Version Changes
Revised. Amendments from Version 1
In Version 2 of this article we have updated the chromosome map in Figure 5 to include axis labels. We have updated the genome assembly evaluation method to use the latest verson of Merqury.FK, and we include the Earth Biogenome Project reference standard.
Abstract
We present a genome assembly from an individual female Nesoenas mayeri (the Pink Pigeon; Chordata; Aves; Columbiformes; Columbidae). The genome sequence is 1,183.3 megabases in span. Most of the assembly is scaffolded into 40 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.97 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,730 protein coding genes. The primary assembly achieves the Earth Biogenome Project reference standard of 6.C.Q62.
Keywords: Nesoenas mayeri, Pink Pigeon, genome sequence, chromosomal, Columbiformes
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; Columbiformes; Columbidae; Nesoenas; Nesoenas mayeri (Prévost, 1843) (NCBI:txid187126).
Background
The Pink Pigeon ( Nesoenas mayeri) is an endemic species of Mauritius distinguished by its soft pinkish-grey feathers and bright pink legs ( Figure 1A). This bird primarily feeds on leaves, seeds, and fruits from native and non-native plants. Pink Pigeons nest on branches, laying clutches of 1 to 2 eggs mainly during the breeding season from September to January. The Pink Pigeon suffered a severe population size decline due to habitat loss and invasive species ( Jackson et al., 2022; Jones, 2013; Pinto et al., 2024). By 1990, the free-living population consisted of only circa 10 individuals ( Jones, 2013; Jones & Swinnerton, 1997). Prior to this population bottleneck, 12 individuals were taken from the last free-living population to establish a captive breeding population at the Gerald Durrell Endemic Wildlife Sanctuary (GDEWS) in Mauritius between 1976 to 1981. This captive-bred population also helped to establish the zoo populations of Pink Pigeons in Europe and America. The population at the GDEWS has also contributed to demographic rescue of the free-living population ( Jackson et al. 2022; Jones, 2013). The current free-living population in Mauritius is estimated to comprise of ~488 adult birds in Mauritius ( Figure 1B) ( BirdLife International, 2021).
Figure 1. The fall and rise of the Pink Pigeon.
( A) A Pink Pigeon ( Nesoenas mayeri; photo credit Gregory Guida) ( B) Demographic trajectory (black line and dots) derived from field monitoring, of the free-living Mauritius Pink Pigeon population over time (bottleneck and recovery), and the bars represent the number of captive-breed individuals released into the free-living population.
The species was assessed as Critically Endangered (between 1994–2000) in the IUCN Red List, and downlisted to Endangered in 2000, and then to Vulnerable in 2018. According to the IUCN’s Green Status assessment ( Tatayah, 2021), the Species Recovery Score equals 17% (Critically Depleted), which is low due to massive forest loss. However, the Pink Pigeon has a High Conservation Legacy, given that without past conservation action, the species would almost certainly be extinct today assessment ( Tatayah, 2021). Genomic-based analysis and computer simulation studies indicate that without genetic rescue, the species is likely to go extinct within the next 50 to 100 years ( Jackson et al., 2022).
Quantitative genetic and conservation genomic analyses show that the Pink Pigeon suffers from severe genomic erosion and a considerable ‘drift debt’ ( Pinto et al., 2024). The species possesses a high genetic load of deleterious mutations, which is estimated to amount to 15 lethal equivalents ( Jackson et al., 2022). Hence, continued genetic drift and inbreeding are predicted to result in severe inbreeding depression by increasing the realised load of deleterious mutations ( Bertorelle et al., 2022; Dussex et al., 2023). Recent genomics research on the Pink Pigeon shows that genomics-informed captive breeding can reduce the realised load by selecting optimal mate-pairs for captive breeding ( Speak et al., 2024). In addition, to improve the long-term viability of the species, three captive-bred birds from the population in Jersey Zoo (British Channel Island) were transported to Mauritius in 2021. Furthermore, in collaboration with the National Parks and Conservation Service (NPCS) and the Mauritian Wildlife Foundation (MWF), a genomics-informed rescue programme is currently being established to inform future releases of captive-bred Pink Pigeons from Jersey Zoo and European zoos to Mauritius. Such genetic rescue is likely to increase diversity in the free-living population, and it will help mask the load of recessive deleterious mutations, thereby increasing fitness and population viability.
