The genome sequence of a caddisfly, Limnephilus auricula (Curtis, 1834)

We present a genome assembly from an individual female Limnephilus auricula (a caddisfly; Arthropoda; Insecta; Trichoptera; Limnephilidae). The genome sequence is 971.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.29 kilobases in length.


Background
Limnephilus is the largest genus of caddisflies (Trichoptera) in the UK, with 29 species recorded.It is also a difficult group to identify to species level, with determination commonly relying on the examination of genitalia.However, in a few cases wing markings can give a good indication; L. auricula has a distinctive pattern consisting of about ten subrectangular pale spots clustered in the centre of the apical third of the forewing.The wing length of this species is 8-12 mm, and it is among the smaller members of the genus in the UK (Barnard & Ross, 2012).This species' distribution is concentrated in north-western Europe, but extends north-east to southern Finland and southeast to eastern Turkey (GBIF Secretariat, 2022).Within the UK the species is widespread and generally common; records become sparser further north but reach as far as Shetland (NBN Atlas Partnership, 2021).The larva, which constructs a tubular case from small pieces of vegetation, does not have strict habitat requirements and can be found in a range of small bodies of standing water (Graf et al., 2008).Adult emergence begins in April in the earliest cases and the latest individuals will remain on the wing in November, although the flight season is punctuated by a period of adult diapause at the height of summer (Barnard & Ross, 2012).
The assembled genome of Limnephilus auricula will facilitate research into aquatic adaptations of caddisflies and contribute to the growing set of resources for studying insect ecology and evolution.

Genome sequence report
The genome was sequenced from one female Limnephilus auricula (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 26-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 13 missing joins or mis-joins and removed 8 haplotypic duplications, reducing the assembly length by 0.4% and the scaffold number by 45%. The final assembly has a total length of 971.3 Mb in 44 sequence scaffolds with a scaffold N50 of 34.8 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 (99.86%) of the assembly sequence was assigned to 30 chromosomal-level scaffolds, representing 29 autosomes and the Z sex chromosome.Chromosome Z was assigned based on read coverage statistics.The sample appears to be ZO as no W could be identified.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.

Sample acquisition and nucleic acid extraction
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.

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     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.

INSDC accession
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 A female Limnephilus auricula (specimen ID Ox002663, ToLID iiLimAuri1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2022-08-15 using a sweep net.The specimen was collected and identified by James McCulloch (University of Oxford) and 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 sample was prepared for DNA extraction at the WSI Tree of Life laboratory: the iiLimAuri1 sample was weighed and dissected on dry ice with

Figure 2 .
Figure 2. Genome assembly of Limnephilus auricula, iiLimAuri1.1: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 971,302,186 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 (47,575,505 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (34,751,523 and 22,144,957 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 endopterygota_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Limnephilus%20auricula/dataset/iiLimAuri1_1/snail.

Figure 3 .
Figure 3. Genome assembly of Limnephilus auricula, iiLimAuri1.1: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/Limnephilus%20auricula/dataset/iiLimAuri1_1/blob.
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.

Figure 4 .
Figure 4. Genome assembly of Limnephilus auricula, iiLimAuri1.1: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/Limnephilus%20auricula/dataset/iiLimAuri1_1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Limnephilus auricula, iiLimAuri1.1:Hi-C contact map of the iiLimAuri1.1 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=W5al477HRX-9waF4zdBRlg.
(Rao et al., 2014))enchmarks are adapted from column VGP-2020 of "Table1: Proposed standards and metrics for defining genome assembly quality" from(Rhie et al., 2021).**ismwasdisruptedusing a Nippi Powermasher fitted with a BioMasher pestle (https://dx.doi.org/10.17504/protocols.io.5qpvo3r19v4o/v1).DNA was extracted at the WSI Scientific Operations core using the Qiagen MagAttract HMW DNA kit, according to the manufacturer's instructions.SequencingPacific 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 a Pacific Biosciences SEQUEL II instrument.Hi-C data were also generated from remaining tissue of iiLimAuri1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.Genome assembly, curation and evaluationAssembly was carried out withHifiasm (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

the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
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.No competing interests were disclosed. YesAre

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
No competing interests were disclosed.