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How do you sequence a tree genome?

How do you sequence a tree genome?


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I'm writing a grant proposal, and part of the research will involve sequencing and comparing DNA from trees in America and Japan. How does one analyze the genome of a tree and compare it to a conspecific?


In journal articles, they are doing many studies every year describing the state of the art tools and procedures for sequencing plant genomes.

by researching 5 minutes you have results of this kind:

http://www.pnas.org/content/95/16/9693.full

Protocols involved commercially available kits (e.g., Qiagen's RNeasy Plant Minikit), non-commercial RNA extraction lab protocols (e.g., CTAB, acid phenol) and hybrid methods that combined components of both commercial kits and lab protocols. The detailed protocols used for all isolations are available online in Appendix S1. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050226

Tissue and organ samples for Northern blot analysis of gene expression patterns were taken during the growing season and frozen in liquid nitrogen, then stored at −80°C. Shoot-tip samples are the terminal 1-2 cm of succulent stem tissue from elongating branches and terminal leaders. Immature xylem was harvested with a vegetable peeler from the surface of woody stems after removal of the bark, and includes cells with primary cell walls derived from the cambial zone through the zone of radial cell expansion. Compression wood and side wood immature xylem RNAs were those used for preparation of the libraries, whereas vertical immature xylem denotes samples taken from stems of control trees growing vertically. The tissue described as “phloem” was collected from the inner surface of the bark of vertical stems and actually includes periderm and other tissues as well as active phloem. Planings were collected from the surface of vertical woody stems with a wood plane after immature xylem was harvested and includes cells that have formed secondary cell walls strong enough to resist harvesting by the vegetable peeler. Needle samples were partially expanded juvenile needles.

here are some more texts for you to check

http://www.pnas.org/content/106/31/12794.full

https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-214

From_field_to_film_Rapid_sequencing_methods_for_field-collected_plant_species

It took me 5 minutes to find these informations by searching articles for

plant sequencing methods


A genome for the olive tree

As an indigenous Mediterranean, I must confess I am an olive oil addict. At home, we acquire this golden and delicious liquid in large quantities, as we use it in almost every dish. Luckily my confessed addiction is nothing to worry much about.

On the contrary, the richness in the mono-unsaturated fatty acids of olive oil has been praised by many dietary studies. Among the many different olive oil varieties, Picual is one of my favorites. I like its strong flavor, particularly when it comes extra virgin, unfiltered, and cold-pressed, from any of the many small producers that still handle their trees and products with sufficient time and care.

History of the olive tree

Olive trees themselves can constitute living monuments. Often reaching ages of over a thousand years, the beauty of these trees is not in their size, which is generally modest, but in the capricious shapes of their trunks, a testimony of a slow growth in a harsh climate.

The Mediterranean olive tree is one of the first domesticated crops, with the first cultivation evidence coming from the early Bronze Age. From the earliest domestication centers in the Levant, the art of cultivating olive trees was spread around the Mediterranean basin by diverse civilizations.

Despite much research, there are still many open questions regarding the history of the domestication of the olive tree, and we know very little about the genetic determinants of selected traits in the different varieties.

Nowadays roughly 3 million tons of olive oil is produced annually and there are many different olive varieties, each with a particular flavor and texture. With a slow growth and decades needed to reach full production, it is striking how the domestication process and the selection of new tree traits and olive varieties were driven across generations.

Despite much research, there are still many open questions regarding the history of the domestication of the olive tree, and we know very little about the genetic determinants of selected traits in the different varieties.

The first olive tree genome

Further advance in our knowledge was precluded in part by a lack of a reference genome for this important crop. This is no longer the case, as the first assembly of the Mediterranean olive tree genome and its annotation is published and described in our article in GigaScience.

The article focuses on the description of the assembly and annotation of a genome obtained from a 1300 year-old tree from the Farga variety. Several additional analyses are ongoing and will form parts of successive publications.

