Comparative Analysis of the Complete Mitochondrial Genomes of <i>Apium graveolens</i> and <i>Apium leptophyllum</i> Provide Insights into Evolution and Phylogeny Relationships
The genus <i>Apium,</i> belonging to the family Apiaceae, comprises roughly 20 species. Only two species, <i>Apium graveolens</i> and <i>Apium leptophyllum,</i> are available in China and are both rich in nutrients and have favorable medicinal properties. However,...
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MDPI AG
2023-09-01
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| author | Xiaoyan Li Mengyao Li Weilong Li Jin Zhou Qiuju Han Wei Lu Qin Luo Shunhua Zhu Aisheng Xiong Guofei Tan Yangxia Zheng |
| author_facet | Xiaoyan Li Mengyao Li Weilong Li Jin Zhou Qiuju Han Wei Lu Qin Luo Shunhua Zhu Aisheng Xiong Guofei Tan Yangxia Zheng |
| author_sort | Xiaoyan Li |
| collection | DOAJ |
| description | The genus <i>Apium,</i> belonging to the family Apiaceae, comprises roughly 20 species. Only two species, <i>Apium graveolens</i> and <i>Apium leptophyllum,</i> are available in China and are both rich in nutrients and have favorable medicinal properties. However, the lack of genomic data has severely constrained the study of genetics and evolution in <i>Apium</i> plants. In this study, Illumina NovaSeq 6000 and Nanopore sequencing platforms were employed to identify the mitochondrial genomes of <i>A. graveolens</i> and <i>A. leptophyllum</i>. The complete lengths of the mitochondrial genomes of <i>A. graveolens</i> and <i>A. leptophyllum</i> were 263,017 bp and 260,164 bp, respectively, and contained 39 and 36 protein-coding genes, five and six rRNA genes, and 19 and 20 tRNA genes. Consistent with most angiosperms, both <i>A. graveolens</i> and <i>A. leptophyllum</i> showed a preference for codons encoding leucine (Leu). In the mitochondrial genome of <i>A. graveolens</i>, 335 SSRs were detected, which is higher than the 196 SSRs found in the mitochondrial genome of <i>A. leptophyllum</i>. Studies have shown that the most common RNA editing type is C-to-U, but, in our study, both <i>A. graveolens</i> and <i>A. leptophyllum</i> exhibited the U-C editing type. Furthermore, the transfer of the mitochondrial genomes of <i>A. graveolens</i> and <i>A. leptophyllum</i> into the chloroplast genomes revealed homologous sequences, accounting for 8.14% and 4.89% of the mitochondrial genome, respectively. Lastly, in comparing the mitochondrial genomes of 29 species, it was found that <i>A. graveolens</i>, <i>A. leptophyllum</i>, and <i>Daucus carota</i> form a sister group with a support rate of 100%. Overall, this investigation furnishes extensive insights into the mitochondrial genomes of <i>A. graveolens</i> and <i>A. leptophyllum</i>, thereby enhancing comprehension of the traits and evolutionary patterns within the <i>Apium</i> genus. Additionally, it offers supplementary data for evolutionary and comparative genomic analyses of other species within the Apiaceae family. |
| first_indexed | 2024-03-10T21:43:25Z |
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| language | English |
| last_indexed | 2024-03-10T21:43:25Z |
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| spelling | doaj.art-265fd489b0b7494c8ea1218b12da30d92023-11-19T14:29:18ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-09-0124191461510.3390/ijms241914615Comparative Analysis of the Complete Mitochondrial Genomes of <i>Apium graveolens</i> and <i>Apium leptophyllum</i> Provide Insights into Evolution and Phylogeny RelationshipsXiaoyan Li0Mengyao Li1Weilong Li2Jin Zhou3Qiuju Han4Wei Lu5Qin Luo6Shunhua Zhu7Aisheng Xiong8Guofei Tan9Yangxia Zheng10College of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaInstitute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, ChinaInstitute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, ChinaCollege of Horticulture, Nanjing Agricultural University, Nanjing 611130, ChinaInstitute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, ChinaCollege of Horticulture, Sichuan Agricultural University, Chengdu 