<i>Cistanche</i> Species Mitogenomes Suggest Diversity and Complexity in <i>Lamiales</i>-Order Mitogenomes
The extreme diversity and complexity of angiosperms is well known. Despite the fact that parasitic plants are angiosperms, little is known about parasitic plant mitogenomic diversity, complexity, and evolution. In this study, we obtained and characterized the mitogenomes of three <i>Cistanche&...
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MDPI AG
2022-10-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/10/1791 |
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| author | Yujing Miao Haimei Chen Wanqi Xu Chang Liu Linfang Huang |
| author_facet | Yujing Miao Haimei Chen Wanqi Xu Chang Liu Linfang Huang |
| author_sort | Yujing Miao |
| collection | DOAJ |
| description | The extreme diversity and complexity of angiosperms is well known. Despite the fact that parasitic plants are angiosperms, little is known about parasitic plant mitogenomic diversity, complexity, and evolution. In this study, we obtained and characterized the mitogenomes of three <i>Cistanche</i> species (holoparasitic plants) from China to compare the repeats, segment duplication and multi-copy protein-coding genes (PCGs), to clarify the phylogenetic and evolution relationship within the <i>Lamiales</i> order, and to identify the mitochondrial plastid insertions (MTPT) in <i>Cistanche</i> mitogenomes. The results showed that the mitogenome sizes of the three <i>Cistanche</i> species ranged from 1,708,661 to 3,978,341 bp. The <i>Cistanche</i> species genome encodes 75–126 genes, including 37–65 PCGs, 31–58 tRNA genes and 3–5 rRNA genes. Compared with other <i>Lamiales</i> and parasitic species, the <i>Cistanche</i> species showed extremely high rates of multi-copy PCGs, ranging from 0.13 to 0.58 percent of the total number of PCGs. In addition, 37–133 Simple Sequence Repeat (SSRs) were found in these three mitogenomes, the majority of which were the mononucleotides Adenine/Thymine. The interspersed repeats contained forward and palindromic repeats. Furthermore, the segment-duplication sequence size ranged from 199,584 to 2,142,551 bp, accounting for 24.9%, 11.7% and 53.9% of the <i>Cistanche deserticola</i>, <i>Cistanche salsa</i> and <i>Cistanche tubulosa</i> mitogenome, respectively. Furthermore, the Ka/Ks analysis suggested that the <i>atp</i>4, <i>ccmB</i>, <i>ccmFc</i> and <i>matR</i> were probably positively selected during <i>Lamiales</i> evolution. The <i>Cistanche</i> plastome suggested the presence of MTPT. Moreover, 6–12 tRNA, 9–15 PCGs fragments and 3 rRNA gene fragments in the <i>Cistanche</i> mitogenomes were found in the MTPT regions. This work reports the <i>Cistanche</i> species mitogenome for the first time, which will be invaluable for study the mitogenome evolution of <i>Orobanchaceae</i> family. |
| first_indexed | 2024-03-09T20:10:40Z |
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| id | doaj.art-680803c2292f4f17a890a691cd28dc69 |
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| last_indexed | 2024-03-09T20:10:40Z |
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| spelling | doaj.art-680803c2292f4f17a890a691cd28dc692023-11-24T00:15:34ZengMDPI AGGenes2073-44252022-10-011310179110.3390/genes13101791<i>Cistanche</i> Species Mitogenomes Suggest Diversity and Complexity in <i>Lamiales</i>-Order MitogenomesYujing Miao0Haimei Chen1Wanqi Xu2Chang Liu3Linfang Huang4Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaKey Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaKey Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaKey Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaKey Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, ChinaThe extreme diversity and complexity of angiosperms is well known. Despite the fact that parasitic plants are angiosperms, little is known about parasitic plant mitogenomic diversity, complexity, and evolution. In this study, we obtained and characterized the mitogenomes of three <i>Cistanche</i> species (holoparasitic plants) from China to compare the repeats, segment duplication and multi-copy protein-coding genes (PCGs), to clarify the phylogenetic and evolution relationship within the <i>Lamiales</i> order, and to identify the mitochondrial plastid insertions (MTPT) in <i>Cistanche</i> mitogenomes. The results showed that the mitogenome sizes of the three <i>Cistanche</i> species ranged from 1,708,661 to 3,978,341 bp. The <i>Cistanche</i> species genome encodes 75–126 genes, including 37–65 PCGs, 31–58 tRNA genes and 3–5 rRNA genes. Compared with other <i>Lamiales</i> and parasitic species, the <i>Cistanche</i> species showed extremely high rates of multi-copy PCGs, ranging from 0.13 to 0.58 percent of the total number of PCGs. In addition, 37–133 Simple Sequence Repeat (SSRs) were found in these three mitogenomes, the majority of which were the mononucleotides Adenine/Thymine. The interspersed repeats contained forward and palindromic repeats. Furthermore, the segment-duplication sequence size ranged from 199,584 to 2,142,551 bp, accounting for 24.9%, 11.7% and 53.9% of the <i>Cistanche deserticola</i>, <i>Cistanche salsa</i> and <i>Cistanche tubulosa</i> mitogenome, respectively. Furthermore, the Ka/Ks analysis suggested that the <i>atp</i>4, <i>ccmB</i>, <i>ccmFc</i> and <i>matR</i> were probably positively selected during <i>Lamiales</i> evolution. The <i>Cistanche</i> plastome suggested the presence of MTPT. Moreover, 6–12 tRNA, 9–15 PCGs fragments and 3 rRNA gene fragments in the <i>Cistanche</i> mitogenomes were found in the MTPT regions. This work reports the <i>Cistanche</i> species mitogenome for the first time, which will be invaluable for study the mitogenome evolution of <i>Orobanchaceae</i> family.https://www.mdpi.com/2073-4425/13/10/1791<i>Cistanche</i>mitogenomeMTPTrepeatsegment duplicationmulti-copy PCGs |
| spellingShingle | Yujing Miao Haimei Chen Wanqi Xu Chang Liu Linfang Huang <i>Cistanche</i> Species Mitogenomes Suggest Diversity and Complexity in <i>Lamiales</i>-Order Mitogenomes Genes <i>Cistanche</i> mitogenome MTPT repeat segment duplication multi-copy PCGs |
| title | <i>Cistanche</i> Species Mitogenomes Suggest Diversity and Complexity in <i>Lamiales</i>-Order Mitogenomes |
| title_full | <i>Cistanche</i> Species Mitogenomes Suggest Diversity and Complexity in <i>Lamiales</i>-Order Mitogenomes |
| title_fullStr | <i>Cistanche</i> Species Mitogenomes Suggest Diversity and Complexity in <i>Lamiales</i>-Order Mitogenomes |
| title_full_unstemmed | <i>Cistanche</i> Species Mitogenomes Suggest Diversity and Complexity in <i>Lamiales</i>-Order Mitogenomes |
| title_short | <i>Cistanche</i> Species Mitogenomes Suggest Diversity and Complexity in <i>Lamiales</i>-Order Mitogenomes |
| title_sort | i cistanche i species mitogenomes suggest diversity and complexity in i lamiales i order mitogenomes |
| topic | <i>Cistanche</i> mitogenome MTPT repeat segment duplication multi-copy PCGs |
| url | https://www.mdpi.com/2073-4425/13/10/1791 |
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