PDF(Pubmed)
Abstract：
Prunus conradinae, a valuable flowering cherry belonging to the Rosaceae family subgenus Cerasus and endemic to China, has high economic and ornamental value. However, a high-quality P. conradinae genome is unavailable, which hinders our understanding of its genetic relationships and phylogenesis, and ultimately, the possibility of mining of key genes for important traits. Herein, we have successfully assembled a chromosome-scale P. conradinae genome, identifying 31,134 protein-coding genes, with 98.22% of them functionally annotated. Furthermore, we determined that repetitive sequences constitute 46.23% of the genome. Structural variation detection revealed some syntenic regions, inversions, translocations, and duplications, highlighting the genetic diversity and complexity of Cerasus. Phylogenetic analysis demonstrated that P. conradinae is most closely related to P. campanulata, from which it diverged ~ 19.1 million years ago (Mya). P. avium diverged earlier than P. cerasus and P. conradinae. Similar to the other Prunus species, P. conradinae underwent a common whole-genome duplication event at ~ 138.60 Mya. Furthermore, 79 MADS-box members were identified in P. conradinae, accompanied by the expansion of the SHORT VEGETATIVE PHASE subfamily. Our findings shed light on the complex genetic relationships, and genome evolution of P. conradinae and will facilitate research on the molecular breeding and functions of key genes related to important horticultural and economic characteristics of subgenus Cerasus.
摘要：
Prunusconradinae,一种珍贵的开花樱桃，属于玫瑰科Cerasus亚属，是中国特有的，具有较高的经济和观赏价值。然而,无法获得高质量的P.conradinae基因组,这阻碍了我们对其遗传关系和系统发育的理解，最终,挖掘重要性状关键基因的可能性。在这里，我们已经成功地组装了一个染色体尺度的油菜基因组，鉴定31,134个蛋白质编码基因，其中98.22%的功能注释。此外，我们确定重复序列占基因组的46.23%.结构变异检测揭示了一些同势区域，倒置,易位,和重复，突出了Cerasus的遗传多样性和复杂性。系统发育分析表明，油菜与斑马的亲缘关系最密切，它偏离了1900万年前(Mya)。鸟疟原虫的分异时间早于蛇尾疟原虫和桔梗。类似于其他李属物种，P.conradinae在〜138.60Mya发生了常见的全基因组复制事件。此外，在P.conradinae中鉴定出79个MADS盒成员，伴随着短营养相亚家族的扩展。我们的发现揭示了复杂的遗传关系，并将促进与Cerasus亚属重要园艺和经济特征相关的关键基因的分子育种和功能的研究。
