| Lagerstroemia L.is a kind of typical genus native to temperate and tropical regions,with China as the center of their geographical distribution and cultivation origin.Lagerstroemia plays an important role in the landscape and gardens around the world,as its many species are of great ornamental value for their beautiful flowers.Many species in Lagerstroemia frequent naturally hybrid making their interspecific relationship chaotic.Up to now,the phylogenetic relationship of Lagerstroemia has not reached a consensus,and the research on the history of species divergence is still blank.Chloroplast phylogenomics can provide effective evidence for phylogenetic relationships,molecular evolution,and divergence of various taxa.Here,based on the chloroplast genomes,this study reconstructed a robust phylogeny of Lagerstroemia,analyzed the evolutionary fate of the chloroplast genome,and interpret the differentiation history of this genus.The main findings are as follows:(1)A total of 15 species of Lagerstroemia and 6 related species were selected to generate three matrices based on the whole chloroplast genome,concatenation of 64 shared protein-coding sequences,and the concatenation of shared protein-coding sequences excluded the third base,respectively.The phylogenetic relationship of Lagerstroemia was reconstructed on the processed molecular matrix by using the concatenative method(maximum likelihood and Bayesian inference)and the coalescent method.The results showed that the ML and BI tree topologies generated by each matrix were the same as each other,but there are subtle differences between different matrices.Lagerstroemia was resolved as monophyly in all reconstructions,including two major clades.Based on the shared protein-coding sequences and the ancestral method,L.intermedia was resolved as a sister group of(L.siamica + L.macrocarpa + L.speciosa + L.venusta),while based on the whole chloroplast genome matrices and the excluded the third base matrices,L.intermedia and L.siamica together formed a minor clade which served as the sister branch of(L.macrocarpa + L.speciosa + L.venusta).The latter one had higher support at this key node,as to be supported in our comparison.In addition,the phylogenetic result was consistent with species ploidy,geographical distribution,and morphological characteristics to some degree.(2)Both the specific single nucleotide variation(SNVs)between Lagerstroemia and relatives,as well as between the two clades within Lagerstroemia were statistically analyzed.The molecular evolution rates of both single protein-coding gene and the chloroplast genome were reflected by measuring the rates of synonymous substitutions and non-synonymous substitutions.The results showed that a total of 114 and 95 special SNVs were identified at the genus and branch level,respectively,among which several genes such as mat K,rpo B,rpo C2,and rrn16 had multiple SNVs with non-synonymous substitutions leading to amino acid alternation.Compared with closely related species,the chloroplast genome of Lagerstroemia had a slower evolution rate,showing no significant difference among the evolution rates of different clades,while the evolution rates of chloroplast protein-coding genes have obvious heterogeneity.(3)Divergence history of Lagerstroemia and its potential driving factors were analyzed by molecular dating.The divergence time between Lagerstroemia and Duabanga was 61 million years ago.The internal divergence of Lagerstroemia into two major clades occurred 57 million years ago during the Paleocene,and the two clades themselves began to diverge rapidly about 7 million years ago,indicating that Lagerstroemia underwent rapid differentiation or evolutionary radiation,and may be related to contemporary dramatic climate fluctuations,such as glacial-interglacial cycles may contribute to the species diversity of Lagerstroemia. |
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