Research Constitutes the First Comprehensive Investigation on the Plastome Structural Variation in Euphorbia
Euphorbia is one of the largest angiosperm genera, compromising some 2000 species. Species in the genus have been used in different aspects of human’s activities, due to their highly ornamental and aesthetic values, important roles in traditional medicine, usages in pharmaceutical industries, as well as being promising biofuel sources. Although plastome sequences of Euphorbia have been sporadically reported in recent years, a comprehensive comparative plastome analysis has not been considered until now.
To help addressing the genomic data-gap in Euphoria, phylogenomic studies based on comprehensively representative sampling are needed. Supervised by Prof. WANG Qingfeng from Wuhan Botanical Garden, Chinese Academy of Sciences, PhD student WEI Neng and Dr. Olwen M. Grace from Royal Botanic Gardens, Kew, carried out phylogenomic and comparative analyses of Euphoria. In the study, they newly sequenced, assembled, and annotated plastomes of Euphorbia species based on a taxonomically representative sampling from the four subgenera.
The plastome sequences of 28 accessions in Euphorbiaceae were sampled, 15 of which were newly sequenced for this study. Phylogenomic and comparative analyses of 22 plastome sequences representing the four subgenera of Euphorbia revealed that the whole plastome are highly variable, with some 42 kb variation ranging from the shortest to the longest. Large-scale expansions of the inverted repeat (IR) region were found in the studied Euphorbia species, 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.
They 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 were recovered in a successive sister relationship.
This 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.
The research entitled “Plastome evolution in the hyperdiverse genus Euphorbia (Euphorbiaceae) using phylogenomic and comparative analyses: large-scale expansion and contraction of the inverted repeat region” was published in Frontiers in Plant Science.
This work was supported by grants from the Sino-Africa Joint Research Center, Chinese Academy of Sciences, China, International Partnership Program of Chinese Academy of Sciences, and the National Science Foundation of China, the University of Chinese Academy of Sciences Joint PhD Training Program, the Swiss Orchid Foundation and the Sainsbury Orchid Trust Fund at the Royal Botanic Gardens, Kew.
The plastid genome comparisons of three representative Euphorbia species (Image by WEI Neng)
Maximum likelihood tree of Euphorbiaceae reconstructed from 76 plastid coding sequences, showing the gene losses/pseudogenizations in the framework of representatives of Euphorbiaceae (Image by WEI Neng)