Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae)
Abstract Background Spiraea L. is a genus comprising approximately 90 species that are distributed throughout the northern temperate regions. China is recognized as the center of species diversity for this genus, hosting more than 70 species, including 47 endemic species. While Spiraea is well-known...
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BMC
2024-01-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-023-04697-8 |
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| author | Shu-Yan Zhang Hai-Fei Yan Lei Wei Tong-Jian Liu Lin Chen Gang Hao Xing Wu Qiao-Ling Zhang |
| author_facet | Shu-Yan Zhang Hai-Fei Yan Lei Wei Tong-Jian Liu Lin Chen Gang Hao Xing Wu Qiao-Ling Zhang |
| author_sort | Shu-Yan Zhang |
| collection | DOAJ |
| description | Abstract Background Spiraea L. is a genus comprising approximately 90 species that are distributed throughout the northern temperate regions. China is recognized as the center of species diversity for this genus, hosting more than 70 species, including 47 endemic species. While Spiraea is well-known for its ornamental value, its taxonomic and phylogenetic studies have been insufficient. Results In this study, we conducted sequencing and assembly of the plastid genomes (plastomes) of 34 Asiatic Spiraea accessions (representing 27 Asiatic Spiraea species) from China and neighboring regions. The Spiraea plastid genome exhibits typical quadripartite structures and encodes 113–114 genes, including 78–79 protein-coding genes (PCGs), 30 tRNA genes, and 4 rRNA genes. Linear regression analysis revealed a significant correlation between genome size and the length of the SC region. By the sliding windows method, we identified several hypervariable hotspots within the Spiraea plastome, all of which were localized in the SC regions. Our phylogenomic analysis successfully established a robust phylogenetic framework for Spiraea, but it did not support the current defined section boundaries. Additionally, we discovered that the genus underwent diversification after the Early Oligocene (~ 30 Ma), followed by a rapid speciation process during the Pliocene and Pleistocene periods. Conclusions The plastomes of Spiraea provided us invaluable insights into its phylogenetic relationships and evolutionary history. In conjunction with plastome data, further investigations utilizing other genomes, such as the nuclear genome, are urgently needed to enhance our understanding of the evolutionary history of this genus. |
| first_indexed | 2024-03-08T16:21:34Z |
| format | Article |
| id | doaj.art-836640090d8e4cf48db4e63d1255d4eb |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-03-08T16:21:34Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-836640090d8e4cf48db4e63d1255d4eb2024-01-07T12:18:54ZengBMCBMC Plant Biology1471-22292024-01-0124111310.1186/s12870-023-04697-8Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae)Shu-Yan Zhang0Hai-Fei Yan1Lei Wei2Tong-Jian Liu3Lin Chen4Gang Hao5Xing Wu6Qiao-Ling Zhang7College of Life Sciences, South China Agricultural UniversityKey Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesKey Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesKey Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesHangzhou Xixi National Wetland Park Service Center (Hangzhou Xixi National Wetland Park Ecology & Culture Research Center)College of Life Sciences, South China Agricultural UniversityKey Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesHangzhou Xixi National Wetland Park Service Center (Hangzhou Xixi National Wetland Park Ecology & Culture Research Center)Abstract Background Spiraea L. is a genus comprising approximately 90 species that are distributed throughout the northern temperate regions. China is recognized as the center of species diversity for this genus, hosting more than 70 species, including 47 endemic species. While Spiraea is well-known for its ornamental value, its taxonomic and phylogenetic studies have been insufficient. Results In this study, we conducted sequencing and assembly of the plastid genomes (plastomes) of 34 Asiatic Spiraea accessions (representing 27 Asiatic Spiraea species) from China and neighboring regions. The Spiraea plastid genome exhibits typical quadripartite structures and encodes 113–114 genes, including 78–79 protein-coding genes (PCGs), 30 tRNA genes, and 4 rRNA genes. Linear regression analysis revealed a significant correlation between genome size and the length of the SC region. By the sliding windows method, we identified several hypervariable hotspots within the Spiraea plastome, all of which were localized in the SC regions. Our phylogenomic analysis successfully established a robust phylogenetic framework for Spiraea, but it did not support the current defined section boundaries. Additionally, we discovered that the genus underwent diversification after the Early Oligocene (~ 30 Ma), followed by a rapid speciation process during the Pliocene and Pleistocene periods. Conclusions The plastomes of Spiraea provided us invaluable insights into its phylogenetic relationships and evolutionary history. In conjunction with plastome data, further investigations utilizing other genomes, such as the nuclear genome, are urgently needed to enhance our understanding of the evolutionary history of this genus.https://doi.org/10.1186/s12870-023-04697-8SpiraeaPhylogenyTime divergenceChloroplast genomePositive selection |
| spellingShingle | Shu-Yan Zhang Hai-Fei Yan Lei Wei Tong-Jian Liu Lin Chen Gang Hao Xing Wu Qiao-Ling Zhang Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae) BMC Plant Biology Spiraea Phylogeny Time divergence Chloroplast genome Positive selection |
| title | Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae) |
| title_full | Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae) |
| title_fullStr | Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae) |
| title_full_unstemmed | Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae) |
| title_short | Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae) |
| title_sort | plastid genome and its phylogenetic implications of asiatic spiraea rosaceae |
| topic | Spiraea Phylogeny Time divergence Chloroplast genome Positive selection |
| url | https://doi.org/10.1186/s12870-023-04697-8 |
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