The comprehensive sample archive and profound understanding of the species’ ecology and its conservation legacy establish it as an exemplary system for studying conservation genomics. Currently, hundreds of whole genomes are being re-sequenced from historical (pre-1900), recent (1990–2000) and contemporary samples to uncover the genomic impacts and enduring consequences of the population's decline and revealing ways to optimize the long-term viability of the Pink Pigeon in Mauritius. This research efforts are part of a collaboration between several universities (University of Kent (UK), University of East Anglia (UK), University of Copenhagen (Denmark)), the Durrell Wildlife Conservation Trust (UK), Jersey Zoo, the Government of Mauritius’ National Parks and Conservation Service (NPCS) and the Mauritian Wildlife Foundation (MWF – conservation NGO, Mauritius). The conservation monitoring and management of the Pink Pigeon is done by the MWF in collaboration with the NPCS with guidance from the university partners; recent conservation actions have also been implemented by Ebony Forest Reserve (conservation group).
This assembly is the first high-quality genome for the genus Nesoenas and one of 12 genomes available for the family Columbidae as of September 2025 (data obtained via NCBI datasets; O’Leary et al., 2024).
Genome sequence report
The genome was sequenced from a female Nesoenas mayeri collected from Jersey Zoo, UK. A total of 32-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 96 missing joins or mis-joins and removed 3 haplotypic duplications, reducing the scaffold number by 32.23%, and increasing the scaffold N50 by 10.48%.
The final assembly has a total length of 1,183.3 Mb in 142 sequence scaffolds with a scaffold N50 of 78.2 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 (98.45%) of the assembly sequence was assigned to 40 chromosomal-level scaffolds, representing 38 autosomes and the Z and W sex chromosomes. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 5; Table 2). 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.
Figure 2. Genome assembly of Nesoenas mayeri, bNesMay2.1: 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 1,183,271,950 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 (214,152,265 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (78,184,682 and 13,300,769 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 aves_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_963082525.1/dataset/CAUJAP01/snail.
Figure 3. Genome assembly of Nesoenas mayeri, bNesMay2.1: 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/GCA_963082525.1/dataset/CAUJAP01/blob.
Figure 4. Genome assembly of Nesoenas mayeri bNesMay2.1: 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/GCA_963082525.1/dataset/CAUJAP01/cumulative.
Figure 5. Genome assembly of Nesoenas mayeri bNesMay2.1: Hi-C contact map of the bNesMay2.1 assembly, visualised using PretextView and PretextSnapshot.
Chromosomes are shown in order of size from left to right and top to bottom and labelled along the axes, with a megabase scale on the bottom axis. An interactive version of this figure in HiGlass may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=U63e71O9TGGSWoX1VPKRfw.
Table 1. Genome data for Nesoenas mayeri, bNesMay2.1.
| Project accession data | ||
|---|---|---|
| Assembly identifier | bNesMay2.1 | |
| Species | Nesoenas mayeri | |
| Specimen | bNesMay2 | |
| NCBI taxonomy ID | 187126 | |
| BioProject | PRJEB64092 | |
| BioSample ID | Genome sequencing: PacBio: SAMEA12922164 | |
| Isolate information | bNesMay2, female: blood (genome sequence, Hi-C and RNA sequencing) | |
| Assembly metrics * | Benchmark | |
| Consensus quality (QV) | Primary: 62.6; alternate: 63.9; combined: 63.3 | ≥ 40 |
| k-mer completeness | Primary: 92.15%; alternate: 68.50%; combined: 99.04% | ≥ 95% |
| BUSCO ** | C:97.3%[S:96.9%,D:0.4%],
F:0.5%,M:2.2%,n:8,338 |
S > 90%; D < 5% |
| Percentage of assembly mapped
to chromosomes |
98.45% | ≥ 90% |
| Sex chromosomes | ZW | localised homologous pairs |
| Organelles | Mitochondrial genome: 16.97 kb | complete single alleles |
| Raw data accessions | ||
| PacificBiosciences Sequel IIe | ERR11673243, ERR11673244 | |
| Hi-C Illumina | ERR11679408 | |
| PolyA RNA-Seq Illumina | ERR11679409 | |
| Genome assembly | ||
| Assembly accession | GCA_963082525.1 | |
| Accession of alternate haplotype | GCA_963082445.1 | |
| Span (Mb) | 1,183.3 | |
| Number of contigs | 652 | |
| Contig N50 length (Mb) | 4.8 | |
| Number of scaffolds | 142 | |
| Scaffold N50 length (Mb) | 78.2 | |
| Longest scaffold (Mb) | 214.15 | |
| Genome annotation | ||
| Number of protein-coding genes | 16,730 | |
| Number of non-coding genes | 1,067 | |
| Number of gene transcripts | 27,410 | |
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from Rhie et al. (2021).
