Whole chloroplast genome (plastome) sequences have become a useful tool with which to estimate the phylogenetic relationships of plant lineages ( Barrett et al., 2016 Hassemer et al., 2019 Li et al., 2019), due to the relative ease at which plastid genomes can be sequenced. Subsequently, the molecular phylogenetic classification for these four subgenera into a global concept of Euphorbia based on the nuclear-ribosomal ITS and the plastid ndhF and matK loci has been established ( Yang et al., 2012 Dorsey et al., 2013 Peirson et al., 2013 Riina et al., 2013). Esula, Athymalus, Chamaesyce, and Euphorbia have been gradually recovered in Euphorbia, although the phylogenetic relationship among them has been in flux ( Steinmann and Porter, 2002 Bruyns et al., 2006, 2011 Park and Jansen, 2007 Zimmermann et al., 2010 Horn et al., 2012). Here, only Euphorbia has been consistently placed in the subtribe Euphorbiinae, for several traditionally segregated genera including Chamaesyce, Cubanthus, Elaeophorbia, Endadenium, Monadenium, Pedilanthus, Poinsettia, and Synadenium are now understood to be deeply nested within Euphorbia ( Steinmann and Porter, 2002 Bruyns et al., 2006 Steinmann et al., 2007 Zimmermann et al., 2010 Horn et al., 2012).įour subgenera, subg. Molecular phylogenetic studies have improved the delimitation of the Euphorbia as well as its infrageneric classification. Many Euphorbia species are key components of tropical ecosystems worldwide ( Yang et al., 2012 Dorsey et al., 2013 Peirson et al., 2013) and its taxonomy is notoriously challenging due to the persistent homoplasy of their morphological characters, species diversity, and its wide distribution ( Webster, 1967 Steinmann and Porter, 2002 Bruyns et al., 2006). 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.Įuphorbia is the largest genus in the family Euphorbiaceae (i.e., the spurge family), comprising some 2,000 species with a nearly global distribution pattern ( Horn et al., 2012, 2014 Webster, 2014). The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. 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. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. 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. 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. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. 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. 8Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.7Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.6Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Chenshan Botanical Garden, Shanghai, China.5East African Herbarium, National Museums of Kenya, Nairobi, Kenya.4University of Chinese Academy of Sciences, Beijing, China.3Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.2Royal Botanic Gardens, Kew, Richmond, United Kingdom.1Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.Musili 5 Wei-Chang Huang 6 Jun-Bo Yang 7 Ai-Qun Hu 2 Guang-Wan Hu 1,3,8 Olwen M.
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