The genome sequence of the Common Sycamore Aphid, Drepanosiphum platanoidis (Schrank, 1801)

We present a genome assembly from an individual female Drepanosiphum platanoidis (the Common Sycamore Aphid; Arthropoda; Insecta; Hemiptera; Aphididae). The genome sequence is 284.5 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.45 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,286 protein coding genes.


Background
The Common Sycamore Aphid, Drepanosiphum platanoidis (Schrank, 1801), is a holocyclic aphid, feeding and reproducing on sycamore, Acer pseudoplatanus L (Wade & Leather, 2002).All adult D. platanoidis are winged, most are green, although a small percentage can be red, and they can develop dark cross-bars on their abdomen (Stroyan, 1977).D. platanoidis is found wherever sycamore occurs, mostly in Europe and the UK, but also in the USA, Canada, New Zealand, central Asia, and North Africa (GBIF Secretariat, 2023).
The lifecycle of D. platanoidis is closely linked to the nutritional value of the sycamore phloem.In the spring, the fundatrices emerge and begin asexual reproduction in response to the high nutritional value of the host phloem associated with bud burst and leaf flushing.Following this period of rapid population growth, they enter a period of aestivation of up to 8 weeks throughout the summer when conditions, such as rainfall, are less favourable (Wellings et al., 1985).In the autumn when the nutritional value increases once again, D. platanoides resumes feeding and reproduction.At this time, sexual male and females are produced, which subsequently mate, resulting in the laying of overwintering eggs (Wade & Leather, 2002;Wynne et al., 1994).This species forms characteristic, uniformly spaced aggregations on the underside of sycamore leaves.The density of these aggregation depends on the palatability of the host and the associated level of intraspecific competition (Dixon & Logan, 1972), with larger leaves supporting a greater number and higher density of aphids (Dixon & McKay, 1970).
The reproductive rate of D. platanoidis is influenced by several factors including temperature, intraspecific competition and the levels of amino acids in host tissue (Wellings, 1981).Due to this aphid's intimate relationship with the climate in which it resides, D. platanoidis is a good model insect for study of the effect of climate change on insect populations (Senior et al., 2020).The availability of the genome will facilitate studies of the underlying genetics behind this aphid's response to climate change.It will also enable genetic comparisons with other tree-dwelling and non-tree dwelling aphids.
The genome of the common sycamore aphid, Drepanosiphum platanoidis, 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 Drepanosiphum platanoidis, based on one female specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one female Drepanosiphum platanoidis (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 64-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 94 missing joins or misjoins and removed 3 haplotypic duplications, reducing the scaffold number by 23.81% and increasing the scaffold N50 by 11.22%. The final assembly has a total length of 284.5 Mb in 63 sequence scaffolds with a scaffold N50 of 24.4 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 (99.76%) of the assembly sequence was assigned to 15 chromosomal-level scaffolds.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).Three super scaffolds align to the M. periscae and A. pisum X chromosome (which is broadly conserved in aphids (Mathers et al., 2021).No male samples were available to determine which chromosome(s) are functionally the sex (X) chromosome in this species.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.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/527648.
The resulting annotation includes 13,442 transcribed mRNAs from 13,286 protein-coding genes.

Sample acquisition and nucleic acid extraction
A female Drepanosiphum platanoidis (specimen ID Ox001587, individual ihDrePlat2) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.33) on 2021-07-14.The specimen was collected and identified by Liam Crowley (University of Oxford) and preserved on dry ice.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

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Drepanosiphum platanoidis assembly (GCA_948098885.1) 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

Felipe Cordeiro Dias
Universidade de São Paulo, São Paulo, Brazil The article provides a complete description of the assembly and annotation of the genome of the common sycamore aphid Drepanosiphum platanoidis, detailing aspects of its composition and structure.The report is well written and provides a good overview.
The background shows some information about the biological aspects of the species, such as the differences brought by the seasons and how this impacts the species and how it would be useful to understand more about the effects of climate change on natural environments.It could include more details about any genetic information that the species already possesses, if applicable, or even about the group in which the species is located.
The methods, including pipelines and programs used, and their results are clear and well presented, following the standard of most genomic notes, including information about the sources and location of raw and processed data.It would be interesting to analyze in the future how using RNASeq data together with protein data would or would not improve genome annotation, considering that here they are only using BRAKER2, adapted only for protein data.
In short, the article is well written and developed in its purposes and presents a good overview of the genome.
Is the rationale for creating the dataset(s) clearly described?Yes 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.
Reviewer Expertise: genetics, entomology, molecular biology, bioinformatics, evolution and phylogenetics 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.

Figure 2 .
Figure 2. Genome assembly of Drepanosiphum platanoidis, ihDrePlat2.1: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 284,524,492 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 (34,895,330 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (24,435,353 and 11,045,042 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 hemiptera_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Drepanosiphum/dataset/CANUER01/snail.

Figure 3 .
Figure 3. Genome assembly of Drepanosiphum platanoidis, ihDrePlat2.1: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/Drepanosiphum/dataset/CANUER01/blob.

Figure 4 .
Figure 4. Genome assembly of Drepanosiphum platanoidis, ihDrePlat2.1: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/Drepanosiphum/dataset/CANUER01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Drepanosiphum platanoidis, ihDrePlat2.1:Hi-C contact map of the ihDrePlat2.1 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=cT_I_pNmQkC6kH1sJdMFsQ.

Table 3
contains a list of relevant software tool versions and sources.

Table 3 . Software tools: versions and sources. Software tool Version Minor concern:
Please, correct this typo: Three super scaffolds align to the M. periscae and A. pisum X chromosome (which is broadly conserved in aphids -> Three super scaffolds align to the M. periscae and A. pisum X chromosome, which is broadly conserved in aphids

Is the rationale for creating the dataset(s) clearly described? Yes 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.Reviewer Expertise: mosquito genetics and genomicsI

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.
https://doi.org/10.21956/wellcomeopenres.22332.r81060© 2024 Cordeiro Dias F. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.