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The Joshua Tree Genome Project

Backed by Willamette University, J B Yoder, Naomi Pierce, Teresa Vanderburg, Barbara Cole, Glenn Svensson, Jennifer Chambers, Wendy Williams, Kendra Mingo, Dan Chitwood, and 274 other backers
Willamette University
Joshua Tree National Park, California
BiologyEcology
Tax Deductible
DOI: 10.18258/6534
Grant: Liberal Arts College
$10,643
Raised
124%
Funded on 3/25/16
Successfully Funded
  • $10,643
    pledged
  • 124%
    funded
  • Funded
    on 3/25/16

About This Project

Joshua trees are perhaps the strangest plants in the world. Their long, spindly branches form twisted candelabras that have become an iconic image of the western American landscape. Ecological modeling suggests that global warming could drive Joshua trees to extinction. We propose to sequence the Joshua tree genome. This powerful research tool will help identify genes that have allowed Joshua trees to adapt to desert environments, and which could help them survive climate change.

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What is the context of this research?

A keystone species of the Mojave Desert, Joshua trees provide habitat for many other species, and there are numerous state and National Parks dedicated to their preservation. Unfortunately, ecological modeling suggests that, due to global warming, many populations are likely to go extinct.

Recent advances in DNA sequencing technology have made it possible to cheaply and efficiently generate genome sequence data. This makes it possible to explore the genetic bases of many features in many different organisms. We will use the Joshua tree genome to identify genes that allow Joshua trees to survive extreme environments. This will inform management strategies to help Joshua tree populations persist in the the face of climate change.

What is the significance of this project?

The Mojave Desert contains the hottest and driest regions of North America. To survive in these inhospitable environments, Joshua trees have developed many physiological adaptations. Sequencing the Joshua tree genome will reveal the genetic basis of these adaptations, and identify strains that may allow Joshua trees to adapt to climate change.

Also, Joshua trees rely on yucca moths for pollination. The moths actively pollinate the trees and lay eggs in the flowers. The eggs become caterpillars that eat some of the seeds. So, the trees pay for pollination by sacrificing seeds to the moths’ larvae. Joshua tree flowers are adapted to promote pollination while limiting the number of seeds that get eaten. Sequencing the genome will identify genes involved in coevolution with yucca moths.

What are the goals of the project?

This project is the first stage in an effort to completely sequence the Joshua tree genome. Ultimately we hope to produce a completed, assembled and annotated reference genome sequence. This phase of the project will involve shotgun sequencing on an Illumina HiSeq platform. This process will produce about 700 million snippets of DNA sequence data. These data will provide useful baseline information about the Joshua tree genome, such as the total amount of genetic variation (heterozygosity), and how much of the genome is composed of large repetitive regions. The data will also be used to complement sequencing to be generated in the next phases of the project, which will involve PacBio sequencing, BioNano optical mapping, and reference based annotation using RNA-seq.

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This project represents the first stage in an effort to completely sequence the Joshua tree genome.

The initial phase involves two steps: library preparation and whole genome sequencing and analysis. We will extract DNA from leaves collected from a single Joshua tree, and prepare whole genome sequencing libraries. This involves fragmentation of the DNA and ligation of special ‘adapters’, bits of synthetic DNA, to the Joshua tree DNA for amplification and sequencing on the Illumina HiSeq 2500 platform.

This initial stage of the project will produce about 105 billion bases of sequence data, enough to read the Joshua tree genome about 35 times over (~35X coverage). These data will tell us about the complexity of the Joshua tree genome, and allow us to characterize repeat content, gene copy number variation, and genetic variation in the genome. This will pave the way for full assembly of a reference genome using PacBio sequencing, BioNano optical mapping and genetic mapping technologies.

Endorsed by

The Joshua Tree is the most dramatic plant in the Mojave Desert, and is a close relative both of yuccas and of lilies. JT is emblematic of the California deserts and is a feature of countless westerns. A sequence of this genome would provide a platform for studying both JT and related plants, and particularly for investigating JT's amazing tolerance to heat and drought. Knowledge of how plants adapt to heat stress is becoming ever more valuable.
This project will produce a very high quality reference genome critical to the understanding their extreme physiological and pollination adaptations. This study also allows for the international scientific community to understand the evolution of Yucca and related succulents. This reference genome will help us understand why there are so many recently evolved species in all these groups, their adaptations, and, why the agaves are useful to produce the traditional drinks of tequila and mezcal.
Drs. Jim Leebens-Mack and Michael McKain are long-time collaborators both with strong expertise in genome assembly and analysis. The Joshua tree genome would be integral in furthering our understanding of co-evolution between insects and plants, a primary factor in generation of biodiversity in both groups.
It is my my pleasure to be able to endorse this work – it is a good project and a great team!
Willamette University is thrilled to support the Joshua Tree Genome Project, a research venture with the potential to define conservation paradigms in the face of climate change, enhance public perception of science, and inform public policy. Chris has been very successful in building an internationally-recognized research program that involves undergraduates and members of the public as equal partners in the work. We’re excited that Chris is extending the reach of his research program to an even larger audience through crowd-funding and social media.
We have entered an exciting new era where we can cost effectively sequence and assemble very large genomes. This allows us to move beyond sequencing model species. Joshua trees have a spectacular phenotype and a bimodal karyotype. They coevolve with their specialist pollinator, yucca moths. This evolutionary interaction is one of the best studied on the planet. The project employs the latest genome sequencing technologies, and the PIs are first rate scientists. I have no doubt that a high quality reference sequence will emerge from this effort.
Joshua trees are keystone features of the Mojave Desert flora, yet little is know of their biology. Their genomes include over 3B nucleotide base pairs. This is the first step towards assembly of a reference genome for all yuccas and closely related agaves. This research team collectively has 60+ years of research experience with yuccas and agaves. The Joshua Tree Genome Project is certain to make major contributions to our understanding of the molecular basis of evolutionary innovations of plant reproduction survival in extreme habitats.

Meet the Team

Christopher Irwin Smith
Christopher Irwin Smith
Associate Professor

Affiliates

Willamette University
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Jeremy B. Yoder
Jeremy B. Yoder
Postdoctoral Research Fellow

Affiliates

University of British Columbia
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Jim Leebens-Mack
Jim Leebens-Mack
Professor of Plant Biology

Affiliates

The University of Georgia
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Michael R. McKain
Michael R. McKain
Postdoctoral Associate

Affiliates

The Danforth Plant Science Center
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Christopher Irwin Smith

I am an Evolutionary Ecologist and Associate Professor at Willamette University. I am interested in coevolution and the biology of desert ecosystems. I am particularly interested in the conservation and ecology of the Joshua tree.

Jeremy B. Yoder

I study evolutionary ecology, population genetics and genomics, and the origins of biodiversity.

Jim Leebens-Mack

I use genomic, phylogenetic and experimental analyses to investigate the genetic and ecology processes that influence diversification. I am especially interested in phylogenomic approaches to explore the ecological, genetic and developmental processes that contribute to the evolution of reproductive characters in flowering plants, including Joshua tree.

Michael R. McKain

I am a Postdoctoral Associate at the Donald Danforth Plant Science Center, studying the effects of polyploidy on the evolution of economically and ecologically important grasses. My research also looks at the role of polyploidy in the evolution of genome structure in plant species from yuccas to orchids.


Project Backers

  • 325Backers
  • 124%Funded
  • $10,643Total Donations
  • $26.59Average Donation
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