Research in the Raubeson Lab

We are interested in plant systematics, evolutionary genetics and comparative genomics. We use DNA-based approaches to address our questions. Primarily our efforts are directed towards developing hypotheses of seed plant relationships (especially within the gymnosperms) and understanding patterns and processes of molecular evolution in the chloroplast genome. Some of our work involves collaborations with scientists at other institutions. Our research has been funded by the National Science Foundation, Central Washington University, the Murdoch Foundation, and the Washington Native Plant Society. Our lab is comprised mostly of undergraduate researchers although students interested in earning a master's degree through work in the lab are encouraged to inquire.

Comparative Chloroplast Genomics

Within the chloroplast is found one of three plant genomes. Usual examples of this genome, within seed plants, range from 120,000 to 160,000 base pairs and contain about 120 genes. Thus (given sufficient funds and the involvement of a sequencing facility) it is tractable for undergraduates to completely sequence and then characterize these genomes. We have been collaborating with scientists at the Joint Genome Institute, University of Texas Austin and other institutions to generate complete sequence data from a number of seed plant chloroplast genomes. Our contribution to this effort has mostly focused on gymnosperms although we wander into the angiosperm world periodically. We are interested in exploring how the genome evolves in terms of both nucleotide change and genome organization. We are also using the distribution of changes at both levels to support phylogenetic hypotheses within seed plants. To learn more about this work, explore the project web site.

Seed Plant Phylogeny

Many aspects of the relationships of seed plants are uncertain, from the overall pattern of relationships among the major extant lineages to the fine scale relationships within families or genera. We use genomic rearrangement and sequence data in our attempts to clarify aspects of the seed plant phylogeny. Some of this work takes place as part of our chloroplast genomics work, some independently, plus some of our future work will take place in the context of a new collaborative project "Gymnosperms on the Tree of Life: Resolving the Phylogeny of Seed Plants". To learn more about this new collaboration, see the GToL web site.

Joining the Lab

If you are a motivated Central undergraduate, interested in participating in this research contact Dr. Raubeson or one of the other current lab members for more information. You should be able to dedicate a minimum of six hours a week to your research project if you expect to make any real progress. Students obtain credit for their research involvement by enrolling in BIOL496, Independent Study.

If you are interested in working on your Master's Degree in Biology under Dr. Raubeson's supervision, contact her via email, describing your background and possible projects of interest to you.

 

Current Lab Members -- more photos in the scrapbook

 

Jianing Yu (Jenny), 06-07 Visiting Scholar, Associate Professor at Shaanxi Normal University

Jenny is working with us to complete and analyze gymnosperm chloroplast genomes. She also is investigating RNA editing in the plastid genomes of Araucaria heterophylla and Ginkgo biloba. When she's at home in China she works on the molecular biology of plant stress responses.

 

Rhiannon Peery, Graduate Researcher (M.S. 2005), Research Technologist I

Rhiannon joined the lab in Summer 2002. Since then she has completed and successfully defended her master's thesis: " Post-glacial recolonization of Tsuga heterophylla". In addition to the phylogeographic work she did for her thesis project, Rhiannon worked on the chloroplast genomic project as a graduate research assistant and, since completing her degree, has continued to be involved in aspects of our comparative genomics research. She has contributed to the completion and analysis of the Nuphar, Ranunculus, and Acorus genomes and is currently working on three genomes from the Apiaceae. She is also managing our sequencing efforts for the Gymnosperm Tree of Life (ToL) project.

 

Stephanie Margheim, Undergraduate Researcher, STEP Program, since Fall 2005

Stephanie has worked to characterize the distribution of chloroplast genome rearrangements in the conifer family Pinaceae. She was a member of the lab in the 2005-6 academic year conducting her Sophomore year research sponsored by the Science Talent Expansion Program (STEP) at CWU. She has continued in the lab working most recently on comparing plastid genomes from closely related plants.

 

 

Skip McCoy, Undergraduate Researcher, Science Honors Research Program, since Winter 2006

Skip began his research characterizing the chloroplast genome of the gnetalean Welwitschia mirabilis winter quarter 2006. He successfully applied to the CWU Science Honors Research Program for support to continue his research through Spring of 2007. He is also contributing to seed plant phylogenetic analyses based on 61 genes from the chloroplast genome and is working on completing his second chloroplast genome from Ephedra.

 

Jayne Johnston, Undergraduate Researcher, since Spring 2006

Jayne first worked as part of a team to complete the Cryptomeria japonica chloroplast genome. She is now investigating rearrangement characters shared among gymnosperm plastomes.

 

Kelli Lackey, Undergraduate Researcher, since Spring 2006

Kelli was part of the team that completed the Cryptomeria japonica chloroplast genome. She is now investigating rearrangement scenarios related to the loss of the inverted repeat in conifers.

 

Nikki Murphy, Undergraduate Researcher, Sp 2005 & since Fall 2006

Initiated work and developed PCR strategies to determine distribution of gene order changes in Pinaceae. Currently working on a pollen imaging project.

 

 

 

Ashley Dutton, Undergraduate Researcher, STEP Program, since Fall 2006

Ashley, along with Cristy Bunnell, is working on the completion of three cycad chloroplast genomes. Ashley is primarily responsible for completing the plastome of Dioon edule. She is also generating cycad VPCR data for the Gymnosperm ToL project.

