A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals

Abstract

Background Ducks have a typical avian karyotype that consists of macro- and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multiplatform scaffolding techniques. Results A major improvement of genome assembly and annotation quality resulted from the successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly. We found that the duck topologically associated domains (TAD) are demarcated by putative binding sites of the insulator protein CTCF, housekeeping genes, or transitions of active/inactive chromatin compartments, indicating conserved mechanisms of spatial chromosome folding with mammals. There are extensive overlaps of TAD boundaries between duck and chicken, and also between the TAD boundaries and chromosome inversion breakpoints. This suggests strong natural selection pressure on maintaining regulatory domain integrity, or vulnerability of TAD boundaries to DNA double-strand breaks. The duck W chromosome retains 2.5-fold more genes relative to chicken. Similar to the independently evolved human Y chromosome, the duck W evolved massive dispersed palindromic structures, and a pattern of sequence divergence with the Z chromosome that reflects stepwise suppression of homologous recombination. Conclusions Our results provide novel insights into the conserved and convergently evolved chromosome features of birds and mammals, and also importantly add to the genomic resources for poultry studies.

A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes

“…S24). Such high trans-contacts between microchromosomes were also found in our companion study on the duck genome (Li et al 2021) and were reported previously for the rattlesnake (Schield et al 2019), as well as for small-sized chromosomes in human cells (Lieberman-Aiden et al 2009), and therefore it is probably a conserved chromosome territorial feature of vertebrates (Perry et al 2020).…”

Genome Stability Is in the Eye of the Beholder: CR1 Retrotransposon Activity Varies Significantly across Avian Diversity

“…The majority of the genomes we have used are of this data type. The recent sequencing of avian genomes using multiplatform approaches have resolved gaps present in short read assemblies, finding these gaps to be rich in interspersed, simple, and tandem repeats ( Li et al 2021 ; Peona et al 2021 ). Of particular note, Li et al (2021 ) resolved gaps in the assembly of Anas platyrhynchos which we analyzed here using long-read sequencing, and found the gaps to be dominated by the two CR1 families that have recently expanded in waterfowl (Anseriformes): CR1-J and CR1-X.…”

“…The recent sequencing of avian genomes using multiplatform approaches have resolved gaps present in short read assemblies, finding these gaps to be rich in interspersed, simple, and tandem repeats ( Li et al 2021 ; Peona et al 2021 ). Of particular note, Li et al (2021 ) resolved gaps in the assembly of Anas platyrhynchos which we analyzed here using long-read sequencing, and found the gaps to be dominated by the two CR1 families that have recently expanded in waterfowl (Anseriformes): CR1-J and CR1-X. Species with low-quality assemblies may have full-length repeats present in their genome, yet the sequencing technology used prevents the assembly of the repeats and hence detection.…”

Genome stability is in the eye of the beholder: recent retrotransposon activity varies significantly across avian diversity

“…The recent sequencing of avian genomes using multiplatform approaches have resolved gaps present in short read assemblies, finding these gaps to be rich in interspersed, simple and tandem repeats (Peona et al 2021;Li et al 2021). Of particular note (Li et al 2021) resolved gaps in the assembly of Anas platyrhynchos which we analyzed here using long read sequencing, and found the gaps to be dominated by the two CR1 families that have recently expanded in waterfowl (Anseriformes): CR1-J and CR1-X. Species with low quality assemblies may have full length repeats present in their genome, yet the sequencing technology used prevents the assembly of the repeats and hence detection.…”

“…The majority of the genomes we have used are of this data type. The recent sequencing of avian genomes using multiplatform approaches have resolved gaps present in short read assemblies, finding these gaps to be rich in interspersed, simple and tandem repeats (Peona et al 2021;Li et al 2021). Of particular note (Li et al 2021) resolved gaps in the assembly of Anas platyrhynchos which we analyzed here using long read sequencing, and found the gaps to be dominated by the two CR1 families that have recently expanded in waterfowl (Anseriformes): CR1-J and CR1-X.…”