Comparison of the chloroplast genomes and phylogenomic analysis of Elaeocarpaceae

Elaeocarpaceae is a vital family in tropical and subtropical forests. Compared with the important position of Elaeocarpaceae species in forest ecosystem and the concern of medicinal value, the most research on Elaeocarpaceae are classification and taxonomy. Molecular systematics has corrected the morphological misjudgment, and it belongs to Oxalidales. Phylogenetic and divergence time estimates of Elaeocarpaceae is mostly constructed by using chloroplast gene fragments. At present, although there are reports on the chloroplast structure of Elaeocarpaceae, a comprehensive analysis of the chloroplast structure of Elaeocarpaceae is lacking. To understand the variation in chloroplast sequence size and structure in Elaeocarpaceae, the chloroplast genomes of nine species were sequenced using the Illumina HiSeq 2500 platform and further assembled and annotated with and (family Elaeocarpaceae) as references. A phylogenomic tree was constructed based on the complete chloroplast genomes of the 11 species representing five genera of Elaeocarpaceae. Chloroplast genome characteristics were examined by using Circoletto and IRscope software. The results revealed the following: (a) The 11 sequenced chloroplast genomes ranged in size from 157,546 to 159,400 bp. (b) The chloroplast genomes of , , and lacked the 32 gene in the small single-copy (SSC) region. The large single-copy (LSC) region of the chloroplast genomes lacked the K gene in , , and . The LSC region of the chloroplast genomes lacked the A gene in genus and . (c) Through inverted repeat (IR) expansion and contraction analysis, a significant difference was found between the LSC/IRB and IRA/LSC boundaries among these species. 3 was detected in the neighboring regions of the LSC and IRb regions in . (d) Phylogenomic analysis revealed that the genus is closely related to on an independent branch and is closely related to , forming a clade with the genus . Structural comparisons showed that Elaeocarpaceae diverged at 60 Mya, the genus diverged 53 Mya and that the genus diverged 0.44 Mya. These results provide new insight into the evolution of the Elaeocarpaceae.