** BUSCO scores based on the aves_odb10 BUSCO set using version 5.4.3. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/GCA_963082525.1/dataset/CAUJAP01/busco.
Table 2. Chromosomal pseudomolecules in the genome assembly of Nesoenas mayeri, bNesMay2.
| INSDC
accession |
Chromosome | Length
(Mb) |
GC% |
|---|---|---|---|
| OY720056.1 | 1 | 214.15 | 40.5 |
| OY720057.1 | 2 | 164.7 | 40.0 |
| OY720058.1 | 3 | 121.94 | 40.5 |
| OY720059.1 | 4 | 78.2 | 40.0 |
| OY720061.1 | 5 | 69.28 | 41.5 |
| OY720062.1 | 6 | 44.46 | 41.5 |
| OY720063.1 | 7 | 40.34 | 42.0 |
| OY720064.1 | 8 | 36.08 | 42.5 |
| OY720065.1 | 9 | 31.79 | 43.5 |
| OY720066.1 | 10 | 24.72 | 44.0 |
| OY720067.1 | 11 | 24.03 | 44.0 |
| OY720068.1 | 12 | 23.58 | 43.5 |
| OY720069.1 | 13 | 21.15 | 43.5 |
| OY720071.1 | 14 | 20.36 | 45.0 |
| OY720072.1 | 15 | 18.29 | 45.5 |
| OY720073.1 | 16 | 16.72 | 46.5 |
| OY720074.1 | 17 | 14.4 | 46.5 |
| OY720075.1 | 18 | 13.3 | 48.5 |
| OY720076.1 | 19 | 13.17 | 47.5 |
| OY720077.1 | 20 | 11.03 | 48.0 |
| OY720078.1 | 21 | 7.92 | 51.0 |
| OY720079.1 | 22 | 7.77 | 49.0 |
| OY720080.1 | 23 | 7.3 | 52.0 |
| OY720081.1 | 24 | 7.27 | 49.0 |
| OY720082.1 | 25 | 6.63 | 53.5 |
| OY720083.1 | 26 | 6.53 | 53.0 |
| OY720084.1 | 27 | 5.15 | 51.0 |
| OY720085.1 | 28 | 4.18 | 55.5 |
| OY720086.1 | 29 | 3.71 | 50.5 |
| OY720087.1 | 30 | 2.43 | 58.5 |
| OY720088.1 | 31 | 1.46 | 60.0 |
| OY720089.1 | 32 | 0.87 | 58.0 |
| OY720090.1 | 33 | 0.58 | 60.0 |
| OY720091.1 | 34 | 0.56 | 54.5 |
| OY720092.1 | 35 | 0.53 | 63.5 |
| OY720093.1 | 36 | 0.41 | 59.0 |
| OY720094.1 | 37 | 0.39 | 59.0 |
| OY720095.1 | 38 | 0.33 | 59.0 |
| OY720070.1 | W | 20.52 | 43.0 |
| OY720060.1 | Z | 78.18 | 40.5 |
| OY720096.1 | MT | 0.02 | 45.5 |
Table 1 lists the assembly metric benchmarks adapted from Rhie et al. (2021) and the Earth BioGenome Project Report on Assembly Standards September 2024. The EBP metric, calculated for the primary assembly, is 6.C.Q62, meeting the recommended reference standard. The primary assembly has a BUSCO completeness of 97.3% (single = 96.9%, duplicated = 0.4%), using the aves_odb10 reference set ( n = 8,338).
Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/187126.
Genome annotation report
The Nesoenas mayeri genome assembly (GCA_963082525.1) was annotated at the European Bioinformatics Institute (EBI) on Ensembl Rapid Release. The resulting annotation includes 27,410 transcribed mRNAs from 16,730 protein-coding and 1,087 non-coding genes ( Table 1; https://beta.ensembl.org/species/1c9a0fd4-e787-4fc9-acca-3aa795602e7e).
Methods
Sample acquisition and nucleic acid extraction
A female Nesoenas mayeri (specimen ID SAN1100036, ToLID bNesMay2) was collected from Jersey Zoo, UK (latitude –2.08, longitude 49.23) on 2021-03-19. The bird was caught in the aviary, blood collected from the jugular vein, and the blood sample was frozen approximately 10 minutes later. The specimen was collected and identified by Harriet Whitford (Durrell Wildlife Conservation Trust).
The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up. The bNesMay2 sample was kept on dry ice ( Jay et al., 2023). For sample homogenisation, blood was cryogenically disrupted using the Covaris cryoPREP ® Automated Dry Pulverizer ( Narváez-Gómez et al., 2023). HMW DNA was extracted using the manual Nucleated Blood Nanobind ® protocol ( Denton et al., 2023a). DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system ( Bates et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation ( Strickland et al., 2023). 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 blood tissue of bNesMay2 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., 2023b).
