Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure
The chloroplast genomes of angiosperms usually have a stable circular quadripartite structure that exhibits high consistency in genome size and gene order. As one of the most diverse genera of angiosperms, Carex is of great value for the study of evolutionary relationships and speciation within its...
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1100876/full |
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| author | Shenjian Xu Ke Teng Hui Zhang Kang Gao Juying Wu Liusheng Duan Yuesen Yue Xifeng Fan |
| author_facet | Shenjian Xu Ke Teng Hui Zhang Kang Gao Juying Wu Liusheng Duan Yuesen Yue Xifeng Fan |
| author_sort | Shenjian Xu |
| collection | DOAJ |
| description | The chloroplast genomes of angiosperms usually have a stable circular quadripartite structure that exhibits high consistency in genome size and gene order. As one of the most diverse genera of angiosperms, Carex is of great value for the study of evolutionary relationships and speciation within its genus, but the study of the structure of its chloroplast genome is limited due to its highly expanded and restructured genome with a large number of repeats. In this study, we provided a more detailed account of the chloroplast genomes of Carex using a hybrid assembly of second- and third-generation sequencing and examined structural variation within this genus. The study revealed that chloroplast genomes of four Carex species are significantly longer than that of most angiosperms and are characterized by high sequence rearrangement rates, low GC content and gene density, and increased repetitive sequences. The location of chloroplast genome structural variation in the species of Carex studied is closely related to the positions of long repeat sequences; this genus provides a typical example of chloroplast structural variation and expansion caused by long repeats. Phylogenetic relationships constructed based on the chloroplast protein-coding genes support the latest taxonomic system of Carex, while revealing that structural variation in the chloroplast genome of Carex may have some phylogenetic significance. Moreover, this study demonstrated a hybrid assembly approach based on long and short reads to analyze complex chloroplast genome assembly and also provided an important reference for the analysis of structural rearrangements of chloroplast genomes in other taxa. |
| first_indexed | 2024-04-10T20:09:54Z |
| format | Article |
| id | doaj.art-336e719992eb4710b0762aef17554ed0 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T20:09:54Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-336e719992eb4710b0762aef17554ed02023-01-26T13:09:45ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-01-011410.3389/fpls.2023.11008761100876Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structureShenjian Xu0Ke Teng1Hui Zhang2Kang Gao3Juying Wu4Liusheng Duan5Yuesen Yue6Xifeng Fan7Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, ChinaInstitute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, ChinaInstitute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, ChinaInstitute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, ChinaInstitute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, ChinaCollege of Plants and Technology, Beijing University of Agriculture, Beijing, ChinaInstitute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, ChinaInstitute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, ChinaThe chloroplast genomes of angiosperms usually have a stable circular quadripartite structure that exhibits high consistency in genome size and gene order. As one of the most diverse genera of angiosperms, Carex is of great value for the study of evolutionary relationships and speciation within its genus, but the study of the structure of its chloroplast genome is limited due to its highly expanded and restructured genome with a large number of repeats. In this study, we provided a more detailed account of the chloroplast genomes of Carex using a hybrid assembly of second- and third-generation sequencing and examined structural variation within this genus. The study revealed that chloroplast genomes of four Carex species are significantly longer than that of most angiosperms and are characterized by high sequence rearrangement rates, low GC content and gene density, and increased repetitive sequences. The location of chloroplast genome structural variation in the species of Carex studied is closely related to the positions of long repeat sequences; this genus provides a typical example of chloroplast structural variation and expansion caused by long repeats. Phylogenetic relationships constructed based on the chloroplast protein-coding genes support the latest taxonomic system of Carex, while revealing that structural variation in the chloroplast genome of Carex may have some phylogenetic significance. Moreover, this study demonstrated a hybrid assembly approach based on long and short reads to analyze complex chloroplast genome assembly and also provided an important reference for the analysis of structural rearrangements of chloroplast genomes in other taxa.https://www.frontiersin.org/articles/10.3389/fpls.2023.1100876/fullmolecular evolutionplastomeplastid genomerepeatsrearrangementthird-generation sequencing |
| spellingShingle | Shenjian Xu Ke Teng Hui Zhang Kang Gao Juying Wu Liusheng Duan Yuesen Yue Xifeng Fan Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure Frontiers in Plant Science molecular evolution plastome plastid genome repeats rearrangement third-generation sequencing |
| title | Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure |
| title_full | Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure |
| title_fullStr | Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure |
| title_full_unstemmed | Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure |
| title_short | Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure |
| title_sort | chloroplast genomes of four carex species long repetitive sequences trigger dramatic changes in chloroplast genome structure |
| topic | molecular evolution plastome plastid genome repeats rearrangement third-generation sequencing |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1100876/full |
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