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Evolution of Cherries (Prunus Subgenus Cerasus) Based on Chloroplast Genomes

Cherries (Prunus Subgenus Cerasus) have economic value and ecological significance, yet their phylogeny, geographic origin, timing, and dispersal patterns remain challenging to understand. To fill this gap, we conducted a comprehensive analysis of the complete chloroplast genomes of 54 subg. Cerasus...

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Autores principales: Shen, Xin, Zong, Wenjin, Li, Yingang, Liu, Xinhong, Zhuge, Fei, Zhou, Qi, Zhou, Shiliang, Jiang, Dongyue
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10650623/
https://www.ncbi.nlm.nih.gov/pubmed/37958595
http://dx.doi.org/10.3390/ijms242115612
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author Shen, Xin
Zong, Wenjin
Li, Yingang
Liu, Xinhong
Zhuge, Fei
Zhou, Qi
Zhou, Shiliang
Jiang, Dongyue
author_facet Shen, Xin
Zong, Wenjin
Li, Yingang
Liu, Xinhong
Zhuge, Fei
Zhou, Qi
Zhou, Shiliang
Jiang, Dongyue
author_sort Shen, Xin
collection PubMed
description Cherries (Prunus Subgenus Cerasus) have economic value and ecological significance, yet their phylogeny, geographic origin, timing, and dispersal patterns remain challenging to understand. To fill this gap, we conducted a comprehensive analysis of the complete chloroplast genomes of 54 subg. Cerasus individuals, along with 36 additional genomes from the NCBI database, resulting in a total of 90 genomes for comparative analysis. The chloroplast genomes of subg. Cerasus exhibited varying sizes and consisted of 129 genes, including protein-coding, transfer RNA, and ribosomIal RNA genes. Genomic variation was investigated through InDels and SNPs, showcasing distribution patterns and impact levels. A comparative analysis of chloroplast genome boundaries highlighted variations in inverted repeat (IR) regions among Cerasus and other Prunus species. Phylogeny based on whole-chloroplast genome sequences supported the division of Prunus into three subgenera, I subg. Padus, II subg. Prunus and III subg. Cerasus. The subg. Cerasus was subdivided into seven lineages (IIIa to IIIg), which matched roughly to taxonomic sections. The subg. Padus first diverged 51.42 Mya, followed by the separation of subg. Cerasus from subg. Prunus 39.27 Mya. The subg. Cerasus started diversification at 15.01 Mya, coinciding with geological and climatic changes, including the uplift of the Qinghai–Tibet Plateau and global cooling. The Himalayans were the refuge of cherries, from which a few species reached Europe through westward migration and another species reached North America through northeastward migration. The mainstage of cherry evolution was on the Qing–Tibet Plateau and later East China and Japan as well. These findings strengthen our understanding of the evolution of cherry and provide valuable insights into the conservation and sustainable utilization of cherry’s genetic resources.
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spelling pubmed-106506232023-10-26 Evolution of Cherries (Prunus Subgenus Cerasus) Based on Chloroplast Genomes Shen, Xin Zong, Wenjin Li, Yingang Liu, Xinhong Zhuge, Fei Zhou, Qi Zhou, Shiliang Jiang, Dongyue Int J Mol Sci Article Cherries (Prunus Subgenus Cerasus) have economic value and ecological significance, yet their phylogeny, geographic origin, timing, and dispersal patterns remain challenging to understand. To fill this gap, we conducted a comprehensive analysis of the complete chloroplast genomes of 54 subg. Cerasus individuals, along with 36 additional genomes from the NCBI database, resulting in a total of 90 genomes for comparative analysis. The chloroplast genomes of subg. Cerasus exhibited varying sizes and consisted of 129 genes, including protein-coding, transfer RNA, and ribosomIal RNA genes. Genomic variation was investigated through InDels and SNPs, showcasing distribution patterns and impact levels. A comparative analysis of chloroplast genome boundaries highlighted variations in inverted repeat (IR) regions among Cerasus and other Prunus species. Phylogeny based on whole-chloroplast genome sequences supported the division of Prunus into three subgenera, I subg. Padus, II subg. Prunus and III subg. Cerasus. The subg. Cerasus was subdivided into seven lineages (IIIa to IIIg), which matched roughly to taxonomic sections. The subg. Padus first diverged 51.42 Mya, followed by the separation of subg. Cerasus from subg. Prunus 39.27 Mya. The subg. Cerasus started diversification at 15.01 Mya, coinciding with geological and climatic changes, including the uplift of the Qinghai–Tibet Plateau and global cooling. The Himalayans were the refuge of cherries, from which a few species reached Europe through westward migration and another species reached North America through northeastward migration. The mainstage of cherry evolution was on the Qing–Tibet Plateau and later East China and Japan as well. These findings strengthen our understanding of the evolution of cherry and provide valuable insights into the conservation and sustainable utilization of cherry’s genetic resources. MDPI 2023-10-26 /pmc/articles/PMC10650623/ /pubmed/37958595 http://dx.doi.org/10.3390/ijms242115612 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Shen, Xin
Zong, Wenjin
Li, Yingang
Liu, Xinhong
Zhuge, Fei
Zhou, Qi
Zhou, Shiliang
Jiang, Dongyue
Evolution of Cherries (Prunus Subgenus Cerasus) Based on Chloroplast Genomes
title Evolution of Cherries (Prunus Subgenus Cerasus) Based on Chloroplast Genomes
title_full Evolution of Cherries (Prunus Subgenus Cerasus) Based on Chloroplast Genomes
title_fullStr Evolution of Cherries (Prunus Subgenus Cerasus) Based on Chloroplast Genomes
title_full_unstemmed Evolution of Cherries (Prunus Subgenus Cerasus) Based on Chloroplast Genomes
title_short Evolution of Cherries (Prunus Subgenus Cerasus) Based on Chloroplast Genomes
title_sort evolution of cherries (prunus subgenus cerasus) based on chloroplast genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10650623/
https://www.ncbi.nlm.nih.gov/pubmed/37958595
http://dx.doi.org/10.3390/ijms242115612
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