- Author: Kat Kerlin
Reposted from UC Davis news
Scientists have successfully sequenced the coast redwood and giant sequoia genomes, completing the first major milestone of a five-year project to develop the tools necessary to study these forests' genomic diversity. The research partners, composed of the University of California, Davis, Johns Hopkins University and the Save the Redwoods League, are making the data publicly available today.
The coast redwood genome is now the second-largest ever sequenced at nearly nine times the size of the human genome. The genome of the giant sequoia is roughly three times that of the human genome.
‘23 and Tree?'
Much like sequencing the human genome opened the door to finding cures for things like sickle cell anemia, sequencing the redwood and sequoia genome could help conserve and restore those species.
“Our patient is the redwood forest,” said David Neale, distinguished professor in the Department of Plant Sciences at UC Davis. “It's not healthy. We seek to make it healthy again, and we need that same foundational resource as a human physician or medical professional needs for their patients.”
Over the past 150 years, 95 percent of the ancient coast redwood range and about one-third of the giant sequoia range have been logged. With this unprecedented loss of old trees and the addition of redwood clones often planted in their place, conservationists have grown concerned that the forests' genomic diversity has fundamentally changed. If diversity has declined, it could leave the redwoods vulnerable to drought, fire and other stressors related to climate change.
By sequencing these trees' genomes, the scientists are providing a tool that resource managers can use to help discern a redwood forest's genetic potential for adapting to its current or future environment.
“We're trying to build a 23andMe for trees, where a manager sends in their samples and gets a risk evaluation of their forest populations, if not individual trees,” Neale said. “Completing the sequences of the coast redwood and giant sequoia genomes is the first step.”
Sequencing conifer ‘mega-genomes'
These conifers have giant genomes, and full sequencing of them has only been possible in the last decade.
The coast redwood has six sets of chromosomes (hexaploid) and 27 billion base pairs of DNA. The giant sequoia has two sets of chromosomes (diploid) and over 8 billion base pairs. For comparison, the largest genome sequenced to date belongs to the axolotl, a North American salamander whose genome was completed in 2018 and has more than 28 billion base pairs.
“We pushed the boundaries of genome-sequencing technology to take on the redwood and sequoia mega-genomes,” said Steven Salzberg, professor of Biomedical Engineering at Johns Hopkins University. “After using our specially developed algorithms to assemble these enormous and complex genome sequences, we have gained a new appreciation for how difficult it is to put together a hexaploid genome, especially one as large as the coast redwood's.”
What's next?
The redwood genome project was launched in late 2017, with a projected five-year timeline. By the end of the project, the genome sequences and screening tools developed will allow field crews to quickly assess adaptive genomic diversity in redwood forests to inform management plans that restore the health and resilience of these forests throughout their natural ranges.
With the genomes sequenced, the League will work to inventory diversity across the landscapes and identify "hot spots" of genomic diversity for enhanced protection and areas of low diversity for restoration.
“Every time we plant a seedling or thin a redwood stand to reduce fuel loads or accelerate growth, we potentially affect the genomic diversity of the forest,” said Emily Burns, director of science for Save the Redwoods League. “With the new genome tools we're developing now, we will soon be able to see the hidden genomic diversity in the forest for the first time and design local conservation strategies that promote natural genomic diversity. This is a gift of resilience we can give our iconic redwood forests for the future.”
The coast redwood and giant sequoia sequence data are available to the scientific community at large through the UC Davis website.
During the next stage of the project, researchers will create a database capturing range-wide genomic variation within each species; develop tools that will allow resource managers to identify coast redwood and giant sequoia genetic variation while in the field; compile forest genetic inventories; and launch pilot restoration projects based on the accrued data.
“When we celebrated the League's 100th anniversary last year, we reaffirmed our commitment to restore entire landscapes of young, recovering redwood forests,” said Sam Hodder, president and CEO of Save the Redwoods League. “Sequencing the coast redwood and giant sequoia genomes for the first time opens a new scientific frontier for our restoration projects. This work will reveal the forests' genetic identity so that we can protect the diversity that's left, and in some areas, restore what was lost.”
Major funding for the research came from Save the Redwoods League. A significant lead gift to the league to fund the initial sequencing of the genomes was provided by Ralph Eschenbach and Carol Joy Provan.
