Complete plastomes of three endemic Mexican pine species (Pinus subsection Australes)

We assembled the plastomes of Pinus greggii, P. jaliscana and P. oocarpa from 100 bp paired-end Illumina reads. We combined de novo (comparing Velvet and SPAdes) with reference-guided assembly and a final step of gap filling. SPAdes performed better than Velvet based on scaffold number (180 vs. 263) and mean length (1886 vs. 560 bp), and number of gaps (2 vs. 4). Annotations were automatically transferred from P. taeda NC_021440 and carefully revised by hand. Phylogenetic analysis with additional plastomes revealed very short branch lengths, supporting a rapid diversification within Australes and close relatedness among pines from Western Mexico.