Comparative and phylogenetic analyses of 26 Magnoliaceae species based on complete chloroplast genome sequences

Magnoliaceae is a family of dicotyledonous plants with primitive flowers and is one of the oldest families of flowering plants. In this paper, the chloroplast genomes of 26 species of Magnoliaceae were contrasted and compared to help clarify the relationships among them. The size of the 26 Magnoliaceae chloroplast genomes ranged from 158 177 bp to 160 183 bp, and approximately 1298 simple-sequence repeats were detected. For long-repeat sequences, 197 repeat loci, including 144 forward repeats, 52 palindromic repeats, and 1 reverse repeat, were detected. In four species, an abnormal gene, rpl22, contained premature stop codons. Moreover, three noncoding regions (ccsA-ndhD, ndhD-psaC, and trnH-psbA) with a nucleotide diversity (Pi) value greater than 0.02 and six coding genes (ycf1, petL, matK, psbT, rps19, and ndhF) with a Pi value of no less than 0.008 were identified (this information is important in resolving relationships within the Magnolia genus). The maximum likelihood (ML) and Bayesian inference (BI) trees had the same topological structures, with high support rates among 20 species, i. e., excluding Magnolia dealbata, Magnolia pyramidata, Magnolia dandyi, Magnolia aromatica, Magnolia conifera, and Magnolia glaucifolia. On the whole, these data represent valuable resources for Magnoliaceae chloroplast genomics and will be useful in future phylogenetic studies.