- Author: Kathy Keatley Garvey
(Embargo lifts at 5 a.m. Pacific Time, July 31, 2018)
There they were--odorant receptor genes, the scent-detecting genes thought to have evolved with winged insects more than 400 million years ago. But this groundbreaking discovery indicates they evolved millions of years earlier.
The sensory gene is considered one of an insect's most important genes, crucial to foraging, mating and avoiding predators.
“It was interesting because a paper published in 2014 claimed that ORs evolved with winged flight and were thus absent in ancestrally wingless (Apterygota) insects,” said Brand, a member of the Population Biology Graduate Group who researches the evolution of olfactory/odorant receptor genes in orchid bees. “Since firebrats are apterygote, we now had proof that this gene family is more ancient than previously thought.”
Brand proposed that they merge their datasets and write a comprehensive paper of higher impact rather than two independent papers. It was a “go.”
The collaborative result: “The Origin of the Odorant Receptor Gene Family in Insects,” a newly published paper by a seven-member team from UC Davis, University of Illinois and the University of Tennessee, in the open-access journal eLife, which prints promising research in the life and medical sciences. The article is online at https://doi.org/10.7554/eLife.38340
“Our finding that the odorant receptor gene family evolved at the evolutionary base of the insects makes it a major evolutionary novelty that presumably contributed to the adaptation of early insects to terrestrial living,” Robertson said.
Said Brand: “Odorant receptors are the largest insect gene family underlying the sense of smell. ORs are thus crucial in the majority of behaviors that involve the sense of smell including foraging, reproduction, and detection of predators.” The cell membranes of odorant receptor neurons are key to detecting scents. In insects, the ORs are usually found in the antennae or mouthparts.
In their abstract, the authors wrote that “The origin of the insect odorant receptor (OR) gene family has been hypothesized to have coincided with the evolution of terrestriality in insects. (Christine) Missbach et al. (2014) suggested that ORs instead evolved with an ancestral OR co-receptor (Orco) after the origin of terrestriality and the OR/Orco system is an adaptation to winged flight in insects. We investigated genomes of the Collembola, Diplura, Archaeognatha,
Zygentoma, Odonata, and Ephemeroptera, and find ORs present in all insect genomes butabsent from lineages predating the evolution of insects. Orco is absent only in the ancestrally wingless insect lineage Archaeognatha. Our new genome sequence of the zygentoman firebrat, Thermobia domestica, reveals a full OR/Orco system. We conclude that ORs evolved before winged flight, perhaps as an adaptation to terrestriality, representing a key evolutionary novelty in the ancestor of all insects, and hence a molecular synapomorphy for the Class Insecta.”
Synapomorphy is defined as a characteristic present in an ancestral species and shared exclusively by its evolutionary descendants.
The research is a UC Davis cross-departmental collaboration involving associate professor Brian Johnson of the Davis Department of Entomology and Nematology, Wei Lin of the Johnson lab and a member of the Entomology Graduate Group; and Brand, who studies with major professor Santiago Ramirez of the Department of Evolution and Ecology.
“A recurring theme in the field of genomics is that incomplete sampling of the relevant taxa often leads to premature conclusions,” said Johnson. “Our work on ORs is a good example of this.” Johnson studies the genetics, behavior, evolution, and health of honey bees. His lab currently focuses on the evolution and genetic basis of social behavior using comparative and functional genomics.”
The seven-member team, in addition to the UC Davis and University of Illinois scientists, included a trio from the University of Tennessee: Ratnasri Pothula, William Klingeman, and Juan Luis Jurat-Fuentes.
Brand recalled that he detected the multiple odorant receptor genes in the firebrat genome in late January or early February. “I was working at home after my normal work day, because this genome work I did with Brian was a side project for me—he knew of my interest in genomics and offered me the opportunity to collaborate on his lab's ongoing projects.”
Brand expects to receive his doctorate from UC Davis in the spring of 2019. A native of Germany and a former research scientist at Ruhr-University, Bochum, he received his master's degree in genetics and evolutionary biology in 2013 from Ruhr-University, and his bachelor's degree in biology in 2010 from Heinrich-Heine University, Düsseldorf, Germany.
