<i>De Novo</i> Hybrid Assembly of the <i>Salvia miltiorrhiza</i> Mitochondrial Genome Provides the First Evidence of the Multi-Chromosomal Mitochondrial DNA Structure of <i>Salvia</i> Species
<i>Salvia miltiorrhiza</i> has been an economically important medicinal plant. Previously, an <i>S. miltiorrhiza</i> mitochondrial genome (mitogenome) assembled from Illumina short reads, appearing to be a single circular molecule, has been published. Based on the recent repo...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-11-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/23/22/14267 |
| _version_ | 1797465059465625600 |
|---|---|
| author | Heyu Yang Haimei Chen Yang Ni Jingling Li Yisha Cai Binxin Ma Jing Yu Jiehua Wang Chang Liu |
| author_facet | Heyu Yang Haimei Chen Yang Ni Jingling Li Yisha Cai Binxin Ma Jing Yu Jiehua Wang Chang Liu |
| author_sort | Heyu Yang |
| collection | DOAJ |
| description | <i>Salvia miltiorrhiza</i> has been an economically important medicinal plant. Previously, an <i>S. miltiorrhiza</i> mitochondrial genome (mitogenome) assembled from Illumina short reads, appearing to be a single circular molecule, has been published. Based on the recent reports on the plant mitogenome structure, we suspected that this conformation does not accurately represent the complexity of the <i>S. miltiorrhiza</i> mitogenome. In the current study, we assembled the mitogenome of <i>S. miltiorrhiza</i> using the PacBio and Illumina sequencing technologies. The primary structure of the mitogenome contained two mitochondrial chromosomes (MC1 and MC2), which corresponded to two major conformations, namely, Mac1 and Mac2, respectively. Using two approaches, including (1) long reads mapping and (2) polymerase chain reaction amplification followed by Sanger sequencing, we observed nine repeats that can mediate recombination. We predicted 55 genes, including 33 mitochondrial protein-coding genes (PCGs), 3 rRNA genes, and 19 tRNA genes. Repeat analysis identified 112 microsatellite repeats and 3 long-tandem repeats. Phylogenetic analysis using the 26 shared PCGs resulted in a tree that was congruent with the phylogeny of Lamiales species in the APG IV system. The analysis of mitochondrial plastid DNA (MTPT) identified 16 MTPTs in the mitogenome. Moreover, the analysis of nucleotide substitution rates in Lamiales showed that the genes <i>atp4</i>, <i>ccmB</i>, <i>ccmFc</i>, and <i>mttB</i> might have been positively selected. The results lay the foundation for future studies on the evolution of the <i>Salvia</i> mitogenome and the molecular breeding of <i>S. miltiorrhiza</i>. |
| first_indexed | 2024-03-09T18:17:06Z |
| format | Article |
| id | doaj.art-d991e673b0b641ba90f101f80d9e7f5e |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T18:17:06Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-d991e673b0b641ba90f101f80d9e7f5e2023-11-24T08:41:26ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-11-0123221426710.3390/ijms232214267<i>De Novo</i> Hybrid Assembly of the <i>Salvia miltiorrhiza</i> Mitochondrial Genome Provides the First Evidence of the Multi-Chromosomal Mitochondrial DNA Structure of <i>Salvia</i> SpeciesHeyu Yang0Haimei Chen1Yang Ni2Jingling Li3Yisha Cai4Binxin Ma5Jing Yu6Jiehua Wang7Chang Liu8School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, ChinaInstitute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, ChinaInstitute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, ChinaInstitute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, ChinaInstitute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, ChinaInstitute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, ChinaInstitute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, ChinaSchool of Environmental Science and Engineering, Tianjin University, Tianjin 300072, ChinaInstitute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China<i>Salvia miltiorrhiza</i> has been an economically important medicinal plant. Previously, an <i>S. miltiorrhiza</i> mitochondrial genome (mitogenome) assembled from Illumina short reads, appearing to be a single circular molecule, has been published. Based on the recent reports on the plant mitogenome structure, we suspected that this conformation does not accurately represent the complexity of the <i>S. miltiorrhiza</i> mitogenome. In the current study, we assembled the mitogenome of <i>S. miltiorrhiza</i> using the PacBio and Illumina sequencing technologies. The primary structure of the mitogenome contained two