A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes)

Abstract

Conservation genomics often relies on non-invasive methods to obtain DNA fragments which limit the power of multi-omic analyses for threatened species. Here, we report multi-omic analyses based on a well-preserved great bustard individual (Otis tarda, Otidiformes) that was found dead in the mountainous region in Gansu, China. We generate a near-complete genome assembly containing only 18 gaps scattering in 8 out of the 40 assembled chromosomes. We characterize the DNA methylation landscape which is correlated with GC content and gene expression. Our phylogenomic analysis suggests Otidiformes and Musophagiformes are sister groups that diverged from each other 46.3 million years ago. The genetic diversity of great bustard is found the lowest among the four available Otidiformes genomes, possibly due to population declines during past glacial periods. As one of the heaviest migratory birds, great bustard possesses several expanded gene families related to cardiac contraction, actin contraction, calcium ion signaling transduction, as well as positively selected genes enriched for metabolism. Finally, we identify an extremely young evolutionary stratum on the sex chromosome, a rare case among birds. Together, our study provides insights into the conservation genomics, adaption and chromosome evolution of the great bustard.

A Bird’s-Eye View of Chromosomic Evolution in the Class Aves

“…Undoubtedly, new prospects in the study of avian genomes are opening up due to the introduction of the latest technologies that make chromosome-level genome assemblies achievable without necessarily involving chromosome preparations [183][184][185][186][187][188][189][190][191]. These are characterized by some recent mammalian genome chromosome level assemblies [189][190][191] and some more recent avian ones [191][192][193]. Technologies include long-read sequencing, optical mapping, and others [194][195][196][197], as well as de novo PacBio long-read and phased avian genome assemblies for complementing and rectifying reference genes previously produced using short and intermediate reads [198].…”

Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe

“…As genomic sequencing technology advances and costs decrease, high-quality reference genomes are becoming increasingly recognized as an essential resource for conservation genomics (Formenti et al 2022;Brandies et al 2019;Theissinger et al 2023;Paez et al 2022). When aligned to a reference genome assembly, high throughput genomic data can contribute to the understanding of past and contemporary population demographics (Gautier et al 2016;du Plessis et al 2023;Luo et al 2023;Campana et al 2016), reveal evolutionary patterns such as adaptive differentiation (Szarmach et al 2021;Martchenko and Shafer 2023), and provide information about the current conservation status of wildlife species of conservation concern (Talla et al 2023;Viluma et al 2022). While reduced-representation sequencing (RRS) methodologies continue to be the more cost-effective and efficient means of generating genome-wide single nucleotide polymorphism (SNP) datasets for large numbers of samples (Wright et al 2020;Peterson et al 2012), alignment of RRS reads to a high-quality reference genome improves both the precision of SNP calls and the quantity of SNPs recovered when compared to de novo read alignment without a genome assembly (Rochette et al 2019;Brandies et al 2019).…”