To determine the structure and sequence variation of the chloroplast genome of genus Aucuba and to reveal their interspecies relationship, the chloroplast genomes of six Aucuba species including A. chinensis and A. japonica var. variegata as well as Garrya buxifolia were sequenced using next-generation sequencing technology. The chloroplast genomes were assembled and annotated using bioinformatics software. The genome characteristics, sequence comparison and phylogeny were analyzed based on the chloroplast genomes. The results were as follows: (1) Six Aucuba species chloroplast genomes exhibited typical quadripartite circular structure (i.e., LSC, SSC, IRB and IRA) and were between 157 891-158 325 bp in length. A total of 114 genes were annotated (except the duplicate genes on IRs), including 80 protein-coding genes (CDS), 30 tRNA genes and 4 rRNA genes. (2) A total of 29 high-frequency codons prefer ending in A/U, and a total of 100 optimal codons of these six sequences were filtered out, including 12 were shared by six Aucuba species. (3) A total of 270 interspersed repeats, 133 tandem repeats and 412 SSR loci were detected in the six Aucuba chloroplast genomes. (4) Comparative analysis result of six Aucuba species revealed a highly conserved chloroplast genome sequence. (5) Ten highly divergent regions were identified based on nucleotide diversity analysis. (6) The phylogenetic trees were constructed using maximum likelihood (ML) and Bayesian (BI) showing a similar topology. The results supported that genus Aucuba was monophyletic with high support rate, as a sister to genus Garrya. The complete chloroplast genomes of these five Aucuba species and one Garrya species is firstly sequenced in the study. The results reveal the interspecies relationships and the taxonomic status of genus Aucuba, and provide references for the classification, identification and phylogeny of the genus Aucuba.
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