Crowdfunding – The Joshua Tree Genome Project

Thanks!

by JTGadmin on March 26, 2016 0 Comments

(Photo: Chris Smith)

Our crowdfunding campaign at Experiment.com concluded last night at midnight, with $10,643 raised — 124% of our original funding goal. That means we’ll have funds for the DNA sequencing we’d wanted to assemble a Joshua tree genome sequence, and some additional funding towards our stretch goal, to develop a gene expression atlas based on that genome sequence. Thanks to every single one of the 325 backers who pledged support, and to everyone who helped spread the word on social media, and to the partner organizations who supported the campaign! We couldn’t have done this without you all.

Let’s stretch!

by JTGadmin on March 20, 2016 0 Comments

Can we go higher yet? (Photo and stunt-man: Chris Smith)

Can we go even higher? (Photo and stunt-man: Chris Smith)

We’re unbelievably gratified by the support for our crowdfunding campaign — we’ve won the Experiment.com challenge to recruit the most backers for a project at a liberal arts college, and the bonus from that blew us past our funding goal. But we’ve still got a few days in the campaign, and assembling a genome is a big project. If we had a little more money, there’s more cool work we could do.

That’s where “stretch goals” come in — Experiment allows projects that meet their goals ahead of schedule to propose additional research, and set a new funding goal to support it. We’ve currently raised $10,523 — with about $3,000 more, we’d be able to go beyond assembling a Joshua tree genome sequence, taking the first steps to understand that sequence. We’d do that by building a gene expression atlas.

An assembled genome sequence is really just a long string of DNA nucleotides. What that code actually means — the proteins it codes for, their responses to different environments — is not simple to understand. We can make some headway in understanding a new Joshua tree genome sequence by using what we know about the general structure of protein-coding genes, and comparing genes found that way to other sequenced plant genomes about which more is known, like maize or Arabidopsis thaliana. But that will only get us so far. To really decode the Joshua tree genome, we need to understand what genes are expressed, or turned on, to form different parts of the plant, or to respond to different environmental conditions.

Every cell in a Joshua tree contains the tree’s complete genomic code, but not every gene in that code is expressed in every cell — genes that are important in a leaf cell are not necessarily the same ones that are important in a flower cell, or a root cell. We can take samples of different types of Joshua tree tissue like leaves, flowers, and roots, and specifically sequence the regions of the genome that are active within the cells in those different samples. Doing this will help us identify what parts of the genome actually are protein-coding genes, but it will also tell us something about those genes’ functions — a gene that is strongly expressed in a leaf, but not in flowers or root tissue, is probably important for the specific functions of leaves. Similarly, sequencing expressed genes in leaves from trees experiencing drought stress and trees that aren’t stressed can identify genes that are important for coping with that stress.

So that’s our stretch goal: funding to do the additional sequencing we’d need to target those expressed genes in an array of tissues and maybe more than one environment, too. In total, it’ll bring our project budget to $13,582 — but we’ve already raised enough that all we still need is $3,059. We’ve got five days left in the campaign. Can we do it? If you haven’t pledged your support yet, now’s the time! And if you have, keep spreading the word on Twitter and Facebook.

We won!

by JTGadmin on March 17, 2016 1 Comment

(Photo by Jeremy Yoder)

We’re delighted to announced that we’ve just gotten word that we won the Experiment.com challenge for projects at liberal arts colleges — of all the projects in the competition, ours received the support of the most individual backers. The prize is $2,000 in bonus funding, which we can put towards more of the expenses of sequencing and analysis that go into assembling a reference genome sequence.

We literally could not have done this without the support of over 300 backers, and all the folks who’ve taken an interest in this project and spread the word on social media and by good old word-of-mouth. Many, many thanks. The collaborators are all excited to get underway.

Keep the momentum going!

by JTGadmin on March 2, 2016 0 Comments

Thanks to all of the folks who have pledged their support for our crowdfunding campaign! We’ve had a very exciting first week. We’re more than 1/3 of the way to our fundraising goal, and are pulling ahead in the competition for the most donors, with 59 backers this week.

One of the challenges for crowdfunding, however, is to keep the momentum going after the initial excitement wears off. That nest egg has to be nurtured if it is ever going to take flight. So, we need your help in spreading the word about the project. Please help us reach more people by inviting your friends to like our Facebook page and tweet about the project using @JTGenome.

