Complete plastid genome of Lippia origanoides (Verbenaceae) and phylogenomic analysis of Lamiales

Abstract

Lippia origanoides (Kunth), also known as salva-de-marajó, is an aromatic shrub distributed from central America to northern South America that presents biomedical potential. Here we sequenced a partial genome dataset for salva-de-marajó using 1/11th of a lane on Illumina Hiseq. The software MIRA was used to assemble the complete plastid using different k-mer sizes and further merging well-assembled regions through manual curation. The plastid genome was 154,310 bp in length, divided in one Large Single Copy region containing 85,156 bp; one Small Single Copy region containing 13,320 bp; and two inverted repeat regions presenting different sizes: IRa, containing 25,955 bp; and IRb, containing 29,879 bp. Genome annotation was automatically performed using GeSeq. Artemis was used to perform manual curation. The plastid presents 88 protein-coding genes, 36 tRNAs and 8 rRNAs. It was deposited in GenBank under the accession number MK248831. Twenty-three species of Lamiales containing complete plastids distributed along nine different families were downloaded to confirm the phylogenetic position of this newly described genome, plus 3 outgroup species. Forty-three genes were found to be present in all plastids. These genes were aligned and concatenated to produce a dataset of 13,959 nucleotidic positions. Modeltest defined the best substitution model as the General Time Reversible. As expected, the phylogenomic analysis grouped L. origanoides together with Aloysia citrodora in a monophyletic clade representing the Verbenaceae family. The complete chloroplast genome of L. origanoides will contribute to support further studies on population genetics, phylogeography, evolutionary, and conservation biology of Verbenaceae.

Keywords

• lippia origanoides
• salva-de-marajó
• plastid genome
• phylogenomics
• verbenaceae
• lamiales