The complete chloroplast genome sequences of three Spondias species reveal close relationship among the species

Abstract

This study reports the complete chloroplast sequences of three Spondias species. The genome sequences were obtained for Spondias tuberosa, Spondias bahienses, and Spondias mombin using the Illumina sequencing technology by a combination of de novo methods and a reference-guided assembly using Sapindus mukorossi as reference. The genomes of S. tuberosa, S. bahiensis, and S. mombin had 162,036, 162,218, and 162,302 bp, respectively. The coding regions exhibited 130 genes, including 34–35 tRNAs and 4 rRNAs. The results revealed synteny among the genomes, with high conservation in the gene order and content and CG content. The inverted repeat regions (IRA and IRB) and the large and small single copies were very similar among the three genomes. The phylogenomic analysis reported similar topologies as that of previous studies, which used partial chloroplast, wherein S. mombin was the first diverging lineage, while S. tuberosa and S. bahiensis were derived, indicating that the phylogenetic analysis using partial or complete genome produces similar results. In summary, (1) we presented the first complete chloroplast genome for the genus Spondias, (2) phylogenies analyzed using the complete chloroplast genomes revealed a robust phylogenetic topology for Spondias, and (3) gene order, content, and orientation in Spondias are highly conserved.