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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Autores principales: Jing Zhang, Yan Wang, Tao Chen, Qing Chen, Lei Wang, Zhen-shan Liu, Hao Wang, Rui Xie, Wen He, Ming Li, Cong-li Liu, Shao-feng Yang, Meng-yao Li, Yuan-xiu Lin, Yun-ting Zhang, Yong Zhang, Ya Luo, Hao-ru Tang, Li-zhi Gao, Xiao-rong Wang
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Publicado: Frontiers Media S.A. 2021
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spelling 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)
institution DOAJ
collection DOAJ
language EN
topic Cerasus
evolutionary pattern
fruiting cherry
genomic variation
plastomes
Rosaceae
Plant culture
SB1-1110
spellingShingle 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
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