mitochondrial chromosomes (MC1 and MC2), which corresponded to two major conformations, namely, Mac1 and Mac2, respectively. Using two approaches, including (1) long reads mapping and (2) polymerase chain reaction amplification followed by Sanger sequencing, we observed nine repeats that can mediate recombination. We predicted 55 genes, including 33 mitochondrial protein-coding genes (PCGs), 3 rRNA genes, and 19 tRNA genes. Repeat analysis identified 112 microsatellite repeats and 3 long-tandem repeats. Phylogenetic analysis using the 26 shared PCGs resulted in a tree that was congruent with the phylogeny of Lamiales species in the APG IV system. The analysis of mitochondrial plastid DNA (MTPT) identified 16 MTPTs in the mitogenome. Moreover, the analysis of nucleotide substitution rates in Lamiales showed that the genes <i>atp4</i>, <i>ccmB</i>, <i>ccmFc</i>, and <i>mttB</i> might have been positively selected. The results lay the foundation for future studies on the evolution of the <i>Salvia</i> mitogenome and the molecular breeding of <i>S. miltiorrhiza</i>.https://www.mdpi.com/1422-0067/23/22/14267<i>Salvia miltiorrhiza</i>lamialesmitogenomemulti-chromosomal structureMTPT |
| spellingShingle | Heyu Yang Haimei Chen Yang Ni Jingling Li Yisha Cai Binxin Ma Jing Yu Jiehua Wang Chang Liu <i>De Novo</i> Hybrid Assembly of the <i>Salvia miltiorrhiza</i> Mitochondrial Genome Provides the First Evidence of the Multi-Chromosomal Mitochondrial DNA Structure of <i>Salvia</i> Species International Journal of Molecular Sciences <i>Salvia miltiorrhiza</i> lamiales mitogenome multi-chromosomal structure MTPT |
| title | <i>De Novo</i> Hybrid Assembly of the <i>Salvia miltiorrhiza</i> Mitochondrial Genome Provides the First Evidence of the Multi-Chromosomal Mitochondrial DNA Structure of <i>Salvia</i> Species |
| title_full | <i>De Novo</i> Hybrid Assembly of the <i>Salvia miltiorrhiza</i> Mitochondrial Genome Provides the First Evidence of the Multi-Chromosomal Mitochondrial DNA Structure of <i>Salvia</i> Species |
| title_fullStr | <i>De Novo</i> Hybrid Assembly of the <i>Salvia miltiorrhiza</i> Mitochondrial Genome Provides the First Evidence of the Multi-Chromosomal Mitochondrial DNA Structure of <i>Salvia</i> Species |
| title_full_unstemmed | <i>De Novo</i> Hybrid Assembly of the <i>Salvia miltiorrhiza</i> Mitochondrial Genome Provides the First Evidence of the Multi-Chromosomal Mitochondrial DNA Structure of <i>Salvia</i> Species |
| title_short | <i>De Novo</i> Hybrid Assembly of the <i>Salvia miltiorrhiza</i> Mitochondrial Genome Provides the First Evidence of the Multi-Chromosomal Mitochondrial DNA Structure of <i>Salvia</i> Species |
| title_sort | i de novo i hybrid assembly of the i salvia miltiorrhiza i mitochondrial genome provides the first evidence of the multi chromosomal mitochondrial dna structure of i salvia i species |
| topic | <i>Salvia miltiorrhiza</i> lamiales mitogenome multi-chromosomal structure MTPT |
| url | https://www.mdpi.com/1422-0067/23/22/14267 |
| work_keys_str_mv | AT heyuyang idenovoihybridassemblyoftheisalviamiltiorrhizaimitochondrialgenomeprovidesthefirstevidenceofthemultichromosomalmitochondrialdnastructureofisalviaispecies AT haimeichen idenovoihybridassemblyoftheisalviamiltiorrhizaimitochondrialgenomeprovidesthefirstevidenceofthemultichromosomalmitochondrialdnastructureofisalviaispecies AT yangni idenovoihybridassemblyoftheisalviamiltiorrhizaimitochondrialgenomeprovidesthefirstevidenceofthemultichromosomalmitochondrialdnastructureofisalviaispecies AT jinglingli idenovoihybridassemblyoftheisalviamiltiorrhizaimitochondrialgenomeprovidesthefirstevidenceofthemultichromosomalmitochondrialdnastructureofisalviaispecies AT yishacai idenovoihybridassemblyoftheisalviamiltiorrhizaimitochondrialgenomeprovidesthefirstevidenceofthemultichromosomalmitochondrialdnastructureofisalviaispecies AT binxinma idenovoihybridassemblyoftheisalviamiltiorrhizaimitochondrialgenomeprovidesthefirstevidenceofthemultichromosomalmitochondrialdnastructureofisalviaispecies AT jingyu idenovoihybridassemblyoftheisalviamiltiorrhizaimitochondrialgenomeprovidesthefirstevidenceofthemultichromosomalmitochondrialdnastructureofisalviaispecies AT jiehuawang idenovoihybridassemblyoftheisalviamiltiorrhizaimitochondrialgenomeprovidesthefirstevidenceofthemultichromosomalmitochondrialdnastructureofisalviaispecies AT changliu idenovoihybridassemblyoftheisalviamiltiorrhizaimitochondrialgenomeprovidesthefirstevidenceofthemultichromosomalmitochondrialdnastructureofisalviaispecies |