De novo assembly and comparative analysis of cherry (Prunus subgenus Cerasus) mitogenomes
Prunus subgenus Cerasus (Mill) A. Gray, commonly known as cherries and cherry blossoms, possesses significant edible and ornamental value. However, the mitochondrial genomes (mitogenomes) of cherry species remain largely unexplored. Here, we successfully assembled the mitogenomes of five cherry spec...
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Frontiers Media S.A.
2025-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1568698/full |
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| author | Tianya Zhai Tianya Zhai Zhuang Zhao Chenlong Fu Chenlong Fu Lizhen Huang Changci Jiang Meng Li Zefu Wang Xiaoyue Yang |
| author_facet | Tianya Zhai Tianya Zhai Zhuang Zhao Chenlong Fu Chenlong Fu Lizhen Huang Changci Jiang Meng Li Zefu Wang Xiaoyue Yang |
| author_sort | Tianya Zhai |
| collection | DOAJ |
| description | Prunus subgenus Cerasus (Mill) A. Gray, commonly known as cherries and cherry blossoms, possesses significant edible and ornamental value. However, the mitochondrial genomes (mitogenomes) of cherry species remain largely unexplored. Here, we successfully assembled the mitogenomes of five cherry species (P. campanulata, P. fruticosa, P. mahaleb, P. pseudocerasus, and P. speciosa), revealing common circular structures. The assembled mitogenomes exhibited sizes ranging from 383,398 bp to 447,498 bp, with GC content varying between 45.54% and 45.76%. A total of 62 to 69 genes were annotated, revealing variability in the copy number of protein-coding genes (PCGs) and tRNA genes. Mitogenome collinearity analysis indicated genomic rearrangements across Prunus species, driven by repetitive sequences, particularly dispersed repeats. Additionally, the five cherry species displayed highly conserved codon usage and RNA editing patterns, highlighting the evolutionary conservation of the mitochondrial PCGs. Phylogenetic analyses confirmed the monophyly of subg. Cerasus, although notable phylogenetic incongruences were observed between the mitochondrial and plastid datasets. These results provide significant genomic resources for forthcoming studies on the evolution and molecular breeding of cherry mitogenomes, enhancing the overall comprehension of mitogenome structure and evolution within Prunus. |
| format | Article |
| id | doaj-art-7c0d1445fe6d4b119bd360def1cbe391 |
| institution | DOAJ |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj-art-7c0d1445fe6d4b119bd360def1cbe3912025-08-20T03:15:06ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-03-011610.3389/fpls.2025.15686981568698De novo assembly and comparative analysis of cherry (Prunus subgenus Cerasus) mitogenomesTianya Zhai0Tianya Zhai1Zhuang Zhao2Chenlong Fu3Chenlong Fu4Lizhen Huang5Changci Jiang6Meng Li7Zefu Wang8Xiaoyue Yang9State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, ChinaState Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, ChinaCollege of Life Sciences, Nanjing Forestry University, Nanjing, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, ChinaCollege of Life Sciences, Nanjing Forestry University, Nanjing, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, ChinaPrunus subgenus Cerasus (Mill) A. Gray, commonly known as cherries and cherry blossoms, possesses significant edible and ornamental value. However, the mitochondrial genomes (mitogenomes) of cherry species remain largely unexplored. Here, we successfully assembled the mitogenomes of five cherry species (P. campanulata, P. fruticosa, P. mahaleb, P. pseudocerasus, and P. speciosa), revealing common circular structures. The assembled mitogenomes exhibited sizes ranging from 383,398 bp to 447,498 bp, with GC content varying between 45.54% and 45.76%. A total of 62 to 69 genes were annotated, revealing variability in the copy number of protein-coding genes (PCGs) and tRNA genes. Mitogenome collinearity analysis indicated genomic rearrangements across Prunus species, driven by repetitive sequences, particularly dispersed repeats. Additionally, the five cherry species displayed highly conserved codon usage and RNA editing patterns, highlighting the evolutionary conservation of the mitochondrial PCGs. Phylogenetic analyses confirmed the monophyly of subg. Cerasus, although notable phylogenetic incongruences were observed between the mitochondrial and plastid datasets. These results provide significant genomic resources for forthcoming studies on the evolution and molecular breeding of cherry mitogenomes, enhancing the overall comprehension of mitogenome structure and evolution within Prunus.https://www.frontiersin.org/articles/10.3389/fpls.2025.1568698/fullcherrymitochondrial genomecomparative analysisevolutionphylogenetic analysis |
| spellingShingle | Tianya Zhai Tianya Zhai Zhuang Zhao Chenlong Fu Chenlong Fu Lizhen Huang Changci Jiang Meng Li Zefu Wang Xiaoyue Yang De novo assembly and comparative analysis of cherry (Prunus subgenus Cerasus) mitogenomes Frontiers in Plant Science cherry mitochondrial genome comparative analysis evolution phylogenetic analysis |
| title | De novo assembly and comparative analysis of cherry (Prunus subgenus Cerasus) mitogenomes |
| title_full | De novo assembly and comparative analysis of cherry (Prunus subgenus Cerasus) mitogenomes |
| title_fullStr | De novo assembly and comparative analysis of cherry (Prunus subgenus Cerasus) mitogenomes |
| title_full_unstemmed | De novo assembly and comparative analysis of cherry (Prunus subgenus Cerasus) mitogenomes |
| title_short | De novo assembly and comparative analysis of cherry (Prunus subgenus Cerasus) mitogenomes |
| title_sort | de novo assembly and comparative analysis of cherry prunus subgenus cerasus mitogenomes |
| topic | cherry mitochondrial genome comparative analysis evolution phylogenetic analysis |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1568698/full |
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