Abstract
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 high-quality 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 1.07-Gb genome, 975Mb (90.4%) was anchored onto 25 pseudochromosomes resulting in a final superscaffold N50 of 68.11Mb. 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.
Highlights
We present a high-quality annotated assembly of the genome of the superb fairy-wren, Malurus cyaneus (Maluridae)
The superb fairy-wren genome is important in that it fills a gap in the passerine tree as it is the first member of the Meliphagides infraorder to have a reference genome
Does it provide a useful resource for species within that clade (Peñalba, Joseph, & Moritz, 2019) and the nonpasserine part of the tree and a useful comparison point in the broader passerine and avian tree for comparative evolution
Summary
We present a high-quality annotated assembly of the genome of the superb fairy-wren, Malurus cyaneus (Maluridae). The superb fairy-wren is an exemplar of the largest clade of that early radiation, the Meliphagides, which has almost 300 species We complement this high-level assembly with a detailed genetic map from which we can infer the variation in recombination across the genome. Providing a genetic map and recombination landscape to accompany a high-quality genome assembly greatly expands the array of possible research questions and avenues We combine both conventional short-read (Illumina shotgun and mate-pair) and long-read sequencing (PacBio) with an extensive pedigree of our long-term study population to achieve a highly contiguous assembly and recombination map. We add prediction-based repeat and gene annotations using existing libraries from other bird species This assembly will greatly facilitate ecological and evolutionary studies of fairy-wrens, and provide a resource for understanding the evolution and diversification of the Meliphagides as a whole
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