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bioRxiv · 10.1101/2025.02.05.636739

Draft Genome of the Endangered Visayan Spotted Deer (Rusa alfredi)

Javier, M. C. F.·Noblezada, A. C.·Sienes, P. M. Q.·Guino-o, R. S.·Palomar-Abesamis, N.·Malay, M. C. D.·del Castillo, C. S.·Ferriols, V. M. E. N.
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Abstract

The Visayan Spotted Deer (Rusa alfredi) is an endangered and endemic species in the Philippines facing significant threats from habitat loss and hunting. It is considered as the worlds most threatened deer species by the International Union for Conservation of Nature (IUCN) thus its conservation has been a top priority. Despite its status, there is a notable lack of genomic information available for R. alfredi and the genus Rusa in general. This study presents the first draft genome assembly of the Visayan Spotted Deer (VSD), Rusa alfredi, using Illumina short-read sequencing technology. The RusAlf_1.1 assembly has a 2.52 Gb total length with a contig N50 of 46 Kb and scaffold N50 size of 75 Mb. The assembly has a BUSCO complete score of 95.5%, demonstrating the genomes completeness, and includes the annotation of 24,531 genes. Phylogenetic analysis based on single-copy orthologs reveals a close evolutionary relationship between the R. alfredi and the genus Cervus. The availability of the RusAlf_1.1 genome assembly represents a significant advancement in our understanding of the VSD. It opens opportunities for further research in population genetics and evolutionary biology, which could contribute to more effective conservation and management strategies for this endangered species. This genomic resource can help in assuring the survival of Rusa alfredi in the country.

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Javier, M. C. F., Noblezada, A. C., Sienes, P. M. Q., Guino-o, R. S., Palomar-Abesamis, N., Malay, M. C. D., del Castillo, C. S., Ferriols, V. M. E. N.. 2025-02-06. Draft Genome of the Endangered Visayan Spotted Deer (Rusa alfredi). https://doi.org/10.1101/2025.02.05.636739

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