An almost chromosome-level assembly and annotation of the Alectoris rufa genome

This is the authors' abstract. We don't add key points for this paper.

The red-legged partridge, Alectoris rufa (n=38 chromosomes) plays a crucial role in the ecosystem of southwestern Europe, and understanding its genetics is vital for conservation and management. Here we sequence, assemble, and annotate a highly contiguous and nearly complete version of it genome (115 scaffolds, L90=23). This assembly contains 96.9% (8078 out of 8332) orthologous genes from the BUSCO aves_odb10 dataset of single copy orthologous genes. We identify RNA and protein genes, 95% of which with functional annotation. This near-chromosome level assembly revealed significant chromosome rearrangements compared to quail ( Coturnix japonica ) and chicken ( Gallus gallus ), suggesting that A. rufa and C. japonica diverged 21 M-years ago and that their common ancestor diverged from G. gallus 37 M-years ago. The reported assembly is a significant step towards a complete reference genome for A. rufa , contributing to facilitate comparative avian genomics, and providing a valuable resource for future research and conservation efforts for the red-legged partridge.