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Genome of an iconic Australian bird: High-quality assembly and linkage map of the superb fairy-wren (Malurus cyaneus)

Penalba, Joshua V.; Deng, Yuan; Fang, Qi; Joseph, Leo G.; Moritz, Craig; Cockburn, Andrew

Description

The superb fairy-wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passer-ines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been repre-sented by a high-quality reference. To rectify that, we present the...[Show more]

dc.contributor.authorPenalba, Joshua V.
dc.contributor.authorDeng, Yuan
dc.contributor.authorFang, Qi
dc.contributor.authorJoseph, Leo G.
dc.contributor.authorMoritz, Craig
dc.contributor.authorCockburn, Andrew
dc.date.accessioned2020-07-14T05:47:51Z
dc.date.available2020-07-14T05:47:51Z
dc.identifier.citationPenalba JV, Deng Y, Fang Q, Joseph L, Moritz C, Cockburn A. Genome of an iconic Australian bird: High-quality assembly and linkage map of the superb fairy-wren (Malurus cyaneus). Mol Ecol Resour. 2019;00:1–19. https://doi.org/10.1111/1755-0998.13124
dc.identifier.issn1755-098X
dc.identifier.urihttp://hdl.handle.net/1885/206161
dc.description.abstractThe superb fairy-wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passer-ines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been repre-sented by a high-quality reference. To rectify that, we present the first high-quality genome assembly of a Meliphagides representative: the superb fairy-wren. We com-bined Illumina shotgun and mate-pair sequences, PacBio long-reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to gener-ate this genome assembly. Of the final assembled 1.07-Gb genome, 975 Mb (90.4%) was anchored onto 25 pseudochromosomes resulting in a final superscaffold N50 of 68.11 Mb. This high-quality bird genome assembly is one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree-based bird genetic maps, we find that the fairy-wren genetic map more closely resembles those of Taeniopygia guttata and Parus major maps, unlike the Ficedula albicollis map which more closely resembles that of Gallus gallus. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high-quality, annotated genome assembly will be an invaluable resource not only regarding the superb fairy-wren species and relatives but also broadly across the avian tree by providing a novel reference point for comparative genomic analyses.
dc.description.sponsorshipFunding was provided by the Australian Research Council (DP150100298), and the office of the DVC (Research) at the Australian National University. E
dc.format.mimetypeapplication/pdf
dc.language.isoen_AU
dc.publisherWiley-Blackwell
dc.rights© 2019 The Authors
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.sourceMolecular Ecology Resources
dc.subjectgenetic map
dc.subjectMalurus cyaneus
dc.subjectMeliphagides
dc.subjectrecombination landscape
dc.subjectreference genome
dc.titleGenome of an iconic Australian bird: High-quality assembly and linkage map of the superb fairy-wren (Malurus cyaneus)
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume20
dcterms.dateAccepted2019-12-02
dc.date.issued2020
local.identifier.absfor060411 - Population, Ecological and Evolutionary Genetics
local.identifier.ariespublicationu3102795xPUB5543
local.publisher.urlhttps://onlinelibrary.wiley.com/
local.type.statusPublished Version
local.contributor.affiliationPenalba, Joshua V., University of Munich
local.contributor.affiliationDeng, Yuan, BGI‐Shenzhen
local.contributor.affiliationFang, Qi, BGI‐Shenzhen
local.contributor.affiliationJoseph, Leo G, CSIRO
local.contributor.affiliationMoritz, Craig, College of Science, ANU
local.contributor.affiliationCockburn, Andrew, College of Science, ANU
dc.relationhttp://purl.org/au-research/grants/arc/DP150100298
local.bibliographicCitation.issue2
local.bibliographicCitation.startpage560
local.bibliographicCitation.lastpage578
local.identifier.doi10.1111/1755-0998.13124
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
dc.date.updated2020-03-23T21:45:08Z
local.identifier.thomsonIDWOS:000505056400001
dcterms.accessRightsOpen Access
dc.provenanceThis is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
dc.rights.licenseCreative Commons Attribution License
CollectionsANU Research Publications

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