A Phylogenomic Toolkit for Resolving One of the Most Recalcitrant Angiosperm Clades: Malpighiales

Malpighiales are an extraordinarily diverse clade of plants, and remain one of the most recalcitrant nodes in the angiosperm Tree of Life. Species in the order comprise around 6% of angiosperm species and exhibit a range of morphologies, including thalloid aquatics (Podostemaceace), holoparasites (Rafflesiaceae), emergent mid-canopy trees (Clusiaceae s.l.), desert succulents (Euphorbiaceae), and mangroves (Rhizophoraceae). Despite their importance and the inclusion of numerous radiating clades spanning the Cretaceous-Tertiary time period, few large scale phylogenomic resources have been developed to resolve the order. The construction of well-resolved phylogenies is essential to addressing larger issues of biogeography, biome evolution, and species diversification within this clade. An approach that is increasingly gaining traction because of its balance of cost and data is sequence capture, which targets a subset of the genome, especially from low copy nuclear genes. As the focus of our study we chose one subclade within the family Calophyllaceae to develop a sequence capture probe set for Malpighiales, (Kielmeyera, Caraipa and Haploclathra). A preliminary phylogeny from this group using chloroplast and nuclear genes indicates that this is a recently evolved radiation and not amenable to resolution using traditional approaches. Our probe set was designed to target 425 low copy genes and 36 ultraconserved-like elements. A total of 80 libraries were prepared, hybridized and sequenced on an Illumina NextSeq for 125x2 bp reads, generating a total of 125 Gbp. The data showed that the targeted loci were recovered and preliminary insights will be presented for the probe set.