College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China.
BMC Genomics. 2024 Jun 19;25(1):617. doi: 10.1186/s12864-024-10522-9.
Sika 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.
Here 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.
Our 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.
梅花鹿（Cervus nippon）在鹿科动物中具有重要地位，最近发表了三个基因组。然而，这些基因组仍然包含数百个缺口，在连续性和准确性方面存在显著差异。这给功能基因组学研究和合适参考基因组的选择带来了挑战。因此，获得高质量的参考基因组对于有效地进行功能基因组学研究至关重要。
我们在此报告了雄性梅花鹿的高质量一致基因组。所有 34 条染色体都组装成单条连续的假染色体，没有任何缺口，这是最完整的组装。基因组大小为 2.7G，包含 23284 个蛋白质编码基因。比较基因组学分析发现，梅花鹿和马鹿的基因组高度保守，约有 2.4G 共线性区域，序列相似度高达 99%。同时，我们观察到马鹿的 Chr23 和 Chr4 在进化过程中融合，形成了梅花鹿的 Chr1。此外，我们在这个一致参考基因组中鉴定了 607 个参与鹿角发育调控的转录因子（TFs），包括 RUNX2、SOX6、SOX8、SOX9、PAX8、SIX2、SIX4、SIX6、SPI1、NFAC1、KLHL8、ZN710、JDP2 和 TWST2。
我们的结果表明，我们获得了高质量的一致参考基因组。这为理解功能基因组学提供了有价值的资源。此外，我们发现了梅花鹿-马鹿杂种生育力的遗传基础，并鉴定了 607 个对鹿角发育有显著影响的 TFs。
