Luo H.; Jiang X.; Li B.; Wu J.; Shen J.; Xu Z.; Zhou X.; Hou M.; Huang Z.; Ou X. and Xu L. 2023. Communications Biology 6(1).

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 near-complete chromosome-level genome assembly. a Genomic features of the great bustard visualized by TBtools¹²⁶. Chromosome IDs are labeled at bottom of chromosome bars. In the “Chr” ring, the “C” label represents the centromere position in each chromosome. In the “GC” ring, the orange bars represent regions (in 50 kb windows) with GC-content higher than the genome average (42.9%), while the blue bars represent the below-average regions. In the “Repeat” ring, red bars represent repeat content in 50 Kb window. In the “Methylation” ring, the orange and blue bars represent regions with 5mC higher or lower than 0.5, respectively. b Hi-C contact heatmap for the assembled chromosomes. The chromosome IDs are shown under the chromosome models. The right panel shows the zoom-in view for dot chromosomes (Chr16, 29–32, 34–38). c Gene synteny blocks among the great bustard, chicken and zebra finch were identified and visualized by MCScan. Horizontal bars represent chromosome models. The synteny blocks highlighted in colors indicate chromosomal fusions.