This publishing strategy accelerates the release of the reference genome to the scientific community without any restrictions, and lets us focus subsequent articles on specific questions of biological relevance. Our assembly approach uses a combination of short-read sequences of fosmid pools and whole genome shotguns, which enables us to reach a high level of completeness with the data.

Although not in our initial plans, the discovery of significant traces of ‘contaminating’ genetic material enabled us to partially assemble the genome of a new variety of the fungus Aerobasilium pullulans, which is known to associate with olive trees. As for the first analyses of the olive tree genome, the most relevant finding is that of an enlarged gene repertoire as compared to other plants, including the yellow monkey flower (Erythranthe guttata), which belongs to the same taxonomic order as the olive tree (lamiales).

A ratio of roughly 2 to 1 in the number of genes between the olive tree and the wild flower, and their patterns of similarity, suggest a recent large-scale gene expansion in the lineage leading to the olive tree

Inflated gene counts can also arise from assembly problems in diploid organisms, when distinct alleles of the same genomic region end up in different contigs. We discarded that factor by confirming that recently duplicated genes in the olive tree did not have a significantly lower level of heterozygosity, as would be expected if resulting from the said assembly artifact.

A ratio of roughly 2 to 1 in the number of genes between the olive tree and the wild flower, and their patterns of similarity, suggest a recent large-scale gene expansion in the lineage leading to the olive tree. Whole genome duplications are common in the evolutionary history of plants, including the most analyzed crops. Determining when and how the olive tree genome expanded its genetic repertoire is one large part of the current focus of our project.

Boosting research

The availability of a reference genome assembly for the species will boost research in the olive tree. Genome re-sequencing, which is more cost-effective than de novo sequencing, will help us in elucidating the past of the olive tree (from the early history of domestication) by comparing several subspecies of wild relatives to the origin of the different varieties, studying genetic makeup and uncovering regions subject to strong selection.

Analysis of the genetic diversity among different cultivars and wild relatives will also help us understand how the different traits are determined, as the underlying molecular bases of phenotypic differences including flavor, size, and oil content, remain poorly understood.

Genome-enabled studies such as the analysis of gene expression to the development of gene markers will certainly benefit from this resource, and will promote the understanding of olive tree physiology and its interactions with pathogens and other associated organisms. Eventually this knowledge will pave the way to improve olive tree handling, and accelerate breeding programs that aim to create novel varieties. I am already salivating, and feeling the need for a crunchy toast covered with olive oil and a bit of salt.


Department of Biology

Commonly known as the water flea, Daphnia pulex is the first crustacean to have its genome sequenced. Although it is the size of a grain of rice, this freshwater organism has the most genes, about 31,000, of any animal studied to date, including humans, who have only 23,000 genes. Scientists from the Daphnia Genomics Consortium (DGC) reported their findings in the Feb. 4 issue of Science.

The consortium, a network of over 475 researchers throughout the world, is led by the IU Bloomington Center for Genomics and Bioinformatics (CGB), and the genome sequence was supported by the U.S. Department of Energy’s Joint Genome Institute.

Daphnia has been studied for over a century, but this microcrustacean still has the ability to surprise. Ten important new findings on Daphnia were reported in the article, “The Ecoresponsive Genome of Daphnia pulex,” written by project leader John K. Colbourne, et al. In addition, nearly 40 companion papers were published based on data found in the study. Findings include the fact that 35% of its genes are new to science, literally undocumented in any other organism, and of all sequenced arthropod genomes (insects, crustaceans, and their relatives) studied so far, Daphnia share the most genes with humans.

“Maturing genomic tools for research, applied to questions that are built on the animal’s ecology and population structures, transform Daphnia into a versatile model species for understanding (1) mechanisms of inheritance and development, (2) the process of physiological acclimation and genetic adaptation to changing environments and (3) the genetic plus environmental basis of complex phenotypic traits,” states the consortium’s website. “A rich literature documents how Daphnia copes with environmental hardship it is known to be a sensitive sentinel species in freshwater ecosystems and is widely used in ecotoxicological studies. Increasingly, Daphnia is being used as a surrogate species to understand genomic responses to environmental stressors that are important factors in human health and well being.”

