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, 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.

中文翻译：

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澳大利亚标志性鸟类的基因组：高品质神仙w（Malurus cyaneus）的高质量装配图和连锁图。

精湛的童话-，Malurus cyaneus，是澳大利亚最具标志性的雀形目物种之一。该物种属于澳大利亚特有的Meliphagides进化枝，该进化枝在oscine passerines进化的早期就多样化了。如今，the曲雀碱几乎占所有鸟类物种多样性的一半。尽管可用鸟类基因组装配的迅速增加，但尚未有高质量参考文献来代表禽树的这一部分。为了纠正这一点，我们提出了Meliphagides代表的第一个高质量基因组组装：精湛的神仙w。我们结合了Illumina shot弹枪和伴侣对序列，PacBio的长读本，以及来自野生种群的密集采样谱系的遗传连锁图谱，以生成此基因组组装体。在最终组装的1.07-Gb基因组中，为975 Mb（90。将4％的人锚定在25个假染色体上，最终产生的超级支架N50为68.11 Mb。这种高质量的鸟类基因组装配是极少数的一种，还伴随着遗传图谱和重组景观。与其他基于谱系的鸟类遗传图谱相比，我们发现，与神仙有关的遗传图谱与Taeniopygia guttata和Parus主要图谱更加相似，而Ficedula albicollis图谱与鸡鸡更相似。最后，我们还提供了一个预测基因并重复注释了基因组。这种新的高质量，带注释的基因组装配将不仅是珍贵的神仙物种和近亲的宝贵资源，而且通过为比较基因组分析提供新颖的参考点，还将在整个鸟类树上成为宝贵的资源。