Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater
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Chromosome-length genome assembly and linkage map of a critically endangered Australian bird : the helmeted honeyeater. / Robledo-Ruiz, Diana A.; Gan, Han Ming; Kaur, Parwinder; Dudchenko, Olga; Weisz, David; Khan, Ruqayya; Lieberman Aiden, Erez; Osipova, Ekaterina; Hiller, Michael; Morales, Hernán E.; Magrath, Michael J. L.; Clarke, Rohan H.; Sunnucks, Paul; Pavlova, Alexandra.
In: GigaScience, Vol. 11, giac025, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Chromosome-length genome assembly and linkage map of a critically endangered Australian bird
T2 - the helmeted honeyeater
AU - Robledo-Ruiz, Diana A.
AU - Gan, Han Ming
AU - Kaur, Parwinder
AU - Dudchenko, Olga
AU - Weisz, David
AU - Khan, Ruqayya
AU - Lieberman Aiden, Erez
AU - Osipova, Ekaterina
AU - Hiller, Michael
AU - Morales, Hernán E.
AU - Magrath, Michael J. L.
AU - Clarke, Rohan H.
AU - Sunnucks, Paul
AU - Pavlova, Alexandra
N1 - Publisher Copyright: © 2022 The Author(s) 2022. Published by Oxford University Press GigaScience.
PY - 2022
Y1 - 2022
N2 - 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 ∼15-fold decline in effective population size 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.
AB - 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 ∼15-fold decline in effective population size 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.
U2 - 10.1093/gigascience/giac025
DO - 10.1093/gigascience/giac025
M3 - Journal article
C2 - 35348671
AN - SCOPUS:85127223985
VL - 11
JO - GigaScience
JF - GigaScience
SN - 2047-217X
M1 - giac025
ER -
ID: 307097470