Biology Professor Peter Cherbas, director of CGB, praises the project’s efforts, saying “Assembling so many experts around a shared research goal is no small feat. We’re obviously proud of the CGB’s catalytic role. The genome project signals the coming-of-age of Daphnia as a research tool for investigating the molecular underpinnings of key ecological and environmental problems.”

Daphnia project leader John Colbourne. Photo: Courtesy of J. Colbourne. CGB Sequencing Director Keithanne Mockaitis is part of the Cacao Project. Photo: Courtesy of the IU College of Arts and Sciences

The flagship paper describing Daphnia’s genome sequence is authored by 20 IU scientists including professors, postdoctoral fellows and graduate students from the schools of Arts and Science, Public and Environmental Affairs, Informatics and Computing, and was supported in part by the METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc. Principal investigators and lab personnel from the biology labs of Mike Lynch, Matt Hahn and Justen Andrews also contributed.

Another large genomics project to which the CGB has substantially contributed is the sequencing and analysis of Theobroma cacao, the tree that produces cocoa beans that are processed into chocolate. In September of last year, candy company Mars Inc., the project’s sponsor, and CGB project leader, Keithanne Mockaitis, announced that the cacao genome had been sequenced. This is the largest genome the CGB has sequenced thus far, with an estimate of roughly 400 million base pairs and 35,000 genes.

The importance of this project is great as farmers and breeders in Asia, South America and West Africa use such genetic findings to improve their planting stocks. With the September announcement, data were released to the public as the Cacao Genome Database. Keithanne Mockaitis, sequencing director of the CGB stated, “When you need to wait three or more years for a tree you plant to bear the beans you sell, you want as much information as possible about the seedlings you’re planting. Making the genome data public further enables breeders, farmers and researchers around the world to use a common set of tools, and to share information that will help them fight the spread of disease in their crops.” The findings could also help reduce poverty in these countries as having more reliable genome data can lead to more sustainable crops.

The Cacao Genome project is a consortium of academic, government and industry partners led by Mars Inc. and the U.S. Department of Agriculture, and including Indiana University, Clemson University, Washington State University, the National Center for Genome Resources, nonprofit organization Public Intellectual Property Resources for Agriculture (PIPRA), the HudsonAlpha Institute, and IBM.

Other IU contributors to the project include CGB research associates James Ford and Zach Smith, data analyst Ram Podicheti, and Don Gilbert, bioinformaticist in the Department of Biology.


Rapidly developing genomic resources in forest trees

Genome resources are developing rapidly in forest trees in spite of the challenges associated with working with large, long-lived organisms and sometimes very large genomes [2]. Complete genome sequencing, however, has been slow to advance in forest trees owing to funding limitations and the large size of conifer genomes. Black cottonwood (Populus trichocarpa Torr. & Gray) was the first forest tree genome to be sequenced by the US Department of Energy Joint Genome Institute (DOE/JGI) [6] (Table 1). Black cottonwood has a relatively small genome (450 Mb) and is a target feedstock species for cellulosic ethanol production, and thus fits into the DOE/JGI priority of sequencing bioenergy feedstock species. The genus Populus has 30+ species (aspens and cottonwoods) with genome sizes of approximately 500 Mb. Several species are being sequenced by DOE/JGI, and other groups around the world, and it seems likely that all members of the genus will soon have a genome sequence (Table 1). The next forest tree to be sequenced was the flooded gum (Eucalyptus grandis BRASUZ1, which is a member of the Myrtaceae family), again by DOE/JGI. Eucalyptus species and their hybrids are important commercial species grown in their native Australia and many regions throughout the southern hemisphere. Several more eucalyptus species are being sequenced (Table 1), each with relatively small genomes (500 Mb), but it will probably take many years before all 700+ members of this genus are completed. Several members of the Fagaceae family are now being sequenced (Table 1). Members of this group include the oaks, beeches and chestnuts, with genome sizes less than 1 Gb.

