Chloroplast genome and historical biogeography of the three Magnolias

Abstract Magnolia officinalis, M. officinalis subsp.biloba and M. hypoleuca are all typical medicinal plants, belonging to genus Magnolia and Family Magnoliaceae. Their molecular information, particularly genetic difference, were known less. In this study, the platform Illumina HiSeq was used to sequence and assemble a novel cp (chloroplast) genome of M. hypoleuca followed by cp purification. Combined with two published cp rawdata, gene cycles and function annotations were comparably performed for the three plant species. The results indicated that 19 791 019 clean reads was assembled for M. hypoleuca cp, Q30 being 91.33%, and genome 160 051 bp. Its GC content is 39.2%, including 37 tRNAs and 8 rRNAs. The M. hypoleuca had smaller chloroplast genome and more introns (or exons) than M. officinalis and M. officinalis subsp.biloba. And there were respectively 11 and 8 more functional genes in M. hypoleuca cp than that in the other two. Based on cp complete genomes sequences, we constructed the phylogenetic relationship and estimated the divergence time of the three species by ML (Maximum likelihood) method, with other 10 published Magnoliaceae species. The results showed that M. officinalis subsp.biloba and M. officinalis might diverge from M. hypoleuca around 18.98 Ma, then they diverged from each other around 15.00 Ma. Additionally, the middle Miocene warming period might play an important role in the demographic and evolutionary histories of the three Magnolias, which provided a novel insight of the origin and dispersal routes of M. hypoleuca.