Winged insects first appeared on earth 406 million years ago, according to research published in a 2014 edition Science by molecular biodiversity researcher Bernhard Misof, a professor at the University of Bonn, Germany.
Fossil records indicate that hexapods diverged from crustaceans 410 to 510 million years ago, according to Misof. “At this time in geological history, land masses were dotted with shallow inland seas, and plant life (mostly algae and bryophytes) was largely restricted to coastal habitats and other sites where water was readily available,” according to a North Carolina State University's Department of Entomology website. “The oldest hexapod fossils are found in rocks of the late Devonian period. These rocks also contain numerous other terrestrial arthropods (mites, spiders, centipedes, scorpions, etc.) suggesting that a major radiation of terrestrial life-forms must have occurred during the Ordovician or Silurian period.”
The first known fossil record of Apterygota insects, which include firebrats, silverfish and jumping bristletails—dates back to the Devonian period, which began 417 years ago.
The firebrat, found throughout the world under rocks and leaf litter, is an indoor pest of dog food, stored foods, fabric and book bindings. It is commonly found in high-humidity environments such as bakeries and boiler rooms.
According to the UC Statewide Integrated Pest Management Program (UC IPM), both firebrats and their cousin silverfish “have enzymes in their gut that digest cellulose, and they choose bookcases, closets, and places where books, clothing, starch, or dry foods are available. Silverfish and firebrats are nocturnal and hide during the day. If the object they are hiding beneath is moved, they will dart toward another secluded place. They come out at night to seek food and water. Both insects prefer dry food such as cereals, flour, pasta, and pet food; paper with glue or paste; sizing in paper including wallpaper; book bindings; and starch in clothing. Household dust and debris, dead insects, and certain fungi also are important sources of food. However, they can live for several months without nourishment.”
“Large numbers of these insects can invade new homes from surrounding wild areas, especially as these areas dry out during the summer,” the UC IPM website says. “They also can come in on lumber, wallboard, and similar products. Freshly laid concrete and green lumber supply humidity, while wallpaper paste provides food.”
Resources:
eLife: https://doi.org/10.7554/eLife.38340
UC IPM Pest Note on Firebrat: http://ipm.ucanr.edu/PMG/PESTNOTES/pn7475.html
Information on hexapods: https://genent.cals.ncsu.edu/bug-bytes/hexapods/
Philipp Brand website: https://evolvingors.wordpress.com
Contacts:
Philipp Brand: pbrand@ucdavis.edu
Brian Johnson: brnjohnson@ucdavis.edu
Hugh Robertson: hughrobe@uiuc.edu
- Author: Pat Bailey
As you're ladling up country-style pinto beans for your weekend barbecue or fixing a cold three-bean salad from kidney, string and navy beans for a summer picnic, pause to remember what a long and storied history these “common bean” varieties share and the new scientific advances that promise to boost their productivity worldwide.
This week, a new genome sequencing is being reported for the common bean, which ranks as the world's 10th most widely grown food crop and includes the culinary favorites above, whose varieties together comprise a $1.2 billion crop in the United States.
“The availability of this new whole-genome sequence for beans is already paying off,” said Paul Gepts, professor in the Department of Plant Sciences at UC Davis and co-author of the new sequencing study.
Gepts, who leads the bean-breeding program at UC Davis, notes that the new sequence is being used to confirm many of the findings made earlier by his UC Davis research group, including identification of the common bean's two points of origin and domestication.
Sequencing and bean ancestry
The common bean is thought to have originated in Mexico more than 100,000 years ago, but -- as the Gepts group earlier discovered – was domesticated separately at two different geographic locations in Mesoamerica and the southern Andes.
“This finding makes the common bean an unusually interesting experimental system because the domestication process has been replicated in this crop,” Gepts said.
The sequencing team compared gene sequences from pooled populations of plants representing these two regions and found that only a small fraction of the genes are shared between common bean species from the two locations. This supports the earlier finding that the common bean was domesticated in two separate events -- one at each location -- but distinct genes were involved in each event.
The new whole-genome sequencing is also helping to identify genetic “markers” that can be used to speed up breeding of new and more productive bean varieties in the United States, East Africa and elsewhere, Gepts said.