The gymnosperm forest trees (such as the conifers) were the last to enter the world of genome sequencing. This was entirely due to their very large genomes (10 Gb and greater) as they are extremely important economically and ecologically, and phylogenetically they represent the ancient sister lineage to that of angiosperm species. Genome resources needed to support a sequencing project were reasonably well developed, but it was not until the introduction of next-generation sequencing (NGS) technologies that sequencing conifer genomes became tractable. Currently, there are at least ten conifer (Pinaceae) genome-sequencing projects under way (Table 1).

Aside from reference genome sequencing in forest trees, there is significant activity in transcriptome sequencing and resequencing for polymorphism discovery (Tables 2 and 3). We have only listed the transcriptome and resequencing projects in Table 1 that are associated with a species that has an active genome-sequencing project.


In a living redwood, just as the oldest branches are near the bottom of a tree and the youngest are near the top, the oldest genetic mutations are located near the bottom of the tree, and the newest mutations are at the top. Moore compares it to an evolutionary tree that shows the relationship between different species. But with a redwood, that plays out on a single tree.

“As the tree grows, literally an evolutionary tree is being built by the actual tree,” he said.

But before he can study how much of its DNA contains mutations, the redwood genome had to be sequenced by the team in the Neale Lab at UC Davis, which includes Moore. The work is funded by the Save the Redwoods League, a nonprofit redwood conservation organization. It’s a project that comes with some unique challenges.

For example, the redwood’s genome contains 32 billion base pairs of DNA. That’s ten times more than the human genome, and it would be 65 feet long if laid out on a table, Moore said. There are also six copies of each chromosome, compared to the typical two in human DNA. To add further complication, the team at UC Davis has been sequencing each genome 100 times to make sure they have every piece of the puzzle.

“This is going to be the largest genome ever sequenced, and it’s probably going to be the most complex,” Moore said.

The sequencing work at UC Davis was completed this year, and now the process moves to Johns Hopkins University, where the genome will be assembled in the correct order. It’s essentially like putting the pieces of a puzzle together, Moore said, and should take another year. After that, he can start looking at where the mutations occur in the DNA. But until then, Moore is studying redwood cell divisions to determine how many cells divide over the course of the tree’s life – “probably many million,” he said.


Sequencing the genome of the virus behind COVID-19

Peter Thielen and Tom Mehoke have spent years sequencing the genome of influenza. Now, as a new strain of coronavirus spreads across the globe, these biologists from Johns Hopkins Applied Physics Laboratory are transitioning their work to better understand the virus that causes COVID-19.

Inside the molecular diagnostics laboratory at Johns Hopkins Hospital, while health care workers and hospital staff work tirelessly to process patient tests, Thielen and Mehoke, members of APL's Research and Exploratory Development Department and the Johns Hopkins Center of Excellence in Influenza Research and Surveillance, are waiting for the positive tests. Certainly, positive tests are no cause for celebration, but for Thielen and Mehoke, they are a key to learning more about the rapidly spreading virus.

With software and molecular biology approaches developed in part at APL, Thielen and Mehoke are using handheld DNA sequencers to conduct immediate on-site genome sequencing of SARS-CoV-2—the virus that causes COVID-19.

"This information allows us to track the evolution of the virus," Thielen said. "It gives us a sense of where the new cases coming into Baltimore could've originated, and insight into how long transmission may have occurred undetected. There are a lot of things we can glean from that."

Topping that list is the ability to see how quickly the virus mutates—integral information for mapping its spread, as well as developing an effective vaccine. Influenza, for example, mutates constantly. That's why it's necessary to vaccinate against different strains of the flu each year.

The virus causing COVID-19, Thielen said, does not appear to be mutating as fast.

"When this virus was first sequenced in China, that information was helpful in starting the process to develop a vaccine," Thielen explained. "What we're doing informs whether or not the virus is mutating away from that original sequence, and how quickly. Based on the mutation rate, early data indicates that this would likely be a single vaccine rather than one that needs to be updated each year, like the flu shot."

