American Campus Tree Genomes
Empowering students through hands-on research of iconic campus trees
Genome sequencing is a rapidly evolving set of technologies that requires an even faster-evolving set of bioinformatic skills to analyze such massive datasets in plant biology. The ACTG: American Campus Tree Genomes initiative was founded on the idea that iconic trees can serve as a gateway for students to interact with the latest genome sequencing technologies and integrate them into collaborative cohorts where they authentically assemble, analyze, and publish these genomes in high-quality journals. In doing so, we immortalize these trees and create opportunities for students to advance their careers with new bioinformatic skills and publications, reducing the barriers that have prevented some students from entering and staying in STEM fields.
Founded in 2021 by Dr. Alex Harkess at HudsonAlpha and Dr. Leslie Goertzen at Auburn University, ACTG is a community resource that provides a curated set of curricula for diverse genome assembly courses (e.g. short-courses, semester-long courses), with the goal of publishing organellar and nuclear genomes in GenBank and manuscript publications with all participants as co-authors.
Our goal is to train thousands of students in cutting-edge genome sequencing technologies and bioinformatic techniques and actively update courses as new technologies emerge. The ACTG project became broadly reproducible thanks to Dr. Stephen Fickling and Dr. Huiting Zhang at Washington State University, who released online documentation and Docker containers for the course. ACTG has recently expanded to animals with a sister project, Campus Mascot Genomes, led by Dr. Ellie Armstrong at UC Riverside.
This project is funded by an NSF CAREER award to Alex Harkess, support from HudsonAlpha Institute for Biotechnology, corporate sponsorship from PacBio for flow cells, and the Genetics Society of America to provide reduced publication fees in G3: Genes, Genomes, Genetics.
We will help you generate all of the short-read and long-read genomic data necessary for this course on-site at the HudsonAlpha Genome Sequencing Center, guide the training of the instructors, and help with in-class assistance when possible.
We have a dedicated program manager who will help modify the curriculum for your university’s cluster or cloud compute, generate the necessary data at HudsonAlpha, assist in guest lecturing, moderate the shared Slack workspace, help with bioinformatic tasks and issues, and ultimately drive the production of the genome manuscript.
In many cases, we will be able to cover some or all of the associated costs of data generation and publishing, and we can assist in fundraising efforts around these iconic tree and mascot genomes.
Courses should be thought of as immensely flexible and can range from one-day short courses to semester-long classes. We have example syllabi that cover some of the most common course types, and we will work with you to structure your course with the appropriate amount of material for the audience size and background knowledge.
Currently, we recommend generating at least these four data types for a typical semester-long genome project course:
- PacBio Revio HiFi reads, at least 30X coverage per haplotype for a typical diploid
- Dovetail Omni-C, at least 30X coverage per haplotype
- Illumina TruSeq PCR-free DNA shotgun sequence, at least 30X coverage per haplotype
- Illumina TruSeq Stranded mRNA-seq, at least four diverse tissue types, 25M read pairs each
- Illumina short-read and PacBio HiFi long-read sequencing data quality control
- Organellar genome assembly (plastid, mitochondria)
- Haplotype-resolved nuclear genome assembly
- Hi-C scaffolding and manual assembly curation
- Repetitive element annotation
- Gene annotation
- Comparative genomics and synteny visualization
- Variant calling and filtering
- Basic unix command line operation
- Basic shell scripting, loops, and error handling
- Docker containers
- Navigating a university compute cluster or Amazon AWS
- PhD students and Postdocs are encouraged to TA courses and drive manuscripts forward as first authors
- Students work closely as a cohort, transforming a classroom into a collaboration
- Access to a shared Slack workspace that connects all students and instructors for networking, collaboration, and problem-solving
- Tiger Giving Day fundraising ($10,770): https://rise.auburn.edu/project/25030
- “Auburn Oak leaves enter the DNA sequencing pipeline” https://www.auburn.edu/cosam/news/articles/2021/05/auburn_oak_leaves_enter_the_dna_sequencing_pipeline.htm
- HudsonAlpha Tiny Expeditions podcast episode “Will science emerge as the real champion in a football rivalry gone wrong?” https://www.hudsonalpha.org/will-science-emerge-as-the-real-champion-in-a-football-rivalry-gone-bad/
“Horticulture students assemble Cosmic Crisp™ apple genome” https://news.wsu.edu/news/2022/11/30/horticulture-students-assemble-cosmic-crisp-apple-genome/
- USCA Biology Projects Research Fund ($10,000 raised) https://giving.usca.edu/sfp/usca-palmetto-project
- “USC Aiken biology students use cutting-edge technology to sequence DNA of the South Carolina state tree” https://www.usca.edu/stories/entry/news/2023/10/09/usc-aiken-biology-students-use-cutting-edge-technology-to-sequence-dna-of-the-south-carolina-state-tree-1
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- Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae https://academic.oup.com/g3journal/article/14/4/jkae034/7608880
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- Using genomics to immortalize and protect McCarty Woods on UF Campus https://www.hudsonalpha.org/using-genomics-to-immortalize-and-protect-mccarty-woods/
For more information or to inquire about developing a course around your tree or mascot genome, please contact:
Alex Harkess (plants) – aharkess@hudsonalpha.org
Ellie Armstrong (animals) ellie.armstrong@ucr.edu