12 September 2017

Herbarium Specimens in Phylogenetics

A herbarium is a collection of dried plant collections, much like a museum for plant specimens. Herbarium specimens are both scientific resource and artistic depiction of plant diversity. In the E.L. Reed Herbarium at Texas Tech, over 20,000 recorded (and many yet-unrecorded) specimens show the diversity of plants in West Texas. Click here for more information about the Herbarium.

Herbaria are underutilized resources for plant research, especially in phylogenetics. Collections made from locations that are now difficult to access, or from threatened or extinct species, would be valuable for phylogenetics analysis. However, it can be difficult to extract high-quality DNA from dried plant material.

Enter targeted sequencing.

The ability to reliably use dried plant material for DNA extraction is one of the most important advantages of targeted sequencing. Because the DNA is used in shotgun sequencing library preparation, degradation of DNA to small fragment sizes does not prohibit sequence recovery! In some instances, we have been able to recover 400+ nuclear genes from a 100-year-old herbarium specimen, even though PCR-based methods failed for the same DNA extraction.

In our lab, we have teamed up with the PAFTOL project at Royal Botanical Gardens, Kew to produce a targeted sequencing kit that will work with any angiosperm! We aim to use more than 350 nuclear protein-coding genes to assess:

  1. How does age and method of preservation affect sequence recovery?
  2. What is the level of sequence variation within genera at these markers?
  3. Can the markers be used as a new method of “barcoding” useful for unidentified specimens?

At Texas Tech, we also aim to characterize the genetic diversity of species native to West Texas and surrounding areas using local collections from the early 20th century.

For more information about the Angiosperms353 kit, see our paper in Systematic Biology. The kit is available for purchase from Arbor Biosciences.

Image: Specimen of Portulaca pilosa (Portulaceae) collected on the campus of what was then Texas Techological College in 1925!