Complete plastomes of three endemic Mexican pine species (<i>Pinus</i> subsection <i>Australes</i>)

2017-08-23T06:37:46Z (GMT) by Xitlali Aguirre-Dugua David S. Gernandt
<p>We assembled the plastomes of <i>Pinus greggii</i>, <i>P. jaliscana</i> and <i>P. oocarpa</i> from 100 bp paired-end Illumina reads. We combined <i>de novo</i> (comparing <i>Velvet</i> and <i>SPAdes</i>) with reference-guided assembly and a final step of gap filling. <i>SPAdes</i> performed better than <i>Velvet</i> 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 <i>P. taeda</i> NC_021440 and carefully revised by hand. Phylogenetic analysis with additional plastomes revealed very short branch lengths, supporting a rapid diversification within <i>Australes</i> and close relatedness among pines from Western Mexico.</p>