Phylogeny of subgenus Yulania (Magnoliaceae) and related taxa based on chloroplast genomes

Abstract

As a candidate basal-most angiosperm, Magnoliaceae has been the subject of keen interest from many botanists who study classical morphology. Although the basal-most position of extant angiosperms is currently Amborella, Magnoliaceae is still spotlighted by many botanists who seek to understand the early-divergence of angiosperms as a second group of basal-most angiosperms as it pertains to phylogenetic, genomic, and evolutionary studies. Although recent molecular phylogenetic studies showed that major lineages exist in this family, the phylogenetic relationships among these lineages remain unclear due to insufficient informative characters, indicating that genome-level phylogenetic analyses are needed. As a series of molecular phylogenetic studies on the Magnoliaceae, this study provides 1) the chloroplast whole genome of Magnolia kobus, a member of subgen. Yulania, using Solexa/Illumina technology, and 2) additional 10 chloroplast genomes included in the subgen. Yulania and related taxa using a conventional PCR-based method. The chloroplast genomes of Magnoliaceae are 158,177bp ~ 160,093bp in length, including IR regions ranging from 25,651bp (M. liliiflora) to 26,602bp (M. acuminata) separated by LSC regions ranging from 87,484bp (M. kobus) to 88,156bp (M. sinica), and SSC regions ranging from 18,722bp (M. sprengeri) to 18,800bp (Mich. odora). Sequence structural analyses based on an aligned matrix showed 1) taxon-specific large gaps such as the 658bp deletion in M. kobus and 952bp deletions including trnV-GAC in M. liliiflora and 2) boarder variations of LSC, SSC, and IR. Various phylogenetic analyses of the entire cp genome region showed strong new phylogenetic relationships among the species of subgen. Yulania and related taxa: 1) M. sprengeri is a sister to the M. kobus/M. salicifolia clade; 2) the M. liliiflora/M. denudata clade is a sister to the clade of M. kobus/M. salicifolia/M. sprengeri; and 3) the Michelia/M. cathcartii clade is a sister to subgen. Yulania, which is a deciduous magnolia group. Combined analyses of eleven chloroplast genomes and two previously reported chloroplast genomes in Magnoliaceae offer a new understanding of the phylogeny and evolution of Magnoliaceae.