期刊
GIGASCIENCE
卷 11, 期 -, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/gigascience/giac025
关键词
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资金
- Australian Research Council [LP160100482]
- University of Canberra, Department of Environment, Land, Water and Planning (DELWP, Victoria)
- Diversity Arrays Technology
- Zoos Victoria
- Environment, Planning & Sustainable Development Directorate (ACT Government)
- Department of Biodiversity, Conservation and Attractions (Western Australia)
- Illumina, Inc.
- IBM
- Pawsey Supercomputing Center
- HelenMacpherson Smith Trust
- Faculty of Science (Monash University)
- Holsworth Wildlife Research Endowment (Ecological Society of Australia)
- Monash Faculty of Science Dean's Postgraduate Research Scholarship (DPRS)
- Monash Faculty of Science Dean's International Postgraduate Research Scholarship (DIPRS)
- European Union [840519]
- Revive & Restore (Catalyst Science Fund)
- University of Western Australia
- Welch Foundation [Q-1866]
- McNair Medical Institute Scholar Award
- NIH Encyclopedia of DNA Elements Mapping Center Award [UM1HG009375]
- US-Israel Binational Science Foundation Award [2019276]
- Behavioral Plasticity Research Institute [NSF DBI-2021795]
- NSF Physics Frontiers Center Award [NSF PHY-2019745]
- NIH Centers of Excellence in Genomic Science grant [RM1HG011016-01A1]
- Marie Curie Actions (MSCA) [840519] Funding Source: Marie Curie Actions (MSCA)
- Australian Research Council [LP160100482] Funding Source: Australian Research Council
The study assembled the chromosome-length genome of the helmeted honeyeater and obtained high-density linkage maps, providing valuable resources for evolutionary studies and guiding conservation efforts for this endangered bird species.
Background The 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. Results We 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 similar to 15-fold decline in effective population size to similar to 60,000 from mid- to late Pleistocene. Conclusions The 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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