The swan genome and transcriptome, it is not all black and white

Abstract

Background The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Results Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. Conclusion Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.

The genome of a globally invasive passerine, the common myna (Acridotheres tristis)

“…A similar pattern is seen in the most closely related species the European starling, and indeed appears to be the most common state of avian proteomes across the species included in our analysis (Fig. 5) and previous similar analysis (Liu et al 2022;Karawita et al 2023) owing to the gene loss that characterises avian genomes (Zhang et al 2014). When considering all gene family changes (not just significant ones) gene family expansion and contraction was more even, a trend not seen in the European starling nor most other avian species (Fig.…”

“…S12). This pattern is seen in other studies of T. guttata (Liu et al 2022;Karawita et al 2023), and is not seen in the zebra finch's nearest relative Lonchura striata domestica despite only 10 million years' divergence (Kumar et al 2022), though this result may also be an artifact of differing annotation approaches.…”

The genome of a globally invasive passerine, the common myna, Acridotheres tristis

“…In general, most avian proteomes across the species included in our analysis ( Fig. 5 ) and previous similar analysis 122 , 123 tend to report more gene family contractions, owing to the gene loss that characterizes avian genomes. 96 The only other avian species included in our analysis that did not conform to this trend was the zebra finch ( Fig.…”

“…5 ). This pattern is seen in other studies of T. guttata , 122 , 123 and is not seen in the zebra finch’s nearest relative Lonchura striata domestica despite only 10 million years’ divergence, 73 though this result may also be an artifact of differing annotation approaches.…”

A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution

“…Indeed, at the advent of genome sequencing in birds, chicken chromosomes were arbitrarily grouped as macrochromosomes (1-5), intermediate chromosomes (5-10), and microchromosomes (11+) (Hillier et al 2004). Subsequent studies have either used these criteria, grouping macrochromosomes and intermediate chromosomes as macrochromosomes, ranging in size from ~23Mb to ~200Mb (O’Connor et al 2018), or established their own criteria for an arbitrary cutoff, such as 10Mb, 30Mb, or 50Mb (Karawita et al 2022; Perry et al 2021; Srikulnath et al 2021; Waters et al 2021). However, these arbitrary categorizations—enforced across vertebrates—make direct comparisons between taxa difficult and may encourage spurious correlations from these artifacts.…”