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<p>Taohongling Sika deer (<i>Cervus nippon kopschi</i>) is classified as a national first-class protected wild animal, and the absence of a high-quality chromosome-scale genome has hindered in-depth studies on its molecular mechanism of adaptive evolution, elucidation of unique biological traits, and identification of its genetic origin. To address this limitation, we finally assembled a 2.87 Gb genome using Pacbio and Illumina sequencing, achieving a scaffold N50 size of 85.86 Mb. Subsequently, we employed Hi-C techniques to assign 97.23% of the sequences from the assembled contigs or scaffolds onto 34 chromosomes. Upon completion of genome annotation, it was determined that repetitive sequences accounted for 46.19%, with a total prediction of 22,890 protein-coding genes, of which 97.16% were functionally annotated. In addition, 63,473 noncoding RNAs were identified. The high-quality chromosome-scale genome obtained in our study can provide a valuable molecular genetic basis for systematic research into the adaptive evolution and genetic characteristics of the Taohongling Sika deer (<i>Cervus nippon kopschi</i>).</p>

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High-quality chromosome-scale genome assembly and annotation of Taohongling Sika deer (Cervus nippon kopschi)

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年11月19日

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  • Qiang Yang,
  • Yongtao Xu,
  • Chang Xiao,
  • Jie Dai,
  • Jianwen Zhan,
  • Weiwei Zhang

摘要

Taohongling Sika deer (Cervus nippon kopschi) is classified as a national first-class protected wild animal, and the absence of a high-quality chromosome-scale genome has hindered in-depth studies on its molecular mechanism of adaptive evolution, elucidation of unique biological traits, and identification of its genetic origin. To address this limitation, we finally assembled a 2.87 Gb genome using Pacbio and Illumina sequencing, achieving a scaffold N50 size of 85.86 Mb. Subsequently, we employed Hi-C techniques to assign 97.23% of the sequences from the assembled contigs or scaffolds onto 34 chromosomes. Upon completion of genome annotation, it was determined that repetitive sequences accounted for 46.19%, with a total prediction of 22,890 protein-coding genes, of which 97.16% were functionally annotated. In addition, 63,473 noncoding RNAs were identified. The high-quality chromosome-scale genome obtained in our study can provide a valuable molecular genetic basis for systematic research into the adaptive evolution and genetic characteristics of the Taohongling Sika deer (Cervus nippon kopschi).