PDF(Pubmed)
Abstract：
BACKGROUND: 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.
RESULTS: 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.
CONCLUSIONS: 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.
RESULTS: 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.
CONCLUSIONS: 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.
摘要：
背景：梅花鹿（Cervusnippon）在子宫颈中具有重要意义，最近出版了三个基因组。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.这对功能基因组学研究和选择合适的参考基因组提出了挑战。因此，获得高质量的参考基因组是有效深入研究功能基因组学的当务之急。
结果：在这里，我们报告了雄性梅花鹿的高质量共有基因组。所有34条染色体都组装成单重叠群假分子，没有任何间隙，这是最完整的组装。基因组大小为2.7G，具有23,284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,具有高达99%的序列相似性的大约2.4G共线区域。同时,我们观察到马鹿的Chr23和Chr4在进化过程中的融合，形成梅花鹿的Chr1。此外,我们确定了607个转录因子（TFs）参与鹿茸发育的调节，包括RUNX2、SOX6、SOX8、SOX9、PAX8、SIX2、SIX4、SIX6、SPI1、NFAC1、KLHL8、ZN710、JDP2和TWST2。
结论：我们的结果表明我们获得了高质量的共有参考基因组。这为理解功能基因组学提供了宝贵的资源。此外,发现了梅花红杂种育性的遗传基础，并确定了607个影响鹿茸发育的重要TFs。
结果：在这里，我们报告了雄性梅花鹿的高质量共有基因组。所有34条染色体都组装成单重叠群假分子，没有任何间隙，这是最完整的组装。基因组大小为2.7G，具有23,284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,具有高达99%的序列相似性的大约2.4G共线区域。同时,我们观察到马鹿的Chr23和Chr4在进化过程中的融合，形成梅花鹿的Chr1。此外,我们确定了607个转录因子（TFs）参与鹿茸发育的调节，包括RUNX2、SOX6、SOX8、SOX9、PAX8、SIX2、SIX4、SIX6、SPI1、NFAC1、KLHL8、ZN710、JDP2和TWST2。
结论：我们的结果表明我们获得了高质量的共有参考基因组。这为理解功能基因组学提供了宝贵的资源。此外,发现了梅花红杂种育性的遗传基础，并确定了607个影响鹿茸发育的重要TFs。
