Research Boot Camp - Sequencing the Marsh Elder Plant Genome
For the past two years, the interns’ Boot Camp experience has allowed them to work with an international team of scientists studying genomic changes during the process of plant domestication. Funded through a National Science Foundation research grant to decode ancient DNA of the Sunflower (Helianthus annuus), our students are working in parallel to sequence the first genome of a related plant, the Marsh Elder (Iva annua). The students receive special guest lectures and interactive discussions (some via video conferencing) on the project from anthropologists at the NMNH and Ohio State University, from plant domestication researchers at the University of California, Berkeley (UCB), and they learn about ancient DNA from the famous Gilbert Lab at the University of Copenhagen, Denmark. In 2014 the students ran genomic DNA of the Marsh Elder on an Ion Torrent Personal Genome Machine (PGM) to recover nearly 3 million reads (or fragments) of DNA sequences ranging from 200–300 base-pairs (bp) in length. Last year’s students ran genomic DNA of the same Marsh Elder plant on the Illumina MiSeq to recover nearly 20 million paired-end reads—sequenced in both directions—to re-assemble into ~600 bp in length fragments. With these data, the scientists hope to reconstruct as much of the Marsh Elder genome as possible, to compare with the ancient DNA during domestication, and with the Sunflower genomes (both ancient and contemporary domesticated plants).
The following YES! GGI student projects are a sample from 2013 – 2015:
Testing Field Preservation Methods for Plant DNA
Three methods of preservation are commonly used to collect plants for research, 1) drying plants in a plant press for classic museum specimens, 2) freezing tissues in liquid nitrogen, and 3) desiccating tissues with silica gel. The latter two methods are used to capture and preserve plant DNA. Using the same specimens to compare preservation methods, this project preserved plant tissue with liquid nitrogen and silica gel and then examined the quality of the DNA that was recovered. The research will continue over time to see whether DNA decomposes more rapidly with silica gel preservation versus being immediately frozen in liquid nitrogen. Silica gel is less expensive and somewhat easier to take into the field than liquid nitrogen.
Arthropod Diversity in Myanmar (Burma)
Arthropods are so diverse, it is estimated they account for 80% of the diversity of life on Earth, so it takes many experts to identify most arthropods to the genus or species and often the family level. A recent collecting expedition to Myanmar collected arthropods from two forest preserves. The specimens were brought back to the National Museum of Natural History and sampled for DNA Barcoding. The barcodes were used to find matches in GenBank, the genome sequence repository at the National Center for Biotechnology Information. When matches were found, the specimens could be more easily identified without requiring arthropod specialists for each taxonomic group.
Using DNA Barcoding for Conservation of Amphibians and Reptiles in Myanmar (Burma)
Frogs, lizards and snakes were collected in remote protected areas of Myanmar, shipped to the National Museum of Natural History and tissues were processed for DNA Barcoding. DNA analysis through barcoding, or sequencing areas of mitochondrial DNA, revealed cryptic species that look alike physically, but are genetically distinct, and helped researchers understand the geographic distribution of species. The amphibian and reptile biodiversity is rich in this poorly known area of southeast Asia; several new species were discovered during this expedition.
Genomic Era: Systematics of Demosponges
Sponges are important organisms in reef systems and on the ocean floor. The goal of this project was to add to our knowledge of the evolutionary history of sponges by adding genomic support to the sponge phylogenetic tree and to place new species onto the tree. Next Generation Sequencing was used to sequence complete mitochondrial genes to identify genes that, in combination, can discriminate closely related species and reveal evolutionary relationships among sponges.
YES! Youth Engagement through Science