Zhang Jing, Wang Yan, Chen Tao, Chen Qing, Wang Lei, Liu Zhen-Shan, Wang Hao, Xie Rui, He Wen, Li Ming, Liu Cong-Li, Yang Shao-Feng, Li Meng-Yao, Lin Yuan-Xiu, Zhang Yun-Ting, Zhang Yong, Luo Ya, Tang Hao-Ru, Gao Li-Zhi, Wang Xiao-Rong
College of Horticulture, Sichuan Agricultural University, Chengdu, China.
Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China.
Front Plant Sci. 2021 Nov 19;12:736053. doi: 10.3389/fpls.2021.736053. eCollection 2021.
Rosaceae comprises numerous types of economically important fruits, ornamentals, and timber. The lack of plastome characteristics has blocked our understanding of the evolution of plastome and plastid genes of Rosaceae crops. Using comparative genomics and phylogenomics, we analyzed 121 Rosaceae plastomes of 54 taxa from 13 genera, predominantly including (true cherry) and its relatives. To our knowledge, we generated the first comprehensive map of genomic variation across Rosaceae plastomes. Contraction/expansion of inverted repeat regions and sequence losses of the two single-copy regions underlie large genomic variations in size among Rosaceae plastomes. Plastid protein-coding genes were characterized with a high proportion (over 50%) of synonymous variants and insertion-deletions with multiple triplets. Five photosynthesis-related genes were specially selected in perennial woody trees. Comparative genomic analyses implied divergent evolutionary patterns between pomaceous and drupaceous trees. Across all examined plastomes, unique and divergent evolution was detected in plastomes. Phylogenomic analyses and molecular dating highlighted the relatively distant phylogenetic relationship between and relatives (, , , and ), which strongly supported treating the monophyletic true cherry group as a separate genus excluding dwarf cherry. High genetic differentiation and distinct phylogenetic relationships implied independent origins and domestication between fruiting cherries, particularly between () and (). Well-resolved maternal phylogeny suggested that cultivated originated from Longmenshan Fault zone, the eastern edge of Himalaya-Hengduan Mountains, where it was subjected to frequent genomic introgression between its presumed wild ancestors and relatives.
蔷薇科包含许多具有重要经济价值的水果、观赏植物和木材。缺乏质体基因组特征阻碍了我们对蔷薇科作物质体基因组和质体基因进化的理解。利用比较基因组学和系统发育基因组学，我们分析了来自13个属的54个分类群的121个蔷薇科质体基因组，主要包括（真樱桃）及其近缘种。据我们所知，我们生成了首张蔷薇科质体基因组全基因组变异图谱。反向重复区域的收缩/扩张以及两个单拷贝区域的序列丢失是蔷薇科质体基因组大小存在巨大基因组变异的基础。质体蛋白质编码基因的特征是同义变异和多个三联体插入缺失的比例很高（超过50%）。在多年生木本植物中特别选择了五个与光合作用相关的基因。比较基因组分析表明，梨果类和核果类树木之间存在不同的进化模式。在所有检测的质体基因组中，在质体基因组中检测到独特且不同的进化。系统发育基因组分析和分子定年突出了与近缘种（、、、和）之间相对较远的系统发育关系，这有力地支持将单系真樱桃组视为一个独立的属，不包括矮樱桃。高遗传分化和明显的系统发育关系意味着结果樱桃之间，特别是（）和（）之间的独立起源和驯化。解析良好的母系系统发育表明，栽培的起源于喜马拉雅-横断山脉东缘的龙门山断裂带，在那里它的假定野生祖先和近缘种之间频繁发生基因组渐渗。
