Data from: Genome of an iconic Australian bird: Chromosome-scale assembly and linkage map of the superb fairy-wren (Malurus cyaneus)

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 passerines 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 represented by a high-quality reference. To rectify that, we present the first chromosome-scale genome assembly of a Meliphagides representative: the superb fairy-wren. We combined Illumina shotgun and mate-pair sequences, PacBio long-reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07Gb genome, 894Mb (84.8%) was anchored onto 25 chromosomes resulting in a final scaffold N50 of 68.11 Mb. This high-quality bird genome assembly is also 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 zebrafinch (Taeniopygia) genetic map more closely resembles the fairy-wren map rather than the map from the more closely-related Ficedula flycatcher. 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 to the superb fairy-wren species and relatives but also broadly across the avian tree by providing a new reference point for comparative genomic analyses.Malurus cyaneus gene annotationGFF file containing the predictive gene annotation of the Malurus cyaneus genome.Malurus_cyaneus.final.withID.gffSliding window recombination rate (50Kb)Recombination rate in 50Kb nonoverlapping windows inferred from smoothing the Marey Map produced from LepMap3.RecombinationRates_LoessSmoothed_50kb.txtSliding window recombination rate (100Kb)Recombination rate in 100Kb nonoverlapping windows inferred from smoothing the Marey Map produced from LepMap3.RecombinationRates_LoessSmoothed_100kb.txtSliding window recombination rate (200Kb)Recombination rate in 200Kb nonoverlapping windows inferred from smoothing the Marey Map produced from LepMap3.RecombinationRates_LoessSmoothed_200kb.txtLM3 pedigree genotype inputInput for LepMap3 for which the genetic map was eventually inferred. Contains genotype likelihoods and family structure of the pedigree.2-LM3_ParentCall2.inputMalurus cyaneus genetic mapPedigree-based genetic map of Malurus cyaneus estimated using LM3. Includes all assembled whole chromosomes, sex averaged genetic distances, and sex-specific genetic distances.Malurus_cyaneus_geneticMap.txtMalurus cyaneus RepeatMasker OutputRepeat content information of the Malurus cyaneus genome.Malurus_cyaneus_RepeatMaskerOutput.tar.g