Also, check out our Experiment.com project page for news about the campaign. We’ll be posting updates over the next week. You can also subscribe on our website to receive email announcements each time our blog here is updated, using the form under “Subscribe by E-mail” in the sidebar.

(Chris Smith)

We’re sequencing the genome of Joshua tree, but we need your help

by JTGadmin on February 24, 2016 1 Comment

(Photo: Chris Smith)

The Joshua Tree Genome Project officially launches today, with a crowdfunding campaign to sequence the genome of one of the most iconic plants in the American southwest. People who love science, Joshua trees, and the Mojave Desert can help finance the development of a Joshua tree genome sequence through Experiment.com.

Why sequence the Joshua tree genome? A reference genome would help answer many important questions about the evolutionary history of this iconic desert species, and about how best to ensure that it survives in a world reshaped by human activity. A sequenced genome will let us:

Discover genes adapted to desert environments. The Mojave Desert contains some of the hottest and driest regions of North America. To survive these inhospitable environments, Joshua trees have an array of physiological and morphological adaptations, from a thick, waxy cuticle on their the leaves, to reduced stomate size and specialized water storage cells. Sequencing the Joshua tree genome will help us find the genes that create these traits, and identify variation in those genes that may allow some Joshua trees to better warmer, drier climates.

Understand the evolution of mutualism. Like all yuccas, Joshua trees rely on highly specialized moths, called yucca moths, to move their pollen from plant to plant. Female moths actively collect and distribute pollen after laying their eggs in Joshua tree flowers; and their larvae eat some of the seeds that develop in the pollinated flower. The moths’ exceptionally reliable pollination service compensates for the loss of a few seeds, and Joshua tree flowers exhibit a suit of adaptations that promote active moth pollination while preventing moth larvae from eating too many seeds. Sequencing of a Joshua tree genome would pave the way to identify genes that contribute to these co-evolved adaptations, and help understand how they have changed over time.

Plan for Joshua tree’s future. Ensuring that Joshua trees will persist into the future means preserving not only the plants themselves, but also the genetic variation that will allow them to adapt to changing climates and environments. We will use a landscape genomics approach to measure the total amount of genetic variation in different populations, and estimate genetic differentiation between populations. This information will let us identify populations of Joshua tree with the greatest potential to adapt to future environmental changes, and give these areas the highest priority for conservation.

Reveal processes of genome evolution. Like all members of the Agavoideae, Joshua trees have a bi-modal karyotype, thought to have resulted from an ancient allopolyploidy event — the combination of two whole genomes by hybridization between species. Sequencing the Joshua tree genome will reveal how genome evolution proceeds following polyploidization events, including the extent of genomic rearrangements among chromosomes of different ancestries, and processes that contribute to diploidization.

The Joshua Tree Genome Project is a collaboration of ecologists, evolutionary biologists, and geneticists, with the support of major Mojave Desert conservation organizations. You can help sequence a Joshua tree genome by donating to the Project through our Experiment.com campaign, and by spreading the word on Twitter and on Facebook.

Calling all fans of science, Joshua trees, and the Mojave Desert!

by JTGadmin on February 22, 2016

In just two days, the Joshua Tree Genome Project is launching a crowdfunding campaign through Experiment.com to help sequence a Joshua tree genome. If you love Joshua trees and understand how much a reference genome would help us learn about their evolutionary past and plan for their future, we hope you’ll pitch in. But as we get ready to launch, we also hope you’ll tell everyone you know about our campaign.

The Joshua Tree Genome Project is part of a special Experiment.com challenge to projects administered by smaller undergraduate institutions, like Willamette University. The challenge is not only to raise the funds required for our project, but to earn the largest number of individual contributions, out of all participating projects. If we win, Experiment.com will kick in another $2,000 — money we can use for other aspects of the genome assembly beyond the DNA sequencing covered by our baseline budget.

So help us spread the word! Click this link to tweet about the project, and encourage folks to follow @JTGenome. And follow this link to like our page on Facebook, and share it to your timeline.

Thanks in advance — every tweet, like, and click brings a Joshua tree genome sequence closer to reality. We’re grateful for the support of conservation organizations and agencies with interest in Joshua trees and the conservation of the Mojave Desert’s unique landscapes. With their help and with yours, we’re hopeful that we can meet our fundraising goal, and win the Experiment.com challenge.