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

Eleiwa, A.; Nadal, J.; Vilaprinyo, E.; Marin-Sanguino, A.; Sorribas, A.; Basallo, O.; Lucido, A.; Richart, C.; Pena, R. N.; Ros-Freixedes, R.; Usie, A.; Alves, R.

doi:10.1101/2024.01.11.575009

bioRxiv · 10.1101/2024.01.11.575009

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

Eleiwa, A.·Nadal, J.·Vilaprinyo, E.·Marin-Sanguino, A.·Sorribas, A.·Basallo, O.·Lucido, A.·Richart, C.·Pena, R. N.·Ros-Freixedes, R.·Usie, A.·Alves, R.

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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 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.

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Eleiwa, A., Nadal, J., Vilaprinyo, E., Marin-Sanguino, A., Sorribas, A., Basallo, O., Lucido, A., Richart, C., Pena, R. N., Ros-Freixedes, R., Usie, A., Alves, R.. 2024-01-11. An almost chromosome-level assembly and annotation of the Alectoris rufa genome. https://doi.org/10.1101/2024.01.11.575009

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