Chloroplast phylogenomics in Bartsia (Orobanchaceae) a subgenomic approach using microfluidic PCR

South American Bartsia (Orobanchaceae), or Bellardia as it will soon be described, is a young clade of plants that grows in the páramos of the Andes.

We studied the phylogenetic relationships of this group by designing 48 primer combinations to amplify the most informative regions in the chloroplast. These regions were amplified using microfluidic PCR technology using a Fluidigm Access Array System, and the amplicons were sequenced in an Illumina MiSeq (nano flow cell – 1 million 250 paired-end reads). This produced a dataset of ~25,000bp of data for 176 samples (44 species or 94% of the species richness in South America) which were selected to represent the four morphological sections of the genus as well as the geographic distribution of the taxa.

We conducted phylogenetic analyses using PartitionFinder, GARLI and MrBayes, which showed that soon after the clade colonized the Andes there was a split between two major clades: the first one mostly comprised of species in the Diffusae section and the second one with members of the other three sections (Strictae, Orthocarpiflorae, and Laxae). We also identified some possible taxonomic disagreements between the molecular and the morphological data, although further analyses including nuclear data are needed before we are able to conclude anything with certainty.

Our sub-genomic approach using microfluidic PCR proofed to be extremely cost effective and time efficient. Additionally, the dataset that was produced is appropriate for phylogenetics as it contains almost no missing data and multiple individuals per species. Finally, we are now in the process of designing primer combinations for 48 single copy nuclear genes, which will result in an ideal dataset for coalescent-based methods, such as species tree estimation and delimitation of species boundaries.