Retrieving the near-complete genome of a threatened bird from wild frozen samples

Abstract

Conservation genomics often relies on non-invasive methods to obtain DNA fragments which limit the power of multi-omic analyses for threatened species. Collecting samples from frozen dead animals in the wild provides an alternative approach to obtaining high-quality nucleic acids. Here, we report multi-omic analyses based on a well-preserved great bustard individual (Otis tarda, Otidiformes) of a recent death found in the mountainous region in Gansu, China. We generated a near-complete genome assembly (OTswu) having only 18 gaps scattering in 8 out of the 40 assembled chromosomes. Unlikely most other bird genome assemblies, OTswu contains complete chromosome models (2n = 80). We demonstrated that the great bustard genome likely retained the ancestral avian karyotype. We also characterized the DNA methylation landscapes of OTswu which are strongly correlated with GC content and gene expression. Our phylogenomic analysis suggested Otidiformes and Musophagiformes were sister groups that diverged from each other 46.3 million years ago. The genetic diversity of great bustard was 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 enriching for metabolism. Finally, we identified an extremely young evolutionary stratum on the sex chromosome, a rare case among Neoaves. Together, our study combining long-read sequencing and RNA-seq technology provides a working strategy for conducting multi-omic analyses for threatened species by retrieving high-quality nucleic acids from dead animals frozen in the wild.

Evolutionary analysis of a complete chicken genome

“…A complete chicken genome (except for the W) is achieved thanks to the Nanopore ultralong and PacBio HiFi sequencing technology and a trio-binning strategy ( 48 ). The capacity of Nanopore sequencers in sequencing through high GC content regions ( 49 , 50 ) allows the assembly of six dot chromosomes missing in older versions of chicken genomes. The dot chromosomes are typically acrocentric, largely compartmentalized into two parts: a compact and gene-rich euchromatin region and a hypermethylated PCH region.…”

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).…”