The genome sequence of the bluish flesh fly, Sarcophaga ( Robineauella) caerulescens (Zetterstedt, 1838)

We present a genome assembly from an individual male Sarcophaga caerulescens (the bluish flesh fly; Arthropoda; Insecta; Diptera; Sarcophagidae). The genome sequence is 597 megabases in span. Most of the assembly is scaffolded into seven chromosomal pseudomolecules, including the assembled X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 21.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,559 protein coding genes.


Background
Sarcophaga caerulescens (Diptera: Sarcophagidae) is a widely distributed flesh fly reported from Nearctic, Palearctic and Oriental regions (Pape, 1996). The species name reflects its bluish colouration (indeed it is sometimes referred to as the bluish flesh fly), and individuals possess the characteristic pigmentation pattern of the genus, with three longitudinal stripes on the thorax and a checked pattern on the abdomen. There are roughly 890 species in the genus Sarcophaga, divided into approximately 169 subgenera (Buenaventura et al., 2017), and S. caerulescens is in the Robineauella subgenus along with around 15 other species, a striking contrast to most other Sarcophagid subgenera, which are monotypic.
Data regarding distribution and abundance of S. caerulescens, as with most, if not all, of the 65 currently recognised UK Sarcophagid species, is relatively sparse, most likely as a result of the difficulty in differentiating highly similar species visually or from photographs. Available data from the National Biodiversity Atlas (NBN) Atlas (https://species.nbnatlas.org/ species/NBNSYS0100005387) shows highest abundance in summer months (June-August), with multiple reports from England and Wales, and a single record from Scotland. As with many flesh fly species, S. caerulescens has been recorded in association with human and animal carcasses, and has been suggested as a candidate for forensic entomology and determination of post-mortem interval (PMI The S. caerulescens genome should be a useful resource for the development of improved DNA barcoding markers, where current COI-based assays can struggle to differentiate some species (Jordaens et al., 2013), and provide useful insights into the evolution of ovoviviparity.

Genome sequence report
The genome was sequenced from one male Sarcophaga caerulescens ( Figure 1) collected from Wytham Woods, Berkshire (latitude 51.77, longitude -1.33). A total of 25-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 57-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 235 missing or mis-joins and removed 10 haplotypic duplications, reducing the assembly length by 0.61% and the scaffold number by 41.03%, and increasing the scaffold N50 by 69.4%.
The final assembly has a total length of 597 Mb in 138 sequence scaffolds with a scaffold N50 of 113.3 Mb (Table 1). Most (98.99%) of the assembly sequence was assigned to seven chromosomal-level scaffolds, representing five autosomes and the X and Y sex chromosomes. Chromosome-scale scaffolds are named by synteny based on the assembly for Sarcophaga peregrina (GCA_014635995.1) (Figure 2- Figure 5; Table 2). The assembly has a BUSCO v5.3.2 (Manni et al., 2021) completeness of 99.1% using the diptera_odb10 reference set. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.

Sample acquisition and nucleic acid extraction
A male S. caerulescens (idSarCaer1) was collected using a net in Wytham Woods, Berkshire, UK (latitude 51.77, longitude -1.33) by Steven Falk (independent researcher). The specimen was identified by Steven Falk and snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The idSarCaer1 sample was weighed and dissected on dry ice with head tissue set aside for Hi-C sequencing. Thorax tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle. High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit. Low molecular weight DNA        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.

Nicolaus Copernicus University, Toruń, Poland
The report of Sarcophaga (Robineauella) caerulescens genome is satisfactory and contains all the necessary information. Introduction covers most important aspects of Sarcophaga caerulescens life history with the most recent references. The genome assembly is of high quality. A brief explanation of larval predatory behaviour and ovoviviparity in Sarcophaga caerulescens will highlight why it is an interesting model for comparative genomics.
I recommend adding more information concerning specimen identification. In particular, a reference to a taxonomic key used for species delimitation, i.e., latest species-level taxonomic literature that contains the currently accepted species concept 1 .