Comparative chloroplast genomes of Annonaceae species: Enlargement of plastomes in size, IR region, and gene content

Abstract

In recent years, the evolution and phylogeny of plastid genomes have attracted much attention from scholars all over the world. Annonaceae is the largest family in Magnoliales with the greatest diversity among and within genera. Thus comparative analyses of its plastomes will be informative. In this study, the complete chloroplast genome of Miliusa glochidioides was sequenced by next-generation sequencing technology. Using two Magnoliaceae species as out-group, a comparative analysis of the existing 13 Annonaceae plastomes was conducted, and a phylogenetic relationship was constructed based on four methods. Our results show that the Annonaceae plastomes have great variation in the evolution process. The genome size is between 159kb and 202kb while the gene content ranges from 127 to 165. The number of genes in the IR region is between 5 and 39. Plastomes underwent significant structural rearrangements, including one inversion and multiple large-scale expansion (6-20kb) in the lR region, and shrinkage and inversions in the SSC region. Compared with Magnoliaceae, two fragments (pafII-atpE and 5'-rps12-psbJ) were inversed in Annonaceae. The phylogenetic relationship based on 78 common protein genes showed that Cananga odorata was located at the base of Annonaceae. Annonoideae was a monophyletic group, and Chieniodendron hainanense was located inside the Malmeoideae. A total of 737 simple sequence repeats (SSRs) were detected in the study, and the distribution of SSRs varied from species. It is mainly dominated by A/T bases (mononucleotide) and is located in the intergenic region. In conclusion, the plastomes of Annonaceae have undergone great variation during evolution, especially the large-scale expansion of the IR region. Our study provides more information for studying the plastome evolution of Annonaceae.