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 IIe (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from the bNesMay2 blood sample using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.
Genome assembly and curation
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 as described previously ( Howe et al., 2021). Manual curation was performed using 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) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
Evaluation of final assembly
The Merqury.FK tool ( Rhie et al., 2020) was run in a Singularity container ( Kurtzer et al., 2017) to evaluate k-mer completeness and assembly quality for the primary and alternate haplotypes using the k-mer databases ( k = 31) computed prior to genome assembly. The analysis outputs included assembly QV scores and completeness statistics.
To produce the HiGlass map, the Hi-C reads are aligned using bwa-mem2 ( Vasimuddin et al., 2019) and the alignment files are combined using SAMtools ( Danecek et al., 2021). The Hi-C alignments are transformed into a contact map with BEDTools ( Quinlan & Hall, 2010) and the Cooler tool suite ( Abdennur & Mirny, 2020), which is then visualised with HiGlass ( Kerpedjiev et al., 2018).
The sanger-tol/blobtoolkit pipeline ( Muffato et al., 2024) is a Nextflow ( Di Tommaso et al., 2017) port of the previous Snakemake Blobtoolkit pipeline ( Challis et al., 2020). It aligns the PacBio reads with SAMtools and minimap2 ( Li, 2018) and generates coverage tracks for regions of fixed size. In parallel, it queries the GoaT database ( Challis et al., 2023) to identify all matching BUSCO lineages to run BUSCO ( Manni et al., 2021). For the three domain-level BUSCO lineage, the pipeline aligns the BUSCO genes to the Uniprot Reference Proteomes database ( Bateman et al., 2023) with DIAMOND ( Buchfink et al., 2021) blastp. The genome is also split into chunks according to the density of the BUSCO genes from the closest taxonomically lineage, and each chunk is aligned to the Uniprot Reference Proteomes database with DIAMOND blastx. Genome sequences that have no hit are then chunked with seqtk and aligned to the NT database with blastn ( Altschul et al., 1990). All those outputs are combined with the blobtools suite into a blobdir for visualisation.
All three pipelines were developed using the nf-core tooling ( Ewels et al., 2020), use MultiQC ( Ewels et al., 2016), and make extensive use of the Conda package manager, the Bioconda initiative ( Grüning et al., 2018), the Biocontainers infrastructure ( da Veiga Leprevost et al., 2017), and the Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017) containerisation solutions.
Table 3 contains a list of relevant software tool versions and sources.
Table 3. Software tools: versions and sources.
Genome annotation
The Ensembl Genebuild annotation system ( Aken et al., 2016) was used to generate annotation for the Nesoenas mayeri assembly (GCA_963082525.1) in Ensembl Rapid Release at the EBI. Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein-to-genome alignments of a select set of proteins from UniProt ( UniProt Consortium, 2019).
Wellcome Sanger Institute – Legal and Governance
The materials that have contributed to this genome note have been supplied by a Tree of Life collaborator. 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 undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Tree of Life collaborator, Genome Research Limited (operating as the Wellcome Sanger Institute) and in some circumstances other Tree of Life collaborators.
Acknowledgements
We thank Houshna Naujeer and colleagues at the National Parks and Conservation Service, Government of Mauritius, for support and permits for sample collection. We are grateful with Carl Jones, Kirsty Swinnerton, Amanda Maujean, Deborah De Chazal and Sion Henshaw for their roles in the Pink Pigeon conservation programme.
Funding Statement
This work was supported by Wellcome through core funding to the Wellcome Sanger Institute [206194, <a href=https://doi.org/10.35802/206194>https://doi.org/10.35802/206194</a>]. Danish National Research Foundation grant DNRF143, European Union's Horizon 2020 Research and Innovation Programme under a Marie Sklodowska-Curie grant (840519), European Research Council (ERODE, 101078303), Royal Society International Collaboration Awards 2020 (ICA∖R1∖201194).
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
[version 2; peer review: 2 approved, 1 approved with reservations]
Data availability
European Nucleotide Archive: Nesoenas mayeri (Pink Pigeon). Accession number PRJEB64092; https://identifiers.org/ena.embl/PRJEB64092 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Nesoenas mayeri genome sequencing initiative is part of the Vertebrate Genomes Project. All raw sequence data and the assembly have been deposited in INSDC databases. Raw data and assembly accession identifiers are reported in Table 1.
Author information
Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.10066175.
Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.10043364.
Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.10066637.
Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.
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