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Watch a summer undergraduate research experience in the Biotechnology Program at NC State. Undergraduate researcher Thomas Morgan compiles a de novo genome for Butterfly Weed in the BIT SURE program working with Dr. Carly Sjogren.
This video was filmed, produced, generously provided by and stars Thomas Morgan: NCSU BIT SURE REU 2022 student researcher.
research projects:
research projects:
Agricultural yields, which we depend upon to feed humanity, are a direct result of stem cell function in plants. Plant stem cells continuously proliferate throughout an entire life cycle to generate new organs like the roots, leaves, flowers, and fruits we consume. The molecular mechanisms that regulate these processes must be better understood in order to increase crop production and assure global food security. For over a decade I used the genetic plant model species, Arabidopsis thaliana, to uncover a greater understanding of how this plant grows and develops. Now I apply these lessons to crop species to learn more about plant diversity and to contribute to enhancing global food security.
Arabidopsis meristems
Arabidopsis meristems
Figure from Sjogren et al. 2017.
Crop transcriptomics
Crop transcriptomics
Images taken by Carly Sjogren 2021
de novo genome assemblies of NC native plants
de novo genome assemblies of NC native plants
Image taken by Thomas Morgan 2022.
Scientific research is people powered
Scientific research is people powered
I have been mentoring undergraduate researchers since 2010 to carry out plant genetic investigations with me. Over this exciting time of discovery I have mentored over 25 undergraduate researchers who have gone on to join the STEM workforce! Currently my research is supported by the wonderful BIT Program resources, I am able to hire undergraduate researchers every summer to carry out plant DNA or RNA sequencing projects. You can learn more about my ongoing research projects (crop transcriptomics project and de novo genomes project) below. Apply for the upcoming Summer Undergraduate Research Experience in the Biotechnology Program (BIT SURE) and tell me about your crop species of interest!
de novo genome assemblies of NC native plants
de novo genome assemblies of NC native plants
The goal of this project is to increase the genetic diversity of sequenced plant genomes in order to better understand plant development and evolution. As we generate more plant genomes as resources for the plant biology research community, we will gain a better understanding of the evolutionary origins or traits that regulate development. Student researchers will select a North Carolina native or endangered plant, collaborate with government agencies and conservation specialists, collect tissue for DNA extraction following wildlife conservation guidelines, and perform de novo genome assembly using our Nanopore MinION bench top sequencer! This is a brand new project without previous data to build upon and with unfettered potential to create something brand new! These exciting plant genetic discoveries can be applied to the development of genetically engineered crops that can help increase crop yields, combating food insecurity and improving the human condition. Interested? Apply for the upcoming Summer Undergraduate Research Experience in the Biotechnology Program (BIT SURE) and tell me about your crop species of interest!
Genome of Asclepias tuberosa (butterfly weed) was sequenced during BIT SURE 2022.
Crop transcriptomics research
Crop transcriptomics research
Identifying relationships of gene networks that regulate stem cell development across multiple plant species resulting in desirable over proliferative traits can uncover new approaches to sustainably increase food stability in an era of climate change. This project generates novel plant RNA-seq data sets that are used in BIT 495/595 Comparative Plant Transcriptomics (BIT CPT) to carry out Linux-based bioinformatic analysis for transcriptomic comparisons.
Student researchers will identify a crop species to grow, collect tissues for RNA extraction, and gain the bioinformatic skills to analyze RNA-seq data as is done in BIT CPT. Currently working with Arabidopsis thaliana, Helianthus annuus (Sunflower), Solanum lycopersicum (Tomato), Lactuca sativa (Lettuce), Gylcine max (Soybean) and (Rabbiteye Blueberry). What species will be next? New crop selections are chosen by BIT SURE researchers and are limited by being: diploid, self-fertile, genome size under 5 megabases, and being able to grow in a lab growth chamber. Interested? Apply for the upcoming Summer Undergraduate Research Experience in the Biotechnology Program (BIT SURE) and tell me about your crop species of interest!
Transcriptomes of Lettuce, Sunflower and Tomato were sequenced during BIT SURE 2021. Transcriptomes of Soybean were sequenced during BIT SURE 2022. Up next: Rabbiteye Blueberry!
meristem research
meristem research
During my doctoral research I uncovered novel and unexpected insights regarding a critical agricultural problem, root growth inhibition due to the depletion of stem cells from aluminum toxicity. Through a mutagenesis screen, I isolated and characterized two suppressor mutants that were both caused by mutations in cell cycle checkpoints. My research has been published in The Plant Cell, Plant, Cell & Environment, and The Plant Journal, won the Faculty of 1000 Best Poster Presentation award at the 2014 Plant Genome Stability and Change Conference, and comprised the preliminary data that won an NSF-funded ERA-CAPS international collaboration.
Figure from Sjogren et al. 2016. showing stem cell depletion in presence of Aluminum (stem cells molecularly marked in blue).
As a postdoctoral researcher I focused on the developmental signaling pathways in pluripotent stem cells in plant shoot apical meristems. My research aimed at understanding stem cell regulation, where I conducted yet another mutagenesis screen. I used a cutting edge genomics mapping approach called mutagenomics to isolate and map over over fifty putative suppressor mutations that regulate stem cell maintenance. Using a synthetic biology approach I also uncovered and translational networks in the CLAVATA signaling pathway. I was named a 2019 Sharon Gray Women's Young Investigator award from the American Society of Plant Biologists.
From left to right: wlidtype Ler, and over proliferation mutants clavata1-4 and clavata3-2. Note the mutants' enlarged size and overproduction of fruits.
Images of Arabidopsis plants taken by Carly Sjogren.
Research Publications
Research Publications
Chen, P, Sjogren, CA, Larsen, PB, and Schnittger, A. (2019). A multi-level response to DNA damage induced by Aluminium. The Plant Journal. doi: 10.1111/tpj.14231.
Sjogren, CA, and Larsen, PB. (2017). SUV2, which encodes an ATR-related cell cycle checkpoint and putative plant ATRIP, is required for aluminium-dependent root growth inhibition in Arabidopsis. Plant, Cell & Environment 40(9):1849-1860. doi: 10.1111/pce.12992.
Sjogren CA, Bolaris SC, Larsen PB. (2015). Aluminum-dependent terminal differentiation of the Arabidopsis root tip is mediated through an ATR-, ALT2-, and SOG1-regulated transcriptional response. Plant Cell (9)2501-15. doi: 10.1105/tpc.15.00172.
Sjogren CA and Larsen PB. (2015). Aluminum-dependent root growth inhibition as mediated by DNA damage machinery. “Aluminum Stress Adaptation in Plants:” Chapter 3; Signaling and Communication in Plants; Springer Publishing.
Nezames CD, Sjogren CA, Barajas JF, Larsen PB. (2012). The Arabidopsis cell cycle checkpoint regulators TANMEI/ALT2 and ATR mediate the active process of aluminum dependent root growth inhibition. Plant Cell (2):608-21. doi: 10.3389/fpls.2018.00118.
This page was last updated by CAS August 2022.
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