DNA sequencing institute

Mapping a Plant Genome

  • December 3, 2019

With nimble fingers and hyper-focused attention, Cal State East Bay graduate student Alisa Mathewson uses tweezers to gently break off a piece of fungus from one petri dish and add it to another. 

There, it will bloom, creating an intricate floral design filling the bottom of the dish. In a few weeks, Mathewson will begin sequencing the fungus’ DNA, mapping its genome down the genus. Data gathered will help her and other scientists worldwide begin creating a phylogenetic tree which will help determine if and how the fungus — which was harvested from the leaves of manzanita — can bolster the plant’s immunity. The process is tedious. But the work is rewarding, carrying the potential to yield results scientists can only imagine. 

Mathewson is a student working at Cal State East Bay’s newest institute, the Green Biome Institute. The institute, which will be housed in the forthcoming Applied Sciences Center, was seed-funded through a gift from alumnus and Cal State East Bay Educational Foundation member Randy Davis (BS '02 Biological Sciences; MS '06, Biological Sciences) and his wife Pat as part of the university’s first comprehensive capital campaign, Rising in the East. 

GBI is the first institute of its kind in the California State University and University of California systems. 

Its goal? 

To help preserve the genetic diversity of plants in California, contribute to the discovery of new and useful biological processes that can improve human lives, and create publicly-available molecular profiles of endangered native California plants. 

Researchers will ask: What if an endangered plant could help cure cancer, improve drought tolerance, or survive poor soils? How do we protect and preserve it before it’s gone? 

"The world of endangered plants has long been ignored, and the GBI positions Cal State East Bay at the forefront of this critical and cutting-edge research,” Davis said. 


DNA sequencing is not new for Cal State East Bay. Beginning in 1996, advanced DNA sequencing has been taught at both the undergraduate and graduate levels in the College of Science, and since then, 300 students have graduated from the university's highly-competitive BioTech program.

One of those graduates? Davis. During a career in the semi-conductor industry, Davis saw his first DNA microarray (or DNA detection chip) while on a sales visit at Hewlett-Packard. It was the late 1990s, and HP was preparing to launch one of the very early DNA microarray scanners. Fast forward to 2014, Davis is the co-founder of Genia Technologies, which was purchased by Roche in 2014 for its innovative electronic DNA sequencing chip.

He hopes his gift and involvement with GBI will help students not unlike himself find where their passions intersect with the industry’s need for diverse, skilled employees.

"The Bay Area has always been at the forefront of DNA sequencing, with the first automated DNA sequencer being developed in Foster City by Applied Biosystems in the late 1980s."

According to the U.S. Bureau of Labor Statistics, California is projected to have nearly 10 percent of the nation’s STEM jobs by 2022. Labor trends predict job growth in health, biomedical and environmental industries by an average of 33 percent over a 10-year span. 

Whether as biologists conserving and genetically preserving endangered plants that may hold the key to curing disease or biochemists who discover formulas for more affordable medications, Cal State East Bay graduates have the potential to influence their communities regionally, throughout the state and around the world.

"The Bay Area has always been at the forefront of DNA sequencing, with the first automated DNA sequencer being developed in Foster City by Applied Biosystems in the late 1980s,” said Kevin Corcoran, vice president, and general manager at Agilent Technologies. “Students are always looking for a sense of what they will be doing once they graduate and join the industry. The GBI will allow them to do meaningful research and provide relevant hands-on education using cutting edge techniques for DNA sequencing and genetic analysis." 


For Mathewson, and many of the other GBI students and the faculty supporting them, finding purpose within the science they study is essential. Yes, there is value to finding out if there are more efficient ways to grow edible plants for food, and yes, there is money in finding out whether another plant can cure cancer. But, there is also the knowledge that by mapping a genome, researchers could be unlocking the key to preserving endangered native California plants.

"We know endophytes aid in plant immunity, we know they help the plant survive and increase its immunity, so I want to know how we can better understand this, especially for the manzanitas that are endangered," Mathewson said. 

