Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry
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 pla...
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oai:doaj.org-article:efdfac681c7a4157ac544076ace4d4702021-11-19T05:08:20ZEvolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry1664-462X10.3389/fpls.2021.736053https://doaj.org/article/efdfac681c7a4157ac544076ace4d4702021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fpls.2021.736053/fullhttps://doaj.org/toc/1664-462XRosaceae 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 Cerasus (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 Cerasus plastomes. Phylogenomic analyses and molecular dating highlighted the relatively distant phylogenetic relationship between Cerasus and relatives (Microcerasus, Amygdalus, Prunus, and Armeniaca), 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 Prunus pseudocerasus (Cerasus pseudocerasus) and P. avium (C. avium). Well-resolved maternal phylogeny suggested that cultivated P. pseudocerasus 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.Jing ZhangJing ZhangYan WangYan WangTao ChenTao ChenQing ChenLei WangLei WangZhen-shan LiuZhen-shan LiuHao WangHao WangRui XieRui XieWen HeWen HeMing LiCong-li LiuShao-feng YangMeng-yao LiYuan-xiu LinYuan-xiu LinYun-ting ZhangYun-ting ZhangYong ZhangYa LuoHao-ru TangHao-ru TangLi-zhi GaoLi-zhi GaoXiao-rong WangXiao-rong WangFrontiers Media S.A.articleCerasusevolutionary patternfruiting cherrygenomic variationplastomesRosaceaePlant cultureSB1-1110ENFrontiers in Plant Science, Vol 12 (2021) |
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Cerasus evolutionary pattern fruiting cherry genomic variation plastomes Rosaceae Plant culture SB1-1110 |
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Cerasus evolutionary pattern fruiting cherry genomic variation plastomes Rosaceae Plant culture SB1-1110 Jing Zhang Jing Zhang Yan Wang Yan Wang Tao Chen Tao Chen Qing Chen Lei Wang Lei Wang Zhen-shan Liu Zhen-shan Liu Hao Wang Hao Wang Rui Xie Rui Xie Wen He Wen He Ming Li Cong-li Liu Shao-feng Yang Meng-yao Li Yuan-xiu Lin Yuan-xiu Lin Yun-ting Zhang Yun-ting Zhang Yong Zhang Ya Luo Hao-ru Tang Hao-ru Tang Li-zhi Gao Li-zhi Gao Xiao-rong Wang Xiao-rong Wang Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry |
description |
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 Cerasus (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 Cerasus plastomes. Phylogenomic analyses and molecular dating highlighted the relatively distant phylogenetic relationship between Cerasus and relatives (Microcerasus, Amygdalus, Prunus, and Armeniaca), 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 Prunus pseudocerasus (Cerasus pseudocerasus) and P. avium (C. avium). Well-resolved maternal phylogeny suggested that cultivated P. pseudocerasus 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. |
format |
article |
author |
Jing Zhang Jing Zhang Yan Wang Yan Wang Tao Chen Tao Chen Qing Chen Lei Wang Lei Wang Zhen-shan Liu Zhen-shan Liu Hao Wang Hao Wang Rui Xie Rui Xie Wen He Wen He Ming Li Cong-li Liu Shao-feng Yang Meng-yao Li Yuan-xiu Lin Yuan-xiu Lin Yun-ting Zhang Yun-ting Zhang Yong Zhang Ya Luo Hao-ru Tang Hao-ru Tang Li-zhi Gao Li-zhi Gao Xiao-rong Wang Xiao-rong Wang |
author_facet |
Jing Zhang Jing Zhang Yan Wang Yan Wang Tao Chen Tao Chen Qing Chen Lei Wang Lei Wang Zhen-shan Liu Zhen-shan Liu Hao Wang Hao Wang Rui Xie Rui Xie Wen He Wen He Ming Li Cong-li Liu Shao-feng Yang Meng-yao Li Yuan-xiu Lin Yuan-xiu Lin Yun-ting Zhang Yun-ting Zhang Yong Zhang Ya Luo Hao-ru Tang Hao-ru Tang Li-zhi Gao Li-zhi Gao Xiao-rong Wang Xiao-rong Wang |
author_sort |
Jing Zhang |
title |
Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry |
title_short |
Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry |
title_full |
Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry |
title_fullStr |
Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry |
title_full_unstemmed |
Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry |
title_sort |
evolution of rosaceae plastomes highlights unique cerasus diversification and independent origins of fruiting cherry |
publisher |
Frontiers Media S.A. |
publishDate |
2021 |
url |
https://doaj.org/article/efdfac681c7a4157ac544076ace4d470 |
work_keys_str_mv |
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