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

Abstract

Lippia origanoides (Kunth), also known as salva-de-maraj o, 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-maraj o 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.

Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine

“…Spach ( Fonseca & Lohmann, 2018 ). The plastome of Lippia origanoides Kunth (Verbenaceae) was also used for comparison (NCBI accession numbers at Table 1 ; Sarzi et al, 2019 ). Verbenaceae is now being consistently recovered as the sister family of Bignoniaceae ( Fonseca, 2021 ), representing a good outgroup for comparative studies.…”

Characterization of the complete chloroplast genome of basswood (Tilia mongolica maxim.)

“…Previous studies on the genetic classification of Tilia populations had focused on the use of random amplified polymorphic DNA (Colagar et al 2013;Filiz et al 2015) and microsatellite (Logan et al 2015) markers. With the development of sequencing technology, chloroplast genomes have been widely used for the identification and phylogenetic analyses of plant species, including some basswoods (Cai et al 2015;Lu et al 2020), owing to the highly conserved genome size and sequence (Sarzi et al 2019;Sun et al 2019). Therefore, it was imperative for the chloroplast genome sequence of T. mongolica to be resolved.…”

Orthologous nuclear markers and new transcriptomes that broadly cover the phylogenetic diversity of Acanthaceae

“…Furthermore, the phylogenetic relationships in several smaller clades are currently not well understood (e.g., in Avicennia L. [Glasenapp et al., ], Barleria L. [Darbyshire et al., ], Dyschoriste Nees [Chumchim et al., ], Thunbergioideae T. Anderson [Borg et al., ], Ruellia L. [Tripp et al., ]). In addition to this obstacle, the rooting of the Acanthaceae phylogeny is uncertain, as interfamilial relationships in Lamiales remain elusive (Schäferhoff et al., ; Refulio‐Rodriguez and Olmstead, ; Stull et al., ; Wikström et al., ; Chase et al., ; Sarzi et al., ; Xu et al., ). These technical barriers prevent targeted investigations of evolutionary questions within this family.…”