In the near-term, the mutations inform how the virus is spreading.

Image caption: APL biologist Tom Mehoke reviews the DNA sequencing analysis of SARS-CoV-2, the virus causing COVID-19, at the molecular diagnostics laboratory at Johns Hopkins Hospital.

Image credit : Johns Hopkins APL / Ed Whitman

With the United States continuing to ramp up testing and mitigation capabilities, the ability to understand how outbreaks are linked gives public health departments another tool for evaluation. Mutations can explain how long the virus may have gone undetected and the supposition that there are likely far more cases than diagnosed, and can advise on what measures to put in place (such as the social-distancing efforts and closings that are ongoing nationwide).

Sequencing of the virus' genome is being performed by scientists all over the globe as they work to trace the source of regional outbreaks. In northern California, for example, news reports suggest that genome sequencing has linked the Bay Area outbreak to the Grand Princess cruise ship, which linked back to the virus found in Washington State, which likely came from China.

That's the type of insight—a DNA fingerprint, if you will—that Thielen and Mehoke will gain as more virus genomes are sequenced from the Baltimore and Washington, D.C., regions.

They've completed analysis of the first four COVID-19 samples, with upward of 100 in the queue from the Baltimore/Washington, D.C. area, and expect many more in the coming weeks.

Johns Hopkins responds to COVID-19

Coverage of how the COVID-19 pandemic is affecting operations at JHU and how Hopkins experts and scientists are responding to the outbreak

Operating remotely with handheld sequencers and laptop computers, Thielen and Mehoke's process required a several day wait before results could be transferred. But, at the end of last week they validated a new process that enables same-day sequencing—one that can be done by the hospital staff members already administering the diagnostic tests.

In the last nine months, Thielen and Mehoke held two workshops with the National Institutes of Health Fogarty International Center to help train scientists from low- and middle-income countries on how to use the handheld sequencers to do this work. The latest workshop was held virtually last week, when they trained stateside researchers to do the same type of on-site sequencing in their own laboratories.

"We were doing that to prepare as many researchers as we can, in the event that there would be a future pandemic," Thielen said. "It's here."


Penn State Geneticist Involved In Effort To Sequence Tree Genome

UNIVERSITY PARK, Pa. -- A molecular geneticist in Penn State's College of Agricultural Sciences was instrumental in the creation of a U.S. Department of Energy (DOE)-funded, ground-breaking effort to sequence the genome of the poplar tree.

"This is the most exciting event that has ever happened in the field of tree molecular genetics," says John Carlson, associate professor of molecular genetics in the School of Forest Resources.

"I have never seen the forest genetics community more excited," says Toby Bradshaw, of the University of Washington, one of the world's foremost tree molecular geneticists.

Bradshaw helped lay the foundation for the project through his discovery of the female cottonwood tree that was chosen for sequencing. Named "Nisqually-1," the tree has been the focus of intensive genetics and physiology studies, and is one of the most successful parent trees for hybrid poplar production.

So what is it about such a seemingly obscure, esoteric tree research project that is so important and exciting? And why the poplar tree (genus Populus)?

"The genome sequence of Populus trichocarpa (cottonwood) is expected to lead to faster-growing trees that produce more biomass for conversion to fuels and paper," explains Carlson. "In addition, trees with unique traits may be useful in phytoremediation, a process whereby trees such as cottonwoods or hybrid poplars could be used to clean up hazardous waste sites."

According to Carlson, Populus trees like cottonwood, hybrid poplar and aspen have emerged as model organisms in forestry for the same reasons that Populus was chosen as the first tree genome to sequence -- rapid growth rate, small genome size and widespread use in plantation forestry and other areas of interest to the forest industry and the DOE.

Cottonwoods, hybrid poplars and aspens also could play a role in improving the environment, displacing imported oil and creating domestic jobs. But first scientists need to better understand the biology of Populus, for which the genome sequence will provide the blueprint.

