ArticleBMC genomics2024
A consensus genome of sika deer (Cervus nippon) and transcriptome analysis provided novel insights on the regulation mechanism of transcript factor in antler development.
Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Transposable element dynamics and regulatory role in sika deer (Cervus nippon) antler development.Mobile DNA · 2026Article
- Article
- Multi-omics integration analysis reveals metabolic changes during sika deer antler growth.BMC genomics · 2026Article
- A comprehensive ruminant microbial catalog (CRMC) reveals convergent selection for key vitamin-synthesizing pathways and genes across ruminants and human.GigaScience · 2026Article
- High-quality chromosome-scale genome assembly and annotation of Taohongling Sika deer (Cervus nippon kopschi).Scientific data · 2025Article
- Comparative transcriptome analysis reveals the patterns of gene expression in different venison cuts of sika deer (Cervus nippon).Animal bioscience · 2025Article
- Conservation of Native Livestock Breeds in Russia: Current State and Promising Prospects.Animals : an open access journal from MDPI · 2025Review
- Draft genome of the endangered visayan spotted deer (GigaByte (Hong Kong, China) · 2025Article
- Article
- Low-molecular-weight peptides from deer antler velvet: Antioxidant potential, biosafety, and synergistic interaction with nanomelanin.Journal of advanced pharmaceutical technology & researchArticle
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundSika deer (Cervus nippon) holds significance among cervids, with three genomes recently published. However, these genomes still contain hundreds of gaps and display significant discrepancies in continuity and accuracy. This poses challenges to functional genomics research and the selection of an appropriate reference genome. Thus, obtaining a high-quality reference genome is imperative to delve into functional genomics effectively.
findingsHere we report a high-quality consensus genome of male sika deer. All 34 chromosomes are assembled into single-contig pseudomolecules without any gaps, which is the most complete assembly. The genome size is 2.7G with 23,284 protein-coding genes. Comparative genomics analysis found that the genomes of sika deer and red deer are highly conserved, an approximately 2.4G collinear regions with up to 99% sequence similarity. Meanwhile, we observed the fusion of red deer's Chr23 and Chr4 during evolution, forming sika deer's Chr1. Additionally, we identified 607 transcription factors (TFs) that are involved in the regulation of antler development, including RUNX2, SOX6, SOX8, SOX9, PAX8, SIX2, SIX4, SIX6, SPI1, NFAC1, KLHL8, ZN710, JDP2, and TWST2, based on this consensus reference genome.
conclusionsOur results indicated that we acquired a high-quality consensus reference genome. That provided valuable resources for understanding functional genomics. In addition, discovered the genetic basis of sika-red hybrid fertility and identified 607 significant TFs that impact antler development.
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