The genome sequence of the chaffinch, Fringilla coelebs Linnaeus, 1758

We present a genome assembly from an individual male Fringilla coelebs (the chaffinch; Chordata; Aves; Passeriformes; Fringillidae). The genome sequence is 1,209.2 megabases in span. Most of the assembly is scaffolded into 40 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.8 kilobases in length.


Background
Linnaeus first described the chaffinch in 1758 as Fringilla coelebs.The specific name coelebs, derived from Latin, means 'single' or 'unmarried', reflecting the then-common belief that only the female birds migrated, leaving the males to lead a bachelor existence.The genus name Fringilla, Latin for 'small bird', can be traced back to ancient authors.The classification of the chaffinch has stayed within the same genus, which also defines the family name Fringillidae for finches.Researchers acknowledge up to 14 subspecies of chaffinch, typically grouped into three distinct clusters based on variations in head pattern and upperpart colouration among males.The British chaffinches are categorised under the nominal subspecies coelebs.
In Britain, chaffinches are predominantly resident; however, during winter, many, including both males and females from Scandinavia, migrate to central and southern regions of the country.Their diet primarily consists of seeds and plant matter, with invertebrates becoming a substantial addition during the breeding season (Snow & Perrins, 1998).
Chaffinches breed in wooded areas, parks, and gardens from mid-April to mid-July.Only the females incubate the eggs and the nestlings, although both parents are involved in feeding them.The incubation period is approximately 13 days, followed by the fledglings leaving the nest after about 14 days, continuing to receive parental care for at least another week (Snow & Perrins, 1998).
The genome of the chaffinch, Fringilla coelebs, 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 Fringilla coelebs, based on one male specimen from Buckinghamshire, UK.

Genome sequence report
The genome was sequenced from one male Fringilla coelebs (Figure 1) supplied by Tiggywinkles Wildlife Hospital, Haddenham, Buckinghamshire, UK (51.78, -0.87).A total of 42-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 50 missing joins or mis-joins, reducing the scaffold number by 7.07%.
The final assembly has a total length of 1,209.2Mb in 459 sequence scaffolds with a scaffold N50 of 73.2 Mb (Table 1).The snail plot 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 (90.11%) of the assembly sequence was assigned to 40 chromosomal-level scaffolds, representing 39 autosomes and the Z sex chromosome.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).The Z chromosome was identified based on alignment with Gallus gallus (GCA_016700215.1).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
A male Fringilla coelebs (specimen ID NHMUK014449386, ToLID bFriCoe1) supplied by Steve Smith of Tiggywinkles Wildlife Hospital on 2021-04-16.The specimen was formally identified by Hein van Grouw (Natural History Museum) and dry frozen at -80 °C.
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, fragmentation, and clean-up.In sample preparation, the bFriCoe1 sample was weighed and dissected on dry ice (Jay et al., 2023).For sample homogenisation, heart tissuewas cryogenically disrupted using the Covaris cryoPREP ® Automated Dry Pulverizer (Narváez-Gómez et al., 2023).HMW DNA was extracted using the Automated MagAttract v1 protocol (Sheerin et al., 2023).DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 30 (Todorovic et al., 2023).Sheared DNA was purified by solid-phase reversible immobilisation (Strickland et al., 2023): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA.The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit.Fragment size distribution was evaluated by running the sample on the FemtoPulse system.
RNA was extracted from heart tissue of bFriCoe1 in the Tree of Life Laboratory at the WSI using the RNA Extraction: Automated MagMax™ mirVana protocol (do Amaral et al., 2023).The RNA concentration was assessed using a      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 1) Why did the authors use a male individual to assemble the genome?A female would allow the assembling for both W and Z sex chromosomes.
2) Parameters used in each tool should be included in the methods section or indicating default settings were used.
3) More aspects of assessment of the assembly should be included, such as the reliable block N50 and genome heterozygosity.
4) Percentage of the assembly mapped to chromosomes (90.11%) is lower than the benchmark indicated in Table 1 (95%).What caused the relatively low number?5) How is the number of chromosomes in the bird determined?
Is the rationale for creating the dataset(s) clearly described?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: Genomics, computational biology, bioinformatics We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above.
Reviewer Report 06 August 2024 https://doi.org/10.21956/wellcomeopenres.23535.r88444 The main comment would be to state the rationale for assembling the genome more clearly in the introduction.While the authors provide valuable ecological context for the bird, the text could be strengthened by briefly summarizing any existing genetic work on the species (or lack thereof), apart from being a target species for the Darwin Tree of Life project.

