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

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 chromosome-scale genome assembly of a Meliphagides representative: the superb fairy-wren. We combined Illumina shotgun and matepair 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 pedigreebased 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.

Chromosome-level genome assembly of the common chaffinch (Aves:Fringilla coelebs): a valuable resource for evolutionary biology

“…In the last decade, the number of bird reference genomes has increased dramatically (e.g. Dalloul et al 2010;Warren et al 2010;Zhang et al 2012;Jarvis et al 2014;Poelstra et al 2014;Frankl-Vilches et al 2015;Friis et al 2018;Louha et al 2019;Peñalba et al 2019;Ducrest et al 2020, Wang et al 2020, providing major scientific breakthroughs in phylogenetics (e.g., Alström et al 2018;Braun et al 2019;Jarvis et al 2015), comparative genomics (Feng et al 2020), adaptation genomics (Wirthlin et al 2014;Lawson & Petren 2017), and genomic architecture (Poelstra et al 2014;Vijay et al 2016), among others. Moreover, the Ten-Thousand Bird Genomes (B10K) consortium is currently sequencing and assembling over 300 avian genomes that correspond to at least one representative per family (Zhang 2015).…”

Beyond genes-for-behaviour: the potential for genomics to resolve questions in avian brood parasitism

“…Furthermore, high-quality reference genomes are now available for brood parasite hosts with rich behavioural data (e.g. superb fairy wren: [61], great reed warbler: [62,63], reed warbler: [64]). Therefore, here we discuss how applying genomic methods to avian brood parasitic systems could be used to better predict (i) where and when brood parasitism should evolve, (ii) when and how hosts defend, or (iii) how coevolutionary trajectories depend on ecological change, three major questions in a field aiming for a deeper understanding of coevolutionary dynamics [32].…”