611130, ChinaThe genus <i>Apium,</i> belonging to the family Apiaceae, comprises roughly 20 species. Only two species, <i>Apium graveolens</i> and <i>Apium leptophyllum,</i> are available in China and are both rich in nutrients and have favorable medicinal properties. However, the lack of genomic data has severely constrained the study of genetics and evolution in <i>Apium</i> plants. In this study, Illumina NovaSeq 6000 and Nanopore sequencing platforms were employed to identify the mitochondrial genomes of <i>A. graveolens</i> and <i>A. leptophyllum</i>. The complete lengths of the mitochondrial genomes of <i>A. graveolens</i> and <i>A. leptophyllum</i> were 263,017 bp and 260,164 bp, respectively, and contained 39 and 36 protein-coding genes, five and six rRNA genes, and 19 and 20 tRNA genes. Consistent with most angiosperms, both <i>A. graveolens</i> and <i>A. leptophyllum</i> showed a preference for codons encoding leucine (Leu). In the mitochondrial genome of <i>A. graveolens</i>, 335 SSRs were detected, which is higher than the 196 SSRs found in the mitochondrial genome of <i>A. leptophyllum</i>. Studies have shown that the most common RNA editing type is C-to-U, but, in our study, both <i>A. graveolens</i> and <i>A. leptophyllum</i> exhibited the U-C editing type. Furthermore, the transfer of the mitochondrial genomes of <i>A. graveolens</i> and <i>A. leptophyllum</i> into the chloroplast genomes revealed homologous sequences, accounting for 8.14% and 4.89% of the mitochondrial genome, respectively. Lastly, in comparing the mitochondrial genomes of 29 species, it was found that <i>A. graveolens</i>, <i>A. leptophyllum</i>, and <i>Daucus carota</i> form a sister group with a support rate of 100%. Overall, this investigation furnishes extensive insights into the mitochondrial genomes of <i>A. graveolens</i> and <i>A. leptophyllum</i>, thereby enhancing comprehension of the traits and evolutionary patterns within the <i>Apium</i> genus. Additionally, it offers supplementary data for evolutionary and comparative genomic analyses of other species within the Apiaceae family.https://www.mdpi.com/1422-0067/24/19/14615<i>Apium graveolens</i><i>Apium leptophyllum</i>mitochondrial genomeSSRsRNA editingphylogeny |
| spellingShingle | Xiaoyan Li Mengyao Li Weilong Li Jin Zhou Qiuju Han Wei Lu Qin Luo Shunhua Zhu Aisheng Xiong Guofei Tan Yangxia Zheng Comparative Analysis of the Complete Mitochondrial Genomes of <i>Apium graveolens</i> and <i>Apium leptophyllum</i> Provide Insights into Evolution and Phylogeny Relationships International Journal of Molecular Sciences <i>Apium graveolens</i> <i>Apium leptophyllum</i> mitochondrial genome SSRs RNA editing phylogeny |
| title | Comparative Analysis of the Complete Mitochondrial Genomes of <i>Apium graveolens</i> and <i>Apium leptophyllum</i> Provide Insights into Evolution and Phylogeny Relationships |
| title_full | Comparative Analysis of the Complete Mitochondrial Genomes of <i>Apium graveolens</i> and <i>Apium leptophyllum</i> Provide Insights into Evolution and Phylogeny Relationships |
| title_fullStr | Comparative Analysis of the Complete Mitochondrial Genomes of <i>Apium graveolens</i> and <i>Apium leptophyllum</i> Provide Insights into Evolution and Phylogeny Relationships |
| title_full_unstemmed | Comparative Analysis of the Complete Mitochondrial Genomes of <i>Apium graveolens</i> and <i>Apium leptophyllum</i> Provide Insights into Evolution and Phylogeny Relationships |
| title_short | Comparative Analysis of the Complete Mitochondrial Genomes of <i>Apium graveolens</i> and <i>Apium leptophyllum</i> Provide Insights into Evolution and Phylogeny Relationships |
| title_sort | comparative analysis of the complete mitochondrial genomes of i apium graveolens i and i apium leptophyllum i provide insights into evolution and phylogeny relationships |
| topic | <i>Apium graveolens</i> <i>Apium leptophyllum</i> mitochondrial genome SSRs RNA editing phylogeny |
| url | https://www.mdpi.com/1422-0067/24/19/14615 |
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