The genome sequence of the chaffinch, Fringilla coelebs Linnaeus, 1758
Hein van Grouw, Zhengchang Su, Siwen Wu, Merly Escalona, Leif Andersson, Jérôme Fuchs, Luohao Xu
TL;DR
This paper provides the genome sequence of the chaffinch, a bird species, including its chromosomal and mitochondrial DNA.
Contribution
The study presents a high-quality genome assembly of the chaffinch, including chromosomal pseudomolecules and the mitochondrial genome.
Findings
The genome assembly spans 1,209.2 megabases and includes 40 chromosomal pseudomolecules.
The mitochondrial genome is 16.8 kilobases in length and has been assembled.
Abstract
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.
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
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Figure 1
Figure 2
Figure 3
Figure 4
Figure 5| Project accession data | ||
|---|---|---|
| Assembly identifier | bFriCoe1.1 | |
| Species |
| |
| Specimen | bFriCoe1 | |
| NCBI taxonomy ID | 37598 | |
| BioProject | PRJEB61919 | |
| BioSample ID | SAMEA9359753 | |
| Isolate information | bFriCoe1 (DNA, Hi-C and RNA sequencing) | |
| Assembly metrics
|
| |
| Consensus quality (QV) | 61.9 |
|
|
| 100.0% |
|
| BUSCO
| C:96.3%[S:96.1%,D:0.2%],
|
|
| Percentage of assembly
| 90.11% |
|
| Sex chromosomes | ZZ |
|
| Organelles | Mitochondrial genome: 16.8 kb |
|
| Raw data accessions | ||
| PacificBiosciences SEQUEL II | ERR11435991, ERR11435992 | |
| Hi-C Illumina | ERR11439646 | |
| PolyA RNA-Seq Illumina | ERR11439647 | |
| Genome assembly | ||
| Assembly accession | GCA_963513975.1 | |
|
| GCA_963513985.1 | |
| Span (Mb) | 1,209.2 | |
| Number of contigs | 1,033 | |
| Contig N50 length (Mb) | 3.7 | |
| Number of scaffolds | 459 | |
| Scaffold N50 length (Mb) | 73.2 | |
| Longest scaffold (Mb) | 153.47 | |
| INSDC
| Chromosome | Length (Mb) | GC% |
|---|---|---|---|
| 1 | 153.47 | 40.0 | |
| 2 | 117.29 | 40.5 | |
| 3 | 114.83 | 40.5 | |
| 4 | 73.43 | 40.5 | |
| 5 | 73.25 | 41.0 | |
| 6 | 63.28 | 42.0 | |
| 7 | 38.68 | 42.5 | |
| 8 | 37.13 | 43.5 | |
| 9 | 32.86 | 44.0 | |
| 10 | 25.64 | 44.5 | |
| 11 | 24.43 | 46.5 | |
| 12 | 22.46 | 45.0 | |
| 13 | 22.39 | 45.5 | |
| 14 | 21.66 | 44.5 | |
| 15 | 19.14 | 46.5 | |
| 16 | 16.5 | 46.5 | |
| 17 | 15.72 | 48.0 | |
| 18 | 15.57 | 48.0 | |
| 19 | 14.4 | 49.5 | |
| 20 | 13.35 | 49.5 | |
| 21 | 12.56 | 49.5 | |
| 22 | 10.4 | 50.0 | |
| 23 | 9.25 | 53.0 | |
| 24 | 8.09 | 54.0 | |
| 25 | 7.69 | 50.5 | |
| 26 | 7.44 | 52.5 | |
| 27 | 7.15 | 54.0 | |
| 28 | 7.05 | 52.0 | |
| 29 | 4.55 | 57.0 | |
| 30 | 4.0 | 57.5 | |
| 31 | 3.43 | 52.5 | |
| 32 | 1.92 | 59.0 | |
| 33 | 1.72 | 62.5 | |
| 34 | 1.22 | 53.5 | |
| 35 | 0.92 | 52.5 | |
| 36 | 0.9 | 56.0 | |
| 37 | 0.9 | 59.0 | |
| 38 | 0.89 | 58.0 | |
| 39 | 0.39 | 55.5 | |
| Z | 83.83 | 41.0 | |
| MT | 0.02 | 46.0 |
| Software
| Version | Source |
|---|---|---|
| BlobToolKit | 4.2.1 |
|
| BUSCO | 5.3.2 |
|
| Hifiasm | 0.16.1-r375 |
|
| HiGlass | 1.11.6 |
|
| Merqury | MerquryFK |
|
| MitoHiFi | 3 |
|
| PretextView | 0.2 |
|
| purge_dups | 1.2.5 |
|
| sanger-tol/
| v1.0 |
|
| sanger-tol/
| 1.1.0 |
|
| TreeVal | - |
|
| YaHS | 1.2a.2 |
|
- —Wellcome Trust
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Taxonomy
TopicsGenomics and Phylogenetic Studies · Genetic diversity and population structure · Chromosomal and Genetic Variations
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Passeriformes; Passeroidea; Fringillidae; Fringillinae; Fringilla; Fringilla coelebs Linnaeus, 1758 (NCBI:txid37598).
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%.
Voucher specimen (NHMUK 2022.10.1) of the Fringilla coelebs (bFriCoe1) specimen used for genome sequencing – study skin prepared by Hein van Grouw.
The final assembly has a total length of 1,209.2 Mb 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.
Table 1.: Genome data for Fringilla coelebs, bFriCoe1.1.
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.
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.
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.
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.
Table 2.: Chromosomal pseudomolecules in the genome assembly of Fringilla coelebs, bFriCoe1.
The estimated Quality Value (QV) of the final assembly is 61.9 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.3.2 completeness of 96.3% (single = 96.1%, duplicated = 0.2%), using the passeriformes_odb10 reference set ( n = 10,844).
Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://tolqc.cog.sanger.ac.uk/darwin/birds/Fringilla_coelebs/.
Methods
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 tissue was 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 Nanodrop spectrophotometer and a Qubit Fluorometer using the Qubit RNA Broad-Range Assay kit. Analysis of the integrity of the RNA was done using the Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.
Protocols developed by the WSI Tree of Life laboratory are publicly available on protocols.io ( Denton et al., 2023).
Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit. DNA and RNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from liver tissue of bFriCoe1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.
Genome assembly, curation and evaluation
Assembly was carried out with Hifiasm ( 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 ( Zhou et al., 2023). The assembly was checked for contamination and corrected using the TreeVal pipeline ( Pointon et al., 2023). Manual curation was performed using JBrowse2 ( Diesh et al., 2023), HiGlass ( Kerpedjiev et al., 2018) and PretextView ( 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.
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 was done using Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a) and “sanger-tol/genomenote” ( Surana et al., 2023b). The genome was analysed within the BlobToolKit environment ( Challis et al., 2020) and BUSCO scores ( Manni et al., 2021; Simão et al., 2015) were calculated.
Table 3 contains a list of relevant software tool versions and sources.
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 doing so we align with best practice wherever possible. The overarching areas of consideration are:
• Ethical review of provenance and sourcing of the material
• Legality of collection, transfer and use (national and international)
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.
The reference list from the paper itself. Each links out to its DOI / PubMed record.
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