Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region
With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic a...
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Frontiers Media S.A.
2021-08-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.712064/full |
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| author | Neng Wei Neng Wei Neng Wei Neng Wei Oscar A. Pérez-Escobar Paul M. Musili Wei-Chang Huang Jun-Bo Yang Ai-Qun Hu Guang-Wan Hu Guang-Wan Hu Guang-Wan Hu Olwen M. Grace Qing-Feng Wang Qing-Feng Wang Qing-Feng Wang |
| author_facet | Neng Wei Neng Wei Neng Wei Neng Wei Oscar A. Pérez-Escobar Paul M. Musili Wei-Chang Huang Jun-Bo Yang Ai-Qun Hu Guang-Wan Hu Guang-Wan Hu Guang-Wan Hu Olwen M. Grace Qing-Feng Wang Qing-Feng Wang Qing-Feng Wang |
| author_sort | Neng Wei |
| collection | DOAJ |
| description | With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within Euphorbia revealed that plastome length in Euphorbia is labile, presenting a range of variation c. 42 kb. Large-scale expansions of the inverted repeat (IR) region were identified, and at the extreme opposite, the near-complete loss of the IR region (with only 355 bp left) was detected for the first time in Euphorbiaceae. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. We screened the most promising molecular markers from both intergenic and coding regions for phylogeny-based utilities, and estimated maximum likelihood and Bayesian phylogenies from four datasets including whole plastome sequences. The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. Our study constitutes the first comprehensive investigation on the plastome structural variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation. |
| first_indexed | 2024-12-16T23:19:00Z |
| format | Article |
| id | doaj.art-9179dce237a74e5a935652133b313312 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-16T23:19:00Z |
| publishDate | 2021-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-9179dce237a74e5a935652133b3133122022-12-21T22:12:12ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-08-011210.3389/fpls.2021.712064712064Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat RegionNeng Wei0Neng Wei1Neng Wei2Neng Wei3Oscar A. Pérez-Escobar4Paul M. Musili5Wei-Chang Huang6Jun-Bo Yang7Ai-Qun Hu8Guang-Wan Hu9Guang-Wan Hu10Guang-Wan Hu11Olwen M. Grace12Qing-Feng Wang13Qing-Feng Wang14Qing-Feng Wang15Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaRoyal Botanic Gardens, Kew, Richmond, United KingdomCenter of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, ChinaUniversity of Chinese Academy of Sciences, Beijing, ChinaRoyal Botanic Gardens, Kew, Richmond, United KingdomEast African Herbarium, National Museums of Kenya, Nairobi, KenyaShanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, ChinaGermplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, ChinaRoyal Botanic Gardens, Kew, Richmond, United KingdomKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaCenter of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaRoyal Botanic Gardens, Kew, Richmond, United KingdomKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, ChinaCenter of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, ChinaSino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, ChinaWith c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within Euphorbia revealed that plastome length in Euphorbia is labile, presenting a range of variation c. 42 kb. Large-scale expansions of the inverted repeat (IR) region were identified, and at the extreme opposite, the near-complete loss of the IR region (with only 355 bp left) was detected for the first time in Euphorbiaceae. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. We screened the most promising molecular markers from both intergenic and coding regions for phylogeny-based utilities, and estimated maximum likelihood and Bayesian phylogenies from four datasets including whole plastome sequences. The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. Our study constitutes the first comprehensive investigation on the plastome structural variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation.https://www.frontiersin.org/articles/10.3389/fpls.2021.712064/fullcomparative genomicsorganellar evolutionphylogenetic inferenceplastome rearrangementspurge familystructural variations |
| spellingShingle | Neng Wei Neng Wei Neng Wei Neng Wei Oscar A. Pérez-Escobar Paul M. Musili Wei-Chang Huang Jun-Bo Yang Ai-Qun Hu Guang-Wan Hu Guang-Wan Hu Guang-Wan Hu Olwen M. Grace Qing-Feng Wang Qing-Feng Wang Qing-Feng Wang Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region Frontiers in Plant Science comparative genomics organellar evolution phylogenetic inference plastome rearrangement spurge family structural variations |
| title | Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region |
| title_full | Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region |
| title_fullStr | Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region |
| title_full_unstemmed | Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region |
| title_short | Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region |
| title_sort | plastome evolution in the hyperdiverse genus euphorbia euphorbiaceae using phylogenomic and comparative analyses large scale expansion and contraction of the inverted repeat region |
| topic | comparative genomics organellar evolution phylogenetic inference plastome rearrangement spurge family structural variations |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.712064/full |
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