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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...
Autores principales: | , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8639594/ https://www.ncbi.nlm.nih.gov/pubmed/34868119 http://dx.doi.org/10.3389/fpls.2021.736053 |
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author | 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 |
author_facet | 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 |
author_sort | Zhang, Jing |
collection | PubMed |
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 | Online Article Text |
id | pubmed-8639594 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-86395942021-12-04 Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry 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 Front Plant Sci Plant Science 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. Frontiers Media S.A. 2021-11-19 /pmc/articles/PMC8639594/ /pubmed/34868119 http://dx.doi.org/10.3389/fpls.2021.736053 Text en Copyright © 2021 Zhang, Wang, Chen, Chen, Wang, Liu, Wang, Xie, He, Li, Liu, Yang, Li, Lin, Zhang, Zhang, Luo, Tang, Gao and Wang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science 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 Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry |
title | 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_short | 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 |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8639594/ https://www.ncbi.nlm.nih.gov/pubmed/34868119 http://dx.doi.org/10.3389/fpls.2021.736053 |
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