Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome.
Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chlor...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0289625&type=printable |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849393765899304960 |
|---|---|
| author | Sang-Chul Kim Young-Ho Ha Beom Kyun Park Ju Eun Jang Eun Su Kang Young-Soo Kim Tae-Hee Kimspe Hyuk-Jin Kim |
| author_facet | Sang-Chul Kim Young-Ho Ha Beom Kyun Park Ju Eun Jang Eun Su Kang Young-Soo Kim Tae-Hee Kimspe Hyuk-Jin Kim |
| author_sort | Sang-Chul Kim |
| collection | DOAJ |
| description | Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis. Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers. |
| format | Article |
| id | doaj-art-8f942dfe67a144e09a3b591a903202cc |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-8f942dfe67a144e09a3b591a903202cc2025-08-20T03:40:18ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01189e028962510.1371/journal.pone.0289625Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome.Sang-Chul KimYoung-Ho HaBeom Kyun ParkJu Eun JangEun Su KangYoung-Soo KimTae-Hee KimspeHyuk-Jin KimChloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis. Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0289625&type=printable |
| spellingShingle | Sang-Chul Kim Young-Ho Ha Beom Kyun Park Ju Eun Jang Eun Su Kang Young-Soo Kim Tae-Hee Kimspe Hyuk-Jin Kim Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome. PLoS ONE |
| title | Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome. |
| title_full | Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome. |
| title_fullStr | Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome. |
| title_full_unstemmed | Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome. |
| title_short | Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome. |
| title_sort | comparative analysis of the complete chloroplast genome of papaveraceae to identify rearrangements within the corydalis chloroplast genome |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0289625&type=printable |
| work_keys_str_mv | AT sangchulkim comparativeanalysisofthecompletechloroplastgenomeofpapaveraceaetoidentifyrearrangementswithinthecorydalischloroplastgenome AT younghoha comparativeanalysisofthecompletechloroplastgenomeofpapaveraceaetoidentifyrearrangementswithinthecorydalischloroplastgenome AT beomkyunpark comparativeanalysisofthecompletechloroplastgenomeofpapaveraceaetoidentifyrearrangementswithinthecorydalischloroplastgenome AT jueunjang comparativeanalysisofthecompletechloroplastgenomeofpapaveraceaetoidentifyrearrangementswithinthecorydalischloroplastgenome AT eunsukang comparativeanalysisofthecompletechloroplastgenomeofpapaveraceaetoidentifyrearrangementswithinthecorydalischloroplastgenome AT youngsookim comparativeanalysisofthecompletechloroplastgenomeofpapaveraceaetoidentifyrearrangementswithinthecorydalischloroplastgenome AT taeheekimspe comparativeanalysisofthecompletechloroplastgenomeofpapaveraceaetoidentifyrearrangementswithinthecorydalischloroplastgenome AT hyukjinkim comparativeanalysisofthecompletechloroplastgenomeofpapaveraceaetoidentifyrearrangementswithinthecorydalischloroplastgenome |