ArticleGigaScience2022
Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater.
Article in GigaScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 29 citations in OpenAlex.
- Neo-sex Chromosomes Track the Mitochondrial Phylogeny and Exhibit an Extensive Added Stratum of Recombination Suppression in Honeyeaters (Aves: Meliphagidae).Genome biology and evolution · 2025Article
- Ephemeral Speciation in a New Guinean Honeyeater Complex (Aves: Melidectes).Molecular ecology · 2025Article
- Genomic origins and evolution of neo-sex chromosomes in Pacific Island birds.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment.Molecular ecology resources · 2025Article
- Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics.Molecular ecology resources · 2025Article
- Germline mutation rates and fine-scale recombination parameters in zebra finch.PLoS genetics · 2025Article
- Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction.Proceedings. Biological sciences · 2025Article
- Mutation and recombination parameters in zebra finch are similar to those in mammals.bioRxiv : the preprint server for biology · 2025Article
- Journeying towards best practice data management in biodiversity genomics.Molecular ecology resources · 2025Article
- Article
- A high-quality genome assembly of the Spectacled Fulvetta (Fulvetta ruficapilla) endemic to China.Scientific data · 2024Article
- A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta).Heredity · 2024Article
- The Genetic Architecture of Recombination Rates is Polygenic and Differs Between the Sexes in Wild House Sparrows (Passer domesticus).Molecular biology and evolution · 2024Article
- Recent secondary contact, genome-wide admixture, and asymmetric introgression of neo-sex chromosomes between two Pacific island bird species.PLoS genetics · 2024Article
- Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap.Genome biology and evolution · 2024Article
- A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes).Communications biology · 2023Article
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Authors and funding
14 authors at 8 institutions in 5 countries.
Funding
Abstract
backgroundThe helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required.
resultsWe used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene.
conclusionsThe annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.
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