Plastid primers for angiosperm phylogenetics and phylogeography1

Ap Applicati tions ons in in Pl Plant t Scien Sciences ces Whole genome sequencing is more available and less expensive than ever before, yet most scientists continue to rely on targeted, comparative sequencing for phylogenetics and phylo-geography. Identifying the most appropriate markers to employ has been challenging. Information for model organisms abounds, and a few studies have specifi cally screened the same set of markers across a diversity of plant groups, ranking the utility of these markers either explicitly or implicitly). These studies are exceedingly valuable, demonstrating there is no one-size-fi ts-all answer to the question " which markers? ". The second critical question to " which markers " is " which primers? ". Hundreds of primer sequences have been published, many designed for specifi c taxo-nomic groups. The work presented here was inspired by " The Tortoise and the Hare II " (Shaw et al., 2005), which was the fi rst study to pull together information on a large number of regions commonly in use (at that time) for plant phylogenetics. Our laboratory was also compiling such information, as were many others. The Tortoise and the Hare II paper was revolutionary in assessing sequence variability for all regions studied across a broad diversity of fl owering plants, and providing a ranking of that variability. In the mid-2000s, a small number of complete chloroplast genome sequences were available for land plants and some of those were not annotated (e.g., Medicago truncat-ula Gaertn. [GenBank NC_003119]; Saski et al., 2005). Grivet et al. (2001) were visionary when they moved beyond analyzing regions commonly being used to design primers for lesser-known and potentially faster-evolving regions of the chloroplast genome. They were the fi rst to take advantage of the new ge-nomic data boom, providing a set of 20 universal chloroplast primers designed around the complete chloroplast data from seven fl owering plant species. Around the same time, I developed nondegenerate primers for 36 noncoding regions in the large and small single-copy regions of the chloroplast genome (published here). These near-universal primers were designed based on the complete chloroplast genome sequences of 16 fl owering plant species (see Appendix 1). Grivet et al. (2001) and I designed primers, but Shaw et al. (2007) took an even more applied approach when they examined sequences for three different taxon pairs (Atropa/Nicotiana , Lotus/Medicago , and Saccharum/Oryza), specifi cally searching for faster-evolving regions. Shaw et al. …