Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer
Abstract The increasing number of plant mitochondrial DNA genomes (mtDNA) sequenced reveals the extent of transfer from both chloroplast DNA genomes (cpDNA) and nuclear DNA genomes (nDNA). This study created a library and assembled the chloroplast and mitochondrial genomes of the leafy sweet potato...
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Nature Portfolio
2024-02-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-024-55150-1 |
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| author | GuoLiang Li Hong Zhang Zhaomiao Lin Huawei Li Guochun Xu Yongqing Xu Rongchang Ji Wenbin Luo Yongxiang Qiu Sixin Qiu Hao Tang |
| author_facet | GuoLiang Li Hong Zhang Zhaomiao Lin Huawei Li Guochun Xu Yongqing Xu Rongchang Ji Wenbin Luo Yongxiang Qiu Sixin Qiu Hao Tang |
| author_sort | GuoLiang Li |
| collection | DOAJ |
| description | Abstract The increasing number of plant mitochondrial DNA genomes (mtDNA) sequenced reveals the extent of transfer from both chloroplast DNA genomes (cpDNA) and nuclear DNA genomes (nDNA). This study created a library and assembled the chloroplast and mitochondrial genomes of the leafy sweet potato better to understand the extent of mitochondrial and chloroplast gene transfer. The full-length chloroplast genome of the leafy sweet potato (OM808940) is 161,387 bp, with 132 genes annotated, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The mitochondrial genome (OM808941) was 269,578 bp in length and contained 69 functional genes, including 39 protein-coding genes, 6 rRNA genes, and 24 tRNA genes. 68 SSR loci were found in the leafy sweet potato organelle genome, including 54 in the chloroplast genome and 14 in the mitochondria genome. In the sweet potato mitochondrial genome, most genes have RNA editing sites, and the conversion ratio from hydrophilic amino acids to hydrophobic amino acids is the highest, reaching 47.12%. Horizontal transfer occurs in the sweet potato organelle genome and nuclear genome. 40 mitochondrial genome segments share high homology with 14 chloroplast genome segments, 33 of which may be derived from chloroplast genome horizontal transfer. 171 mitochondrial genome sequences come from the horizontal transfer of nuclear genome. The phylogenetic analysis of organelle genes revealed that the leafy sweet potato was closely related to the tetraploid wild species Ipomoea tabascana and the wild diploid species Ipomoea trifida. |
| first_indexed | 2024-03-07T15:07:45Z |
| format | Article |
| id | doaj.art-f9d351674c5d4983b4d50c57a11688e1 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-07T15:07:45Z |
| publishDate | 2024-02-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj.art-f9d351674c5d4983b4d50c57a11688e12024-03-05T18:51:28ZengNature PortfolioScientific Reports2045-23222024-02-0114111110.1038/s41598-024-55150-1Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transferGuoLiang Li0Hong Zhang1Zhaomiao Lin2Huawei Li3Guochun Xu4Yongqing Xu5Rongchang Ji6Wenbin Luo7Yongxiang Qiu8Sixin Qiu9Hao Tang10Institute of Crop Sciences, Fujian Academy of Agricultural SciencesInstitute of Crop Sciences, Fujian Academy of Agricultural SciencesInstitute of Crop Sciences, Fujian Academy of Agricultural SciencesInstitute of Crop Sciences, Fujian Academy of Agricultural SciencesInstitute of Crop Sciences, Fujian Academy of Agricultural SciencesInstitute of Crop Sciences, Fujian Academy of Agricultural SciencesInstitute of Crop Sciences, Fujian Academy of Agricultural SciencesInstitute of Crop Sciences, Fujian Academy of Agricultural SciencesInstitute of Crop Sciences, Fujian Academy of Agricultural SciencesInstitute of Crop Sciences, Fujian Academy of Agricultural SciencesInstitute of Crop Sciences, Fujian Academy of Agricultural SciencesAbstract The increasing number of plant mitochondrial DNA genomes (mtDNA) sequenced reveals the extent of transfer from both chloroplast DNA genomes (cpDNA) and nuclear DNA genomes (nDNA). This study created a library and assembled the chloroplast and mitochondrial genomes of the leafy sweet potato better to understand the extent of mitochondrial and chloroplast gene transfer. The full-length chloroplast genome of the leafy sweet potato (OM808940) is 161,387 bp, with 132 genes annotated, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The mitochondrial genome (OM808941) was 269,578 bp in length and contained 69 functional genes, including 39 protein-coding genes, 6 rRNA genes, and 24 tRNA genes. 68 SSR loci were found in the leafy sweet potato organelle genome, including 54 in the chloroplast genome and 14 in the mitochondria genome. In the sweet potato mitochondrial genome, most genes have RNA editing sites, and the conversion ratio from hydrophilic amino acids to hydrophobic amino acids is the highest, reaching 47.12%. Horizontal transfer occurs in the sweet potato organelle genome and nuclear genome. 40 mitochondrial genome segments share high homology with 14 chloroplast genome segments, 33 of which may be derived from chloroplast genome horizontal transfer. 171 mitochondrial genome sequences come from the horizontal transfer of nuclear genome. The phylogenetic analysis of organelle genes revealed that the leafy sweet potato was closely related to the tetraploid wild species Ipomoea tabascana and the wild diploid species Ipomoea trifida.https://doi.org/10.1038/s41598-024-55150-1 |
| spellingShingle | GuoLiang Li Hong Zhang Zhaomiao Lin Huawei Li Guochun Xu Yongqing Xu Rongchang Ji Wenbin Luo Yongxiang Qiu Sixin Qiu Hao Tang Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer Scientific Reports |
| title | Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer |
| title_full | Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer |
| title_fullStr | Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer |
| title_full_unstemmed | Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer |
| title_short | Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer |
| title_sort | comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer |
| url | https://doi.org/10.1038/s41598-024-55150-1 |
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