The chloroplast genome of Hancornia speciosa Gomes: structural organization and phylogenomic studies in Rauvolfioideae (Apocynaceae)

The chloroplast genomes have been utilized in many studies of evolution, population structure and molecular identification. The aim of this study was to assemble the chloroplast genome of Hancornia speciosa Gomes, an economically important fruit species from Brazil, using next-generation sequencing data in order to reconstruct the phylogenetic analysis of Rauvolfioideae. Twenty-four million Illumina short paired-end reads were used for de novo assembly, and the chloroplast contig was identified by BLAST. The chloroplast genome of H. speciosa contains 155,357 bp, with 25,755 bp of inverted repeat A, 25,654 bp of inverted repeat B, 85,702 bp of large single copy and 18,229 bp of small single copy. The coding regions contained 83 genes, eight rRNAs and 36 tRNAs. The phylogenomic analysis reported similar topologies as in previous studies, which used partial chloroplast genomes, and demonstrated that Rauvolfioideae is paraphyletic. In summary, we demonstrated: (1) the first complete chloroplast genome of H. speciosa ; (2) phylogenies analyzed using the complete chloroplast genomes revealed a robust phylogenetic topology for Rauvolfioideae; and (3) the phylogenetic analysis showed that the subfamily Rauvolfioideae is paraphyletic.