The genome sequence of the European turtle dove, Streptopelia turtur Linnaeus 1758

We present a genome assembly from an individual female Streptopelia turtur (the European turtle dove; Chordata; Aves; Columbidae). The genome sequence is 1.18 gigabases in span. The majority of the assembly is scaffolded into 35 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled.


Introduction
The European turtle dove, Streptopelia turtur, breeds throughout Europe, Central Asia, the Middle East and North Africa, overwintering in north Sub-Saharan Africa.Populations in the Atlantic archipelago of Britain and Ireland are primarily located in southern and eastern England.S. turtur populations are in rapid decline in the UK, having fallen by 98% between 1970 and 2018, making them critically endangered; they are also vulnerable to global extinction (Burns et al., 2020).Several causes have been put forward for this collapse in population.Changes in farming practices and agricultural intensification in the UK have reduced the availability of wild plant seeds, increasing the reliance of S. turtur on anthropogenic seed sources (Browne & Aebischer, 2003); a negative association between nestling condition and consumption of seeds from anthropogenic sources has been reported, although this association was positive for adult birds (Dunn et al., 2018).Additionally, infection with the protozoan parasite Trichomonas gallinae has been identified as a cause of death in adults and nestlings (Stockdale et al., 2015).The length of breeding seasons and the number of breeding attempts of S. turtur have markedly reduced, meaning that fewer young are hatched each year (Browne & Aebischer, 2004).Large populations of migrating birds are also hunted in Mediterranean countries, such as France, Spain and Morocco, compounding this decline in numbers.The genome sequence described here will be of utility to researchers assessing the vulnerability of S. turtur to parasitic infections, and to those interested in population genomics and supporting the numbers of this declining species.

Genome sequence report
The genome was sequenced from a blood sample collected from a single live female S. turtur during routine population health checks.A total of 34-fold coverage in Pacific Biosciences single-molecule long reads (N50 22 kb) and 45-fold coverage in 10X Genomics read clouds (from molecules with an estimated N50 of 34 kb) were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.The Hi-C scaffolds were validated using BioNano Genomics long range restriction maps (106-fold effective coverage).Manual assembly curation corrected 54 missings/misjoins and removed 1 haplotypic duplication, reducing the scaffold number by 23.59%, increasing the scaffold N50 by 19.08% and decreasing the assembly length by 0.01%.The final assembly has a total length of 1.18 Gb in 357 sequence scaffolds with a scaffold N50 of 81.4 Mb (Table 1).The majority, 98.3%, of the assembly sequence was assigned to 35 chromosomal-level scaffolds representing 33 autosomes (numbered by synteny to the chicken, Gallus gallus domesticus: GCA_000002315.5), and the W and Z sex chromosomes (Figure 1-Figure 4; Table 2).The assembly has a BUSCO v5.1.2 (Simão et al., 2015) completeness of 95.7% using the aves_odb10 reference set.While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.BioSample ID SAMEA994735

Isolate information
Female, blood sample

Methods
The European turtle dove specimen was taken from blood collected from a live bird during routine health checks of populations in Marks Tey, Essex, UK (latitude 51.874N, longitude 0.729E; grid reference TL8823).The sample was taken under Home Office (Animals Scientific Procedures Act, ASPA) licence number PPL 7007641); the bird was caught and handled under a British Trust for Ornithology ringing license.
DNA was extracted using an agarose plug extraction from a blood sample following the BioNano Genomics Prep Blood and Cell Culture DNA Isolation Protocol.Pacific Biosciences  et al., 2016) as described previously (Howe et al., 2021).Manual curation was performed using evidence from BioNano Genomics (using the BioNano Access viewer), using HiGlass and Pretext.Figure 1-Figure 3 and BUSCO v5.1.2scores were generated using BlobToolKit (Challis et al., 2020).Table 3 gives version numbers of the software tools used in this work.Reviewer Expertise: Evolutionary genetics, ornithology, comparative genomics, retinal cell biology 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.
Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA In this article, the authors present a genome assembly of the European turtle dove.The methods are clear and well detailed.The authors use a variety of sequence data types, including several long-read technologies in order to present a solid assembly.The article is clear and straightforward, and the genome assembly and associated raw data will be of use to the scientific community.Is the rationale for creating the dataset(s) clearly described?YesAre the protocols appropriate and is the work technically sound?YesAre sufficient details of methods and materials provided to allow replication by others?YesAre the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.

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.