Assembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transfer
Abstract Background Red raspberry (Rubus idaeus L.) is a renowned fruit plant with significant medicinal value. Its nuclear genome and chloroplast genome (plastome) have been reported, while there is a lack of genetic information on its mitogenome. We sequenced and assembled the complete mitogenome...
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2025-01-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-024-05969-7 |
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| author | Huajie Zhang Minghui Yan Lijuan Li Zhuo Jiang Ye Xiong Yusheng Wang Caleb Onoja Akogwu Olutayo Mary Tolulope Hao Zhou Yanxia Sun Hengchang Wang |
| author_facet | Huajie Zhang Minghui Yan Lijuan Li Zhuo Jiang Ye Xiong Yusheng Wang Caleb Onoja Akogwu Olutayo Mary Tolulope Hao Zhou Yanxia Sun Hengchang Wang |
| author_sort | Huajie Zhang |
| collection | DOAJ |
| description | Abstract Background Red raspberry (Rubus idaeus L.) is a renowned fruit plant with significant medicinal value. Its nuclear genome and chloroplast genome (plastome) have been reported, while there is a lack of genetic information on its mitogenome. We sequenced and assembled the complete mitogenome of R. idaeus, and conducted a series of genetic investigations comparing it with the nuclear and chloroplast genomes, so as to better gain a comprehensive understanding of the species’ genetic background. Results The mitogenome is represented by one circular chromosome of 438,947 bp. Twenty-four core genes, nine variable genes, 26 tRNAs, and three rRNAs were annotated. A total of 52 SSRs and 38 tandem repeat sequences were identified. 533 pairs of dispersed repeats were detected, among which three pairs were found to have mediated the homologous recombination, resulting in one major conformation and seven minor conformations. Furthermore, 52 homologous sequences between the mitogenome and plastome were identified, including six complete protein-coding genes and 12 tRNA genes. We also detected 828 homologous fragments between the nuclear genome and mitogenome, including one trnM-CAU gene. Conclusions In this study, we presented the mitogenome of R. idaeus for the first time based on data obtained from Illumina and Oxford Nanopore sequencing platforms. Key characteristics of the mitogenome were examined, including its gene composition, repetitive elements, and homologous DNA fragments. Additionally, we identified multiple recombination events in the mitogenome mediated by repetitive sequences The high-quality and well-annotated mitogenome for the known fruit red raspberry will provide essential genetic information for species classification, evolution analysis, and even genetic improvement in Rubus in the future. |
| format | Article |
| id | doaj-art-7422b852c42540ee90d84532bc4056a3 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-7422b852c42540ee90d84532bc4056a32025-01-26T12:23:23ZengBMCBMC Plant Biology1471-22292025-01-0125111210.1186/s12870-024-05969-7Assembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transferHuajie Zhang0Minghui Yan1Lijuan Li2Zhuo Jiang3Ye Xiong4Yusheng Wang5Caleb Onoja Akogwu6Olutayo Mary Tolulope7Hao Zhou8Yanxia Sun9Hengchang Wang10CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, WuhanDabie Mountain Laboratory, College of Tea and Food Science, Xinyang Normal University, XinyangCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, WuhanCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, WuhanCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, WuhanSchool of Horticulture and Gardening, Yangtze University, JingzhouCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, WuhanCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, WuhanKey Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and TechnologyCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, WuhanCAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, WuhanAbstract Background Red raspberry (Rubus idaeus L.) is a renowned fruit plant with significant medicinal value. Its nuclear genome and chloroplast genome (plastome) have been reported, while there is a lack of genetic information on its mitogenome. We sequenced and assembled the complete mitogenome of R. idaeus, and conducted a series of genetic investigations comparing it with the nuclear and chloroplast genomes, so as to better gain a comprehensive understanding of the species’ genetic background. Results The mitogenome is represented by one circular chromosome of 438,947 bp. Twenty-four core genes, nine variable genes, 26 tRNAs, and three rRNAs were annotated. A total of 52 SSRs and 38 tandem repeat sequences were identified. 533 pairs of dispersed repeats were detected, among which three pairs were found to have mediated the homologous recombination, resulting in one major conformation and seven minor conformations. Furthermore, 52 homologous sequences between the mitogenome and plastome were identified, including six complete protein-coding genes and 12 tRNA genes. We also detected 828 homologous fragments between the nuclear genome and mitogenome, including one trnM-CAU gene. Conclusions In this study, we presented the mitogenome of R. idaeus for the first time based on data obtained from Illumina and Oxford Nanopore sequencing platforms. Key characteristics of the mitogenome were examined, including its gene composition, repetitive elements, and homologous DNA fragments. Additionally, we identified multiple recombination events in the mitogenome mediated by repetitive sequences The high-quality and well-annotated mitogenome for the known fruit red raspberry will provide essential genetic information for species classification, evolution analysis, and even genetic improvement in Rubus in the future.https://doi.org/10.1186/s12870-024-05969-7De-novo assemblyMitogenomePhylogenetic analysisRecombinationSequence collinearity |
| spellingShingle | Huajie Zhang Minghui Yan Lijuan Li Zhuo Jiang Ye Xiong Yusheng Wang Caleb Onoja Akogwu Olutayo Mary Tolulope Hao Zhou Yanxia Sun Hengchang Wang Assembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transfer BMC Plant Biology De-novo assembly Mitogenome Phylogenetic analysis Recombination Sequence collinearity |
| title | Assembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transfer |
| title_full | Assembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transfer |
| title_fullStr | Assembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transfer |
| title_full_unstemmed | Assembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transfer |
| title_short | Assembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transfer |
| title_sort | assembly and comparative analysis of the complete mitochondrial genome of red raspberry rubus idaeus l revealing repeat mediated recombination and gene transfer |
| topic | De-novo assembly Mitogenome Phylogenetic analysis Recombination Sequence collinearity |
| url | https://doi.org/10.1186/s12870-024-05969-7 |
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