Cristy Bunnell , Undergraduate Researcher, since Fall 2006

Cristy, in collaboration with Ashley Dutton, is investigating chloroplast genome evolution in cycads. Cristy is primarily responsible for the plastid genome of Zamia integrifolia.

Kevin Wilcox, Undergraduate Researcher, since Spring 2007

Contributing to the sequence effort for the Gymnosperm Tree of Life Project.

Jamie Petersen, Undergraduate Researcher, since Spring 2007

Contributing to the sequence effort for the Gymnosperm Tree of Life Project.

Jessica Garrity , Undergraduate Researcher, since Spring 2007

Contributing to the sequence effort for the Gymnosperm Tree of Life Project.

Chris Escott (far left), Undergraduate Researcher Spring 2006, Research Assistant since Fall 2006

Chris started in the lab as part of the team finishing the Cryptomeria japonica plastome (that's the team pictured -- Chris, Kelli, Jayne and Jack). This year Chris has served as Rhiannon's trusty assistant and generally helps keep the lab up and running.

 

 

 

Former Lab Members [let us know what you're up to!] Also check out the Photo Gallery

 

Chris Dzuibek, Undergraduate Researcher, Sp 2005, 2005-6 Academic Year

Chris performed a detailed nucleotide-level comparison of the Nuphar and Nymphaea chloroplast genomes. Along with other more predictable results, he found that some non-coding regions of the genome evolved more slowly than some protein-coding genes. He also investigated codon usage patterns in Nuphar.

Josh Leigh , Undergraduate Researcher, W - Su 2006

Josh's primary project was the completion of the Ginkgo chloroplast genome. Among his more interesting findings -- a large gene has been lost from one copy of the inverted repeat and trnC has been tandemly duplicated (6 copies some partial). He also contributed to the completion of the Welwitschia and Cycas genomes.

Nichole Fine , Undergraduate Researcher, Sp03-W05

Nichole generated mitochondrial (nad5 intron) and chloroplast (atpB,atpE) sequence data to investigate generic level relationsihps in the conifer family Podocarpaceae.

Melissa Phillips , Undergraduate Researcher, Sp03-W04

Melissa compared the plastome trnH-psbA intergenic region among numerous conifers particularly those from the Podocarpaceae and Araucariaceae in an attempt to determine the nature and pattern of insertion-deletion mutational events. About half of the events could be characterized as a form of slip-strand mispairing but the mechanism giving rise to the remainder could not be determined.

Peter Feysa , Undergraduate Researcher, Sp-Su03

Peter characterized the remant inverted repeat in the chloroplast genome from five members of Pinaceae.

Kathy McGinnis, Undergraduate Researcher Sp02- W03

Kathy's research involved using SSR analysis to detect somatic mosaicism in long-lived tree species. Kathy is currently working on her PhD in pharmacology.

Sallie Herman, Graduate Researcher (M.S. 2002) F99-Su02

Sallie investigated the level of genetic diversity retained in a rare endemic buttercup species (Ranunculus triternatus a.k.a. R. reconditus) using a RAPD approach and comparison to the widespread related species Ranunculus glaberrimus. Somewhat surprisingly, the rare species had much higher levels of variation than the widespread species. Sallie currently splits her year between working for the Forest Service and helping to launch an ecological preserve in Mexico.

Laurie Schneble, Undergraduate Researcher, Su-F00

Distribution of genome rearrangements in Podocarpaceae

Andrea Oestreich , Undergraduate Researcher, F99-Su00

Andrea generated sequence data from the chloroplast gene matK for 18 representatives of the angiosperm family Campanulaceae, which she analyzed phylogenetically in combination with data from rbcL and atpB.

Mira Mishkin, Undergraduate Researcher, F99-Sp00

Genetic diversity in a rare buttercup species.

Vickie DiMaggio, Undergraduate Researcher, W97-Su99

Vickie applied a PCR-RFLP strategy to investigate relationships with the conifer family Araucariaceae. She also generated sequence data to determine the distribution of the remnant inverted repeat in conifer chloroplast genomes.

Brad Smith , Undergraduate Researcher, F99

Assisted with ongoing projects.

Fred Schmitt , Undergraduate Researcher, Su98, W-Sp99

Assisted with ongoing projects.

Ryanne Fry , Undergraduate Researcher, W99

Developed and applied a PCR strategy for determining gene order patterns in chloroplast genomes of Podocarpaceae.

K-T Oxford, Undergraduate Researcher, W-Sp97

Assisted with ongoing projects, particularly IR extent in seed plant chloroplast genomes.

Tami Sawyer, Undergraduate Researcher, Su96-W97

Assisted with ongoing projects, particularly IR extent in basal angiosperm chloroplast genomes..

 

Links

DOGMA (tool to aid in annotating chloroplast and animal mitochondrial genomes)

NCBI (various tools that we use a lot even if occasionally we wished they worked better)

EMBOSS (suite of bioinformatics tools)

ClustalW (one of many ports to this alignment tool)

MUSCLE (an alignment alternative)

MULAN (graphic genome comparison tool, not the Disney movie)

Chloroplast genome data base (dePamphilis Lab, Penn State)

GOBASE (The Organelle Genome DataBase, Montreal)

 

 

 

 

 

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