Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomes
Abstract Background Gene transfer between the organelles and the nucleus plays a central role in shaping plant genome evolution. The identification and analysis of nuclear DNA of plastid (NUPTs) and mitochondrial (NUMTs) origins are important for exploring the extent of intracellular DNA transfer in...
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2025-02-01
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| Online Access: | https://doi.org/10.1186/s12864-025-11230-8 |
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| author | Seongjun Park Yong Hwang Heesoo Kim KyoungSu Choi |
| author_facet | Seongjun Park Yong Hwang Heesoo Kim KyoungSu Choi |
| author_sort | Seongjun Park |
| collection | DOAJ |
| description | Abstract Background Gene transfer between the organelles and the nucleus plays a central role in shaping plant genome evolution. The identification and analysis of nuclear DNA of plastid (NUPTs) and mitochondrial (NUMTs) origins are important for exploring the extent of intracellular DNA transfer in genomes. Results We report the complete plastid and mitochondrial genomes (plastome and mitogenome) of Cicuta virosa (Apiaceae) as well as a draft nuclear genome using high-fidelity (HiFi) PacBio sequencing technologies. The C. virosa plastome (154,449 bp) is highly conserved, with a quadripartite structure, whereas the mitogenome (406,112 bp) exhibits two chromosomes (352,718 bp and 53,394 bp). The mitochondrial-encoded genes (rpl2, rps14, rps19, and sdh3) were successfully transferred to the nuclear genome. Our findings revealed extensive DNA transfer from organelles to the nucleus, with 6,686 NUPTs and 6,237 NUMTs detected, covering nearly the entire plastome (99.93%) and a substantial portion of the mitogenome (77.04%). These transfers exhibit a range of sequence identities (80–100%), suggesting multiple transfer events over evolutionary timescales. Recent DNA transfer between organelles and the nucleus is more frequent in mitochondria than that in plastids. Conclusions This study contributes to the understanding of ongoing genome evolution in C. virosa and underscores the significance of the organelle-nuclear genome interplay in plant species. Our findings provide valuable insights into the evolutionary processes that shape organelle genomes in Apiaceae, with implications for broader plant genome evolution. |
| format | Article |
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| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-02-01 |
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| series | BMC Genomics |
| spelling | doaj-art-2dd6ce33c21a4731a507911ba800c58d2025-02-09T12:13:54ZengBMCBMC Genomics1471-21642025-02-0126111210.1186/s12864-025-11230-8Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomesSeongjun Park0Yong Hwang1Heesoo Kim2KyoungSu Choi3Institute of Natural Science, Yeungnam UniversityBiological Specimen Conservation Division, Diversity Conservation Research Department, Nakdonggang National Institute of Biological ResourcesDivesity Forecast & Evaluation Division, Diversity Conservation Research Department, Nakdonggang National Institute of Biological ResourcesDepartment of Biology, College of Natural Science, Kyungpook National UniversityAbstract Background Gene transfer between the organelles and the nucleus plays a central role in shaping plant genome evolution. The identification and analysis of nuclear DNA of plastid (NUPTs) and mitochondrial (NUMTs) origins are important for exploring the extent of intracellular DNA transfer in genomes. Results We report the complete plastid and mitochondrial genomes (plastome and mitogenome) of Cicuta virosa (Apiaceae) as well as a draft nuclear genome using high-fidelity (HiFi) PacBio sequencing technologies. The C. virosa plastome (154,449 bp) is highly conserved, with a quadripartite structure, whereas the mitogenome (406,112 bp) exhibits two chromosomes (352,718 bp and 53,394 bp). The mitochondrial-encoded genes (rpl2, rps14, rps19, and sdh3) were successfully transferred to the nuclear genome. Our findings revealed extensive DNA transfer from organelles to the nucleus, with 6,686 NUPTs and 6,237 NUMTs detected, covering nearly the entire plastome (99.93%) and a substantial portion of the mitogenome (77.04%). These transfers exhibit a range of sequence identities (80–100%), suggesting multiple transfer events over evolutionary timescales. Recent DNA transfer between organelles and the nucleus is more frequent in mitochondria than that in plastids. Conclusions This study contributes to the understanding of ongoing genome evolution in C. virosa and underscores the significance of the organelle-nuclear genome interplay in plant species. Our findings provide valuable insights into the evolutionary processes that shape organelle genomes in Apiaceae, with implications for broader plant genome evolution.https://doi.org/10.1186/s12864-025-11230-8Nuclear DNAs of plastid and mitochondrial originIntracellular DNA transfer |
| spellingShingle | Seongjun Park Yong Hwang Heesoo Kim KyoungSu Choi Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomes BMC Genomics Nuclear DNAs of plastid and mitochondrial origin Intracellular DNA transfer |
| title | Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomes |
| title_full | Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomes |
| title_fullStr | Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomes |
| title_full_unstemmed | Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomes |
| title_short | Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomes |
| title_sort | insights into the nuclear organelle dna integration in cicuta virosa apiaceae provided by complete plastid and mitochondrial genomes |
| topic | Nuclear DNAs of plastid and mitochondrial origin Intracellular DNA transfer |
| url | https://doi.org/10.1186/s12864-025-11230-8 |
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