For Davis, aside from the science, he’s excited Cal State East Bay students will now have a chance to find their place in the biotech world. A place where their interests align with industry needs and have the potential to unlock solutions to the problems our world will face in the coming decades. 

"It is a great thing to help people realize their dreams," Davis said. "There's nothing better than bringing a group of like-minded, curious people together to ask important questions and, if you're lucky, gives students a chance to do hands-on research that has the potential to change lives." 



What type of classes do you teach? 

First year molecular biology and senior level lab classes in molecular biology techniques and PCR/DNA sequencing 

What is your research area of focus? 

Genome Evolution in the Liliaceae (flowering plants within the lily family) 

What will your involvement with GBI be? 

Director of GBI and active researcher 

What are you most excited about for GBI? 

This is an opportunity to apply advanced molecular techniques to answer important questions in evolutionary biology. This will also provide very high-level training for our students, both undergraduates and graduates. 

What do you want people to know about GBI? 

Cal State East Bay is doing highly sophisticated research in plant biology, working with rare and endangered species.


What classes do you teach? 

Mostly, I teach evolution, molecular biology, and genomics, as well as graduate courses on science communication and foundations of scientific research.

What is your research area of focus? 

My research focuses on plant development and evolution. I use molecular techniques to understand how developmental processes change over evolutionary time, and how these changes affect the form and function of plant structures, ultimately resulting in the diversity of forms we see in nature.

What will your involvement with GBI be? 

My research group and I generate and analyze genomic, transcriptomic, epigenetic and microbiome data for endangered plant species. At the moment, we have been mostly focusing on several species of manzanitas endemic to California.

What are you most excited about for GBI? 

I'm most excited about the amazing opportunities for mentoring students in cutting-edge molecular techniques and data analysis. I strongly believe these skills will greatly improve students' competitiveness in the job market once they graduate.

What do you think people need to know about GBI or the research you do? 

I think GBI embodies a unique opportunity for combining excellence in research and teaching at Cal State East Bay while at the same time helping gather important information about California's endangered plant species. It is a win-win-win initiative of education, research, and environmental conservation.


What classes do you teach? 

Fungal biology, fungal diversity, plant biology, population biology, evolution, and phylogenetic methods 

What is your research area of focus? 

My research program focuses on fungal systematics, evolution and diversity. 

What will your involvement with GBI be? 

I am currently one of the associate directors of the institute. My students and I will be studying the fungal microbiomes that are associated with our target plant species. All plants harbor fungi within their leaves and other tissues, known as endophytes. My students will be documenting the composition and dynamics of endophyte communities within the leaves and other plant tissues. Additionally, we will eventually be looking at the fungal communities present in the soil that interact with the plant roots. 

What are you most excited about for GBI? 

For me, the most exciting thing about the GBI is that we are providing our students with unparalleled opportunities to work as a team to both document and understand “whole-plant” biology using some of the most current, cutting edge technologies in molecular biology. To my knowledge, no other group of researchers with diverse backgrounds, training, and areas of specialization are working together with students in such a holistic approach to understanding plant biology. The GBI researchers are truly working from the ground up and from the inside out to understand our target plants and their ecological interactions. 

What do you think people need to know about GBI or the research you do? 

I really want people to understand the importance of the work our students are doing. Our target plant species are all considered rare, threatened or endangered. The data and results that our students generate have the potential to truly change the management and conservation approaches we take to managing and conserving these organisms.


During the next several years, Cal State East Bay students and faculty will be mapping the following plants’ genetic profiles: 

Prosartes parvifolia (Siskiyou Bells) **

Arctostaphylos pallida (Oakland Hills, Alameda Manzanita)**

Scoliopus bigelovii (Fetid Adder’s Tongue or Slink pod)

Carex albida (White Sedge) 

Abronia alpina (Ramshaw Meadows Sand Verbena) **

Calochortus raichei (Cedar’s Mariposa Lily)**

Fritillaria liliacea (Fragrant Fritillary)**

Lilium maritimum (Coast Bog Lily)**

Arctostaphylos species one (Manzanita Genus)**

 ** Endangered