Comparative Chloroplast Genomes of Six Magnoliaceae Species Provide New Insights into Intergeneric Relationships and Phylogeny

SIMPLE SUMMARY: Magnoliaceae is one of the most endangered families of angiosperms. The systematic classification of Magnoliaceae has been controversial for a long time due to minor differences in morphology. In the present study, six new chloroplast genomes of Magnoliaceae were sequenced, and the 37 published chloroplast genomes of the family were subjected to phylogenetic analyses. The results showed that all these chloroplast genomes possess the typical quadripartite structure with a conserved genome arrangement and gene structures, yet their lengths varied due to the expansion/contraction of the IR/SC boundaries. Phylogenetic relationships within Magnoliaceae were determined using complete cp genome sequences. These findings will provide a theoretical basis for adjusting the phylogenetic position of Magnoliaceae at the molecular level. ABSTRACT: Magnoliaceae plants are industrial tree species with high ornamental and medicinal value. We published six complete chloroplast genomes of Magnoliaceae by using Illumina sequencing. These showed a typical quadripartite structure of angiosperm and were 159,901–160,008 bp in size. A total of 324 microsatellite loci and six variable intergenic regions (Pi > 0.01) were identified in six genomes. Compared with five other genomes, the contraction and expansion of the IR regions were significantly different in Manglietia grandis. To gain a more thorough understanding of the intergeneric relationships in Magnoliaceae, we also included 31 published chloroplast genomes of close relative species for phylogenetic analyses. New insights into the intergeneric relationships of Magnoliaceae are provided based on our results and previous morphological, phytochemical and anatomical information. We suggest that the genus Yulania should be separated from the genus Michelia and its systematic position of should be restored; the genera Paramichelia and Tsoongiodendron should be merged into the genus Michelia; the genera Pachylarnax and Parakmeria should be combined into one genus. These findings will provide a theoretical basis for adjusting the phylogenetic position of Magnoliaceae at the molecular level.