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ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Systematics and Evolution
Volume 15 - 2024 |
doi: 10.3389/fpls.2024.1404071
This article is part of the Research Topic Rise to the Challenges in Plastome Phylogenomics, Volume II View all articles
The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history
Provisionally accepted- 1 College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi Province, China
- 2 Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- 3 College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
- 4 College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
- 5 Department of Agricultural Biology, College of Agricultural Sciences, Colorado State University, Fort Collins, Colorado, United States
Prunus mume in the Rosaceae and commonly referred to as mei or Chinese plum is widely used as a traditional ornamental flowering plant and fruit tree in China. Although some population and genetic analyses have been conducted for this species, no extensive comparisons of genetic variation from plastomes have yet been investigated. Here, we de novo assembled the plastomes of 322 P. mume accessions and constructed a pan-plastome level resource of population structure and genetic diversity. The assembled plastomes exhibited a typical quadripartite structure and ranged from 157,871 bp to 158,213 bp in total size with a GC content ranging from 36.73 to 36.75%. A total of 112 unique genes were identified. Single nucleotide variants (SNVs) were the most common variants found among the plastomes, followed by nucleotide insertions/deletions (InDels), and block substitutions with the intergenic spacer (IGS) regions containing the greatest number of variants. From the pan-plastome data six well-supported genetic clusters were resolved using multiple different population structure analyses. The different cultivars were unevenly distributed among multiple clades. We also reconstructed a phylogeny for multiple species of Prunus to better understand genus level diversity and history from which a complex introgressive relationship between mei and other apricots/plums was resolved. This pattern indicates that the domestication of P. mume involved multiple genetic origins and possible matrilineal introgression from other species. These results provide an important maternal history for Prunus and lay groundwork for future studies on intergenomic sequence transfers, cytonuclear incompatibility, and conservation genetics.
Keywords: Pan-plastome, phylogeny, population structure, Prunus, P. mume
Received: 20 Mar 2024; Accepted: 29 Apr 2024.
Copyright: © 2024 Wang, Kan, Wang, Yan, Li, Soe, Tembrock, Xing, Wu, Li and Jia. 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) or licensor 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.
* Correspondence:
Jie Wang, College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi Province, China
Junhu Kan, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
Jie Wang, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, 6150, Western Australia, Australia
Xinlin Yan, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, China
Yi Li, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
Thida Soe, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
Guoming Xing, College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi Province, China
Minlong Jia, College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi Province, China
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