Minor comments:
In the background, the third sentence, "The genus name Fringilla, Latin for 'small bird', can be traced back to ancient authors," could either be omitted, as it does not provide useful information, or alternatively, rewritten to provide more specific details about the etymology.'Ancient authors' is ambiguous.

1.
In sentence 4 of the background, replace 'upperpart colouration' with 'colouration of the upper part of the head.'

2.
In the third paragraph of the background, edit: "Chaffinches breed in wooded areas, parks, and gardens from mid-April to mid-July.Only females incubate the eggs, but both parents feed the nestlings." 3.
In the section Genome sequence report, please change the first sentence to: "We sequenced the genome of a male.."

4.
In the section Genome sequence report, replace 'number' with 'reducing the proportion of scaffolds' in the sentence: "Manual assembly curation corrected 50 missing joins or mis-joins, reducing the scaffold number by 7.07%."

5.
Please be more specific with the genome assembly metrics presented in Table 1.Do the values for the "Assembly metrics" section in Table 1 correspond to the primary haplotype of the assembly, or do they represent values for the diploid assembly? 1.
Are the metrics for the "Genome assembly" section in Table 1 for the primary haplotype? 2.

6.
Is the rationale for creating the dataset(s) clearly described?Partly 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: genome assembly, bioinformatics 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.

USA
This report provides a high-quality assembly of the chaffinch which is an abundant passerine in Europe and Western Asia.The methods and resulting data are well documented.This is an important resource for genomic studies of this species.
I assume that chromosomes have been numbered according to the length of the chromosomal pseudomolecules but that should be stated.Also, it would be of interest to provide information on the correspondence between these chromosome numbers in chaffinch and chromosome numbers in the zebra finch, a well-studied genome.
I also have one minor comment and that it would be nice to include the correct citation to Linnaeus first description of the species.The chaffinch is an ecologically and evolutionarily important songbird.I am glad its genome is now assembled at the chromosome level with high quality.I only have a few minor comments.

Is
The authors determined 40 chromosome models, but it is unclear how it was done.Was it just selecting the top 40 largest scaffolds, or using zebra finch/chicken chromosomes as a reference?

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: Evolutionary genomics 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 Fringilla coelebs, bFriCoe1.1:metrics.The BlobToolKit snail plot 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 1,209,243,761 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 (153,465,205 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (73,246,393 and 3,427,555 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 passeriformes_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAUPSF01/dataset/CAUPSF01/snail.

Figure 3 .
Figure 3. Genome assembly of Fringilla coelebs, bFriCoe1.1:BlobToolKit GC-coverage plot.Sequences are coloured by phylum.Circles are sized in proportion to sequence length.Histograms show the distribution of sequence length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAUPSF01/dataset/CAUPSF01/blob.

Figure 4 .
Figure 4. Genome assembly of Fringilla coelebs, bFriCoe1.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all sequences.Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAUPSF01/dataset/CAUPSF01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Fringilla coelebs, bFriCoe1.1:Hi-C contact map of the bFriCoe1.1 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=Pvknk_JaSoykRDNPZU3R6Q.

Reviewer Report 06
August 2024 https://doi.org/10.21956/wellcomeopenres.23535.r88442© 2024 Andersson L. 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.Leif Andersson 1 Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA 2 Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas,

Darwin Tree of Life Project Sampling Code of Prac- tice', 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.

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: Evolutionary genomics 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.
○-number of snps in the genome and per chromosome ○ -number of protein coding genes ○ It would also be worth comparing this genome assembly with the one assembled byRecuerda et  al. (2021; doi.org/10.1093/gbe/evab034)for the same species (synteny plot, number of CDS ?).

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.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.
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.MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing, Chongqing, China https://doi.org/10.21956/wellcomeopenres.23535.r88440© 2024 Xu L.