This project builds upon the success that the DOE has had in mapping the human genome, a decade-long effort that is expected to lead to cures and the prevention of diseases in people. While sequencing the human genome took years, researchers at the Joint Genome Institute at the DOE's Oak Ridge National Laboratory in Tennessee and cooperating institutions expect to make the genetic blueprint of Populus available within 18 months. And they expect the payback to be significant.

"This effort will furnish scientists in this country and abroad with an unprecedented molecular 'parts list' for a tree," said Jerry Tuskan, the lead Populus genetics researcher in Oak Ridge National Lab's Environmental Sciences Division. "Such a list will provide the scientific community with a catalog of genes, knowledge as to what these genes do in trees and an exciting opportunity to better understand how trees grow."

"The information we gain from this effort will open the doors to countless other opportunities to use woody plants in the production of new and traditional forest products and even in ecological preservation," says Carlson. "The sequencing of the poplar genome will be a bonanza for researchers seeking to understand how individual genes influence the growth of trees and their adaptation to the natural environment. This knowledge eventually might be applied to the breeding of fast-growing trees capable of producing wood, fiber and energy on a smaller amount of land."

Worldwide, support for the project is high, according to Carlson, as more than 100 scientists have indicated via a Web survey that they believe a poplar tree genome sequencing effort should be a top priority of forest research. Already, cottonwoods, hybrid poplars and aspens are being used in a variety of ways ranging from paper production to carbon sequestration to the development of fast-growing trees as a source of feedstocks for renewable bio-based products.

Carlson describes his role in the project this way: "After I gave a talk in December of 2000, David Luke, former CEO of the forest industry giant Westvaco and a native of Tyrone, Pa., suggested that I prepare a case statement describing the need for and benefits of sequencing the poplar genome. I did, and that document started a wider discussion of the concept among forest geneticists, but none of us imagined that within a few months the project might become a reality. My colleagues Bradshaw and Tuskan turned the ideas in the case statement into a great proposal that the DOE quickly adopted."

Carlson serves on a steering committee for the International Poplar Genome Consortium, which is helping DOE chart a path for the sequencing effort and facilitate public access and use of the data. Participants in the consortium include the DOE's Oak Ridge National Laboratory, the DOE°s Joint Genome Institute, Genome Canada, The Swedish Populus Genome Project, Penn State, Oregon State, Michigan State and the University of Washington.


DOE begins international effort to sequence tree genome

Trees like cottonwood, hybrid poplar and aspen have long been used as model organisms in forestry, and the choice of Populus as the first tree genome to sequence is due in large part to their rapid growth rate, small genome size and widespread use in areas of interest to the forest industry and DOE.

"This effort will furnish scientists both in this country and abroad with an unprecedented molecular 'parts list' for a tree," said Jerry Tuskan, a researcher in ORNL's Environmental Sciences Division. "Such a list will provide the scientific community with a catalog of genes, knowledge as to what these genes do in trees and an exciting opportunity to better understand how trees grow."

Ultimately, this information will allow scientists to more effectively use trees to carry out important functions like carbon sequestration and enhanced production of biomass for fuels and fiber.

This project builds upon the success that DOE has had in mapping the human genome, a decade-long effort that is expected to lead to cures and the prevention of diseases in people. While sequencing the human genome took years, researchers at DOE's Joint Genome Institute, ORNL and cooperating institutions expect to make the genetic blueprint of Populus available within 18 months. And they expect the payback to be significant.

"Genetic sequencing of Populus is expected to lead to faster growing trees, trees that produce more biomass for conversion to fuels, while also sequestering carbon from the atmosphere," said Stan Wullschleger of ORNL's Environmental Sciences Division. "In addition, trees with unique traits may be used in phytoremediation, a process whereby trees such as cottonwoods or hybrid poplars could be used to clean up hazardous waste sites.

"Clearly, the information we gain from this effort will benefit ongoing and future projects within DOE and open the doors to countless other opportunities to use woody plants in the pursuit of goals related to traditional forest products and even ecological preservation."

