An almost chromosome-level assembly and annotation of theAlectoris rufagenome

Abstract

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 thatA. rufaandC. japonicadiverged 21 M-years ago and that their common ancestor diverged fromG. gallus37 M-years ago. The reported assembly is a significant step towards a complete reference genome forA. rufa, contributing to facilitate comparative avian genomics, and providing a valuable resource for future research and conservation efforts for the red-legged partridge.