Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae
The Annonaceae stands as the most species rich family in the Magnoliales, a basal group of angiosperms. Widely distributed in tropical and subtropical regions, it holds significant ecological and economic value. The plastid genome (plastome) is often employed in studies related to plant phylogenetic...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2024-04-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1351388/full |
| _version_ | 1797202894457405440 |
|---|---|
| author | Jingyao Ping Jing Hao Ting Wang Yingjuan Su Yingjuan Su |
| author_facet | Jingyao Ping Jing Hao Ting Wang Yingjuan Su Yingjuan Su |
| author_sort | Jingyao Ping |
| collection | DOAJ |
| description | The Annonaceae stands as the most species rich family in the Magnoliales, a basal group of angiosperms. Widely distributed in tropical and subtropical regions, it holds significant ecological and economic value. The plastid genome (plastome) is often employed in studies related to plant phylogenetics, comparative genomics, evolutionary biology, and genetic engineering. Nonetheless, research progress on plastid genomics in the Annonaceae has been relatively slow. In this study, we analyzed the structure and repetitive sequence features of plastomes from 28 Annonaceae species. Among them, Mitrephora tomentosa and Desmos chinensis were newly sequenced, with sizes of 160,157 bp and 192,167 bp, and GC contents of 38.3% and 38.4%, respectively. The plastome size in the Annonaceae ranged from 158,837 bp to 202,703 bp, with inverted repeat (IR) region sizes ranging from 64,621 bp to 25,861 bp. Species exhibiting expansion in the IR region showed an increase in plastome size and gene number, frequent boundary changes, different expansion modes (bidirectional or unidirectional), and an increase in repetitive sequences. Specifically, a large number of dispersed repetitive sequences lead to an increase in the size of the LSC region in Goniothalamus tamirensis. Phylogenetic analysis revealed Annonoideae and Malmeoideae as monophyletic groups and sister clades, with Cananga odorata outside of them, followed by Anaxagorea javanica. This research uncovers the structural variation characteristics of plastomes in the Annonaceae, providing valuable information for understanding the phylogeny and plastome evolution of Annonaceae. |
| first_indexed | 2024-04-24T08:10:41Z |
| format | Article |
| id | doaj.art-8612ad3e37184f1f938bbf59ea33cdf5 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-24T08:10:41Z |
| publishDate | 2024-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-8612ad3e37184f1f938bbf59ea33cdf52024-04-17T04:57:45ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-04-011510.3389/fpls.2024.13513881351388Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the AnnonaceaeJingyao Ping0Jing Hao1Ting Wang2Yingjuan Su3Yingjuan Su4School of Life Sciences, Sun Yat-Sen University, Guangzhou, ChinaSchool of Life Sciences, Sun Yat-Sen University, Guangzhou, ChinaCollege of Life Sciences, South China Agricultural University, Guangzhou, ChinaSchool of Life Sciences, Sun Yat-Sen University, Guangzhou, ChinaResearch Institute of Sun Yat-Sen University, Shenzhen, ChinaThe Annonaceae stands as the most species rich family in the Magnoliales, a basal group of angiosperms. Widely distributed in tropical and subtropical regions, it holds significant ecological and economic value. The plastid genome (plastome) is often employed in studies related to plant phylogenetics, comparative genomics, evolutionary biology, and genetic engineering. Nonetheless, research progress on plastid genomics in the Annonaceae has been relatively slow. In this study, we analyzed the structure and repetitive sequence features of plastomes from 28 Annonaceae species. Among them, Mitrephora tomentosa and Desmos chinensis were newly sequenced, with sizes of 160,157 bp and 192,167 bp, and GC contents of 38.3% and 38.4%, respectively. The plastome size in the Annonaceae ranged from 158,837 bp to 202,703 bp, with inverted repeat (IR) region sizes ranging from 64,621 bp to 25,861 bp. Species exhibiting expansion in the IR region showed an increase in plastome size and gene number, frequent boundary changes, different expansion modes (bidirectional or unidirectional), and an increase in repetitive sequences. Specifically, a large number of dispersed repetitive sequences lead to an increase in the size of the LSC region in Goniothalamus tamirensis. Phylogenetic analysis revealed Annonoideae and Malmeoideae as monophyletic groups and sister clades, with Cananga odorata outside of them, followed by Anaxagorea javanica. This research uncovers the structural variation characteristics of plastomes in the Annonaceae, providing valuable information for understanding the phylogeny and plastome evolution of Annonaceae.https://www.frontiersin.org/articles/10.3389/fpls.2024.1351388/fullAnnonaceaeplastomesphylogenyIR expansionrepetitive sequences |
| spellingShingle | Jingyao Ping Jing Hao Ting Wang Yingjuan Su Yingjuan Su Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae Frontiers in Plant Science Annonaceae plastomes phylogeny IR expansion repetitive sequences |
| title | Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae |
| title_full | Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae |
| title_fullStr | Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae |
| title_full_unstemmed | Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae |
| title_short | Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae |
| title_sort | comparative analysis of plastid genomes reveals rearrangements repetitive sequence features and phylogeny in the annonaceae |
| topic | Annonaceae plastomes phylogeny IR expansion repetitive sequences |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1351388/full |
| work_keys_str_mv | AT jingyaoping comparativeanalysisofplastidgenomesrevealsrearrangementsrepetitivesequencefeaturesandphylogenyintheannonaceae AT jinghao comparativeanalysisofplastidgenomesrevealsrearrangementsrepetitivesequencefeaturesandphylogenyintheannonaceae AT tingwang comparativeanalysisofplastidgenomesrevealsrearrangementsrepetitivesequencefeaturesandphylogenyintheannonaceae AT yingjuansu comparativeanalysisofplastidgenomesrevealsrearrangementsrepetitivesequencefeaturesandphylogenyintheannonaceae AT yingjuansu comparativeanalysisofplastidgenomesrevealsrearrangementsrepetitivesequencefeaturesandphylogenyintheannonaceae |