Worldwide, support for the project is high, as more than 100 scientists have indicated via the Web that they believe a poplar genome sequencing effort should be a top priority of forest research. Already, cottonwoods, hybrid poplars and aspens are being used in a variety of ways ranging from paper production to carbon sequestration to the development of fast-growing trees as a source of feedstocks for renewable bio-based products.

"I have never seen the forest genetics community more excited," said Toby Bradshaw, a molecular biologist with the University of Washington, which helped DOE lay the foundation for this effort. "The sequencing of the poplar genome will be a bonanza for researchers seeking to understand how individual genes influence the growth of trees and their adaptation to the natural environment. This knowledge might eventually be applied to the breeding of fast-growing trees capable of producing wood, fiber and energy sustainably on a small amount of land."

In addition to ORNL, participants in the international project include the Joint Genome Institute, the University of Washington, Genome Canada and the Swedish University of Agricultural Sciences. The Joint Genome Institute sequencing facility will produce half of the sequence this year and another half in 2003.

Other ORNL researchers involved in the project are Frank Larimer of the Life Sciences Division and Lee Gunter and Zamin Yang of the Environmental Sciences Division. The research was funded by DOE's Office of Biological and Environmental Research.

ORNL is a Department of Energy multiprogram research facility managed by UT-Battelle.


Nothing in Biology Makes Sense!

Remember Joshua trees? If you read this blog, you probably do. They’re an ecological keystone species — and a cultural icon — in the Mojave desert, and they have a fascinating, co-evolving relationship with yucca moths. Some contributors to this very blog, have been studying that pollination relationship and its evolutionary consequences for a decade, building on natural history research that goes back to the time of Charles Darwin.

Up to now, though, modern genetic tools have been of limited use for Joshua trees, because no one has assembled the complete DNA sequence of a Joshua tree. Having a “reference genome” would let those of us who study the trees identify specific genes involved in coevolution with yucca moths, compare the evolutionary effects of that pollination mutualism to natural selection exerted by the harsh environments in which the trees grow, and even use genome-scale data to inform Joshua tree conservation planning.

Well, we’ve decided it’s time to do all of that, and we’re asking for help. A team of folks with expertise in Joshua trees’ natural history, Mojave Desert ecology, and genomic data analysis launched the Joshua Tree Genome Project a couple weeks ago, with a crowd-funding campaign on Experiment.com to pay for part of the DNA sequencing we’d need to assemble a reference genome.

We’re approaching 50% of our funding goal, and leading a competition among projects based at undergraduate universities to recruit the most donors, which could win us $2,000 in matching funds — so even if you give as little as $1, you’re providing a big boost to the project. Go check out the Joshua Tree Genome Project website, and then head on over and pledge your support.


Fort Collins roots

Moore said that the skills he learned at CSU have helped him in this project. For example, Moore learned about plant anatomy and morphology techniques from David Steingraeber, an associate professor in the Department of Biology. As Steingraeber’s student, Moore also studied the rare Mimulus gemmiparus, or Rocky Mountain monkeyflower, which reproduces clonally like the redwood. He said it’s one of the reasons he became interested in redwood mutations.

As an undergraduate, Moore was awarded the College of Natural Sciences’ Marilyn and Ron Tuttle Undergraduate Research Scholarship. The scholarship was established by CSU biology and botany alumna Marilyn Tuttle and her husband Ron and provides support to biochemistry and biology undergraduates to conduct research.

Moore credits this scholarship with allowing him to pursue his own research on redwoods, which no one else at CSU was doing. Some of that work was featured in stories by National Geographic, NPR and theWashington Post.

When he graduates from UC Davis, Moore plans to keep studying other long-lived trees, such as the bristlecone pine, which can live for more than 5,000 years. Moore said that he is fascinated by how these trees deal with such a long lifespan.

“The older a tree gets, the more it gets beat up, just smashed by life,” he said. “Yet they can persist through that. I love that about it because it shows life’s resilience.”


Watch the video: How to Sequence a Genome: 2. Building Libraries (May 2022).