has a total length of 1,170 Mb in 81 sequence scaffolds with a scaffold N50 of 172 Mb (Table 1). The majority of the assembly sequence (99.78%) was assigned to 8 chromosomal-level scaffolds, representing 6 autosomes (numbered by sequence length), and the X and Y sex chromosome (Figure 2- Figure 5; Table 2). The assembly has a BUSCO v5.1.2 (Manni et al., 2021) completeness of 99.3% (single 97.6%, duplicated 1.7%) using the hemiptera_odb10 reference set. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.

Methods
Sample acquisition, DNA extraction and sequencing A single male A. acuminata (ihAelAcum1) was collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), Figure 1. Image of the Aelia acuminata specimen (ihAelAcum1) used for genome sequencing, taken during preservation and processing. The specimen is shown alongside a FluidX sample tube 43.9 mm in length. Museum, by hand. The sample was identified by the same individual and was snap-frozen in liquid nitrogen.
DNA was extracted from the whole organism of ihAelAcum1 at the Wellcome Sanger Institute Scientific Operations core from the whole organism using the Qiagen MagAttract HMW Institute on Pacific Biosciences SEQUEL II and Illumina HiSeq X instruments. Hi-C data were generated from the head/thorax tissue of ihAelAcum5 and whole organism tissue of ihAelAcum1 using the Arima Hi-C+ kit and sequenced on an Illumina NovaSeq 6000 instrument.   ( 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 BlobToolKit environment (Challis et al., 2020). Table 3 contains a list of all software tool versions used, where appropriate. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.