Draft genome of the endangered visayan spotted deer (Rusa alfredi), a Philippine endemic species.

GigaByte (Hong Kong, China) Pub Date : 2025-02-24 eCollection Date: 2025-01-01 DOI:10.46471/gigabyte.150

Ma Carmel F Javier, Albert C Noblezada, Persie Mark Q Sienes, Robert S Guino-O, Nadia Palomar-Abesamis, Maria Celia D Malay, Carmelo S Del Castillo, Victor Marco Emmanuel N Ferriols

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Abstract

The Visayan Spotted Deer (VSD), or Rusa alfredi, is an endangered and endemic species in the Philippines. Despite its status, genomic information on R. alfredi, and the genus Rusa in general, is missing. This study presents the first draft genome assembly of the VSD using the Illumina short-read sequencing technology. The resulting 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 genome's completeness, and includes the annotation of 24,531 genes. Our phylogenetic analysis based on single-copy orthologs revealed a close evolutionary relationship between R. alfredi and the genus Cervus. RusAlf_1.1 represents a significant advancement in our understanding of the VSD. It opens opportunities for further research in population genetics and evolutionary biology, potentially contributing to more effective conservation and management strategies for this endangered species.

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濒危的菲律宾特有物种鄢陵斑鹿（Rusa alfredi）的基因组草案。

维萨扬斑点鹿（VSD），或Rusa alfredi，是菲律宾的一种濒临灭绝的特有物种。尽管它的地位，R. alfredi的基因组信息，以及一般的Rusa属，都是缺失的。本研究提出了利用Illumina短读测序技术的VSD基因组组装草图。得到的RusAlf_1.1组装体全长2.52 Gb，序列N50为46 Kb，支架N50大小为75 Mb。该组装体的BUSCO完成度为95.5%，显示了基因组的完整性，包含24,531个基因的注释。基于单拷贝同源基因的系统发育分析揭示了鹿角鹿属与鹿角鹿属之间的密切进化关系。RusAlf_1.1代表了我们对VSD的理解的重大进步。这为种群遗传学和进化生物学的进一步研究提供了机会，可能有助于更有效地保护和管理这种濒危物种。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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