Genome of an iconic Australian bird: High‐quality 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 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.

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

“…( Supplementary Table S2). A similar dynamic was observed also during the assembly process of 611 the superb fairy-wren Malarus cyaneus (Peñalba et al 2019) where BUSCO values dropped with 612 long-read gap-filling but were restored after sequence polishing. 613…”

“…Finally, contig N50 should be used as a measure of contiguity, rather than scaffold N50, 597 as contig length measures sequences not interrupted by gaps. 598 599 Most of the currently available avian genomes score more than 94% of BUSCO gene completeness 600(Peñalba et al 2019) with various degrees of fragmentation, suggesting that it has become 601 straightforward to generate short-read assemblies with high BUSCO values. On the other hand, 602 BUSCO seems to be limited by the sequencing errors introduced by PacBio in the identification of 603 gene models(Watson and Warr 2019).…”

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

“…Most of the currently available avian genomes score more than 95% of BUSCO gene completeness (Peñalba et al., 2019) with various degrees of fragmentation, suggesting that it has become straightforward to generate short‐read assemblies with high BUSCO values. On the other hand, BUSCO seems to be limited by the sequencing errors introduced by PacBio in the identification of gene models (Watson & Warr, 2019).…”

Genome-Wide Analyses of the Relict Gull (Larus Relictus) Insights Into Evolutionary Implications

“…Among them, long-read sequencing technologies such as Paci c Biosciences (PacBio) [13] can produce average lengths of over 10,000 bp [12]. PacBio technology has been used to obtain high-quality genome assemblies for several avian species, such as Gallus gallus (Galliformes) [14] and Malurus cyaneus (Passeriformes) [15].…”