The nitrogen connection
All of bean varieties that belong to the “common bean” group share with the closely related soybean the highly valued ability to form symbiotic relationships with “nitrogen-fixing” bacteria in the soil.
The plants and the bacteria work together to convert nitrogen in the atmosphere into ammonia – which includes nitrogen in a form that enriches the soil and feeds crops. Nitrogen-fixing crop plants can actually reduce or eliminate the need for farmers to apply expensive fertilizers.
One goal of the new sequencing project was to better understand the genetic basis for how such symbiotic relationships between nitrogen-fixing plants and bacteria are formed and sustained, with an eye toward increasing fuel- and food-crop productivity.
The research team successfully identified a handful of genes involved with moving nitrogen around, which could be helpful to farmers who intercrop beans with other crops that don't fix nitrogen.
Findings from this study are reported this week online in the journal Nature Genetics. The sequencing project was led by researchers at the University of Georgia, U.S. Department of Energy Joint Genome Institute, Hudson Alpha Institute for Biotechnology and North Dakota State University.
- Posted By: Jeannette E. Warnert
- Written by: Diane Nelson, (530) 752-1969, denelson@ucdavis.edu
The stripe rust disease of wheat caused by the highly specialized fungal pathogen Puccinia striiformis f. sp. tritici has been responsible for recurrent episodes of large yield losses and economic hardship among grain-based agricultural societies for centuries. Current epidemics of new aggressive races of Puccinia striiformis that appear after the year 2000 pose significant threats to food security worldwide and, in particular, in developing countries in Africa and central Asia. In spite of its economic importance, the Puccinia striiformis genomic sequence is not currently available.
In order to get access to the genes of this pathogen, a team of researchers – including Professor Jorge Dubcovsky (also a Howard Hughes Medical Institute researcher) and Professor Richard Michelmore, director of the UC Davis Genome Center, Project Scientist Dario Cantu and Manjula Govindarajulu, a postdoctoral researcher in Michelmore’s lab - used cutting-edge technology to rapidly sequence a large portion of the genome of one of the Puccinia striiformis more virulent and aggressive races. They assembled long stretches of the Puccinia striiformis genome and established a preliminary automatic annotation of its genes, with a special focus on those likely to be involved in pathogenicity.
This information is available in the open-access article published by the Public Library of Science and made publically available through the National Center of Biotechnology information and a dedicated web page.
“This shotgun sequence assembly does not substitute for the need of a complete and annotated Puccinia striiformis genome, but it provides immediate access to a large proportion, more than about 88 percent, of the genes from this pathogen,” said Cantu. “This public information has the potential to accelerate a new wave of studies to determine the mechanisms used by this pathogen to infect wheat, and hopefully to reduce current yield loses caused by this pathogen.”
These researchers, in collaboration with others at the John Innes Institute in the UK, are currently sequencing new and old races of Puccinia striiformis to investigate their differences in virulence and aggressiveness.
This project was supported in part by funds provided through a grant from the Bill & Melinda Gates Foundation, and the National Research Initiative Competitive Grants from the USDA National Institute of Food and Agriculture.
- Author: Jeannette E. Warnert
Roger Beachy, the director of the USDA National Institute of Food and Agriculture, was at UC Davis yesterday to announce grants for agricultural research amounting to $40 million, calling them "significant investments," said a UC Davis news release.
Together with UC Davis officials, Beachy announced that:
- Wheat geneticist Jorge Dubcovsky will receive $25 million to develop new varieties of wheat and barley. Dubcovsky and his 55 university and USDA colleagues will focus on biological and environmental stresses to wheat that are caused, at least in part, by global climate change.
- Forest geneticist David Neale will receive $14.6 million to head a team that will work to sequence the genomes of loblolly pine and two other conifers. Neale and his research colleagues plan to accelerate breeding efforts for fast-growing varieties of these trees to enhance their use as feedstocks for biofuels and biopower.
"We look forward to the practical solutions for agriculture and for the environment that will arise from these collaborative projects," UC Davis Chancellor Linda Katehi said at the press conference.
A story about the grants written by Rick Daysog of the Sacramento Bee said they come as UC Davis has stepped up efforts to attract research grants following Katehi's appointment as chancellor in 2009. During its fiscal year ending June 30, 2010, the university received a record $679 million in research grants.