Plant Virus Jumps 1.6-Billion-Year Species Barrier To Infect Honeybees

The mystery of colony collapse disorder in honeybees has a remarkable new suspect – a plant virus that has made a spectacular jump across 1.6 billion years of evolution to infect insects.

The potential hive killer is tobacco ringspot virus, named for the discoloured circles it forms on infected leaves. It has at least 90 different plant hosts and is so difficult to get rid of that some farmers have stopped raising susceptible crops.

It often travels on pollen from one host to another by thumbing a ride in insects, including varroa mites, aphids and bees. But such viral hitchhikers usually stay in the gut or salivary glands, ready to make a quick jump to the next plant host.

So when a team of scientists from the US Department of Agriculture and China’s Academy of Agricultural Science spotted it in honeybees they were not expecting to find that it had spread throughout the animals’ bodies, and was doing particularly well in wings, antennae, trachea, hemolymph (insect blood) and nerves. 

a bee at work (Photo credit: Andreas.

Such jumps are not unheard of. Rhabodoviridae, the family of viruses that includes rabies, has members that have both plant and animal hosts. Shorter hops are routinely made between species by influenza and HIV famously transferred to humans from apes.

Common to all these viruses is the use of RNA rather than DNA to encode their genetic templates. RNA is the messenger molecule that tells cells how to build proteins. It is not as rigorously policed as DNA, and so is far more likely to have copying errors. As a result, viruses that rely on RNA mutate more often.

Tobacco ringworm virus was also found in varroa mites, which parasitize honeybees, and may play a role in spreading the disease.

The prime suspect in colony collapse disorder remains neonicotinoid pesticides, which were banned in the European Union in November 2013.

However, the case against them is far from proven, and researchers continue to hunt for other candidates, including viruses.

The US-China team screened six strong and four weak colonies over a year for tobacco ringspot and other viruses, deformed wing bee virus, black queen cell virus and Israel acute paralysis virus and found that higher concentrations presaged colony collapse, although no apparent disease symptoms were spotted in individual bees. The four weak colonies studied had collapsed by February.

What remains unclear is whether the viruses are causing the decline, contributing to it or just taking advantage of it.

Honeybees pollinate 90 commercial crops worldwide and their services in the US alone are valued at $14.6bn a year.

ORIGINAL: Forbes

1/31/2014

Genome sequencing meets chocolate

ORIGINAL: IBM Research

How analyzing cacao plant genes could save chocolate

Plants have DNA, too. So just as genome sequencing has been conducted on fruit flies and humans, scientists have also discovered the genomes of rice, mustard, and a few trees - including as of 2010, the cacao.

IBM, the United States Department of Agriculture’s Agricultural Research Service (USDA-ARS), and candy-maker Mars Inc. teamed up in 2008 to sequence the cocoa genome in an effort to help farmers grow tastier, more disease-resistant and more productive cocoa trees. The initial phase of work yielded a surprising result: identifying the genes that dictate the color of the plant may be the best indicator for better-tasting, healthier plants.

Why sustain cocoa?

• 70 percent of today’s global cocoa is produced in equatorial Africa
• 2,000,000 small-scale cocoa farms in West Africa depend on this crop
• 1/3 of all cocoa produced in Africa is lost to drought, pests and fungal disease
• $800 million (U.S.) lost due to failed cocoa crops

IBM and Mars use Deep Analytics to Map the Cocoa Genome

IBM and Mars use Deep Analytics to Map the Cocoa Genome(2:52)

Genome sequencing: how computers deciphers genetic code

In order to sequence the cacao’s genetic material, scientists had to first crush the leaves, pods and other parts of the plant at the USDA’s Agricultural Research Service lab. A DNA sequencer then extracted the nucleotides that make up the plants unique set of genes. And while the team at IBM, Mars and the USDA finished the sequence three years ahead of schedule, the real work is in deciphering the more than 30,000 estimated cacao genes.

The 30,000 is arrived at by using algorithms to identify patterns of genes embedded in the genome. The algorithms “spot” the genes by comparing similarities with known genes from other species.

While this fully automated process can estimate the total number of genes, specific genes are handled by in silico-in vitro screenings – a combination of experimental biology and computer analysis. The analysis is a delicate problem that, in IBM's efforts to identify cacao pod color, demanded algorithmic precision at a different scale (a sort of “genome whisperer”) that analyzed hundreds of pods collected from different geographies.

“Typically, the hardest task is in finding gene(s) responsible for a phenotype in the "mass" of genes in the genomes. The breakthrough here is being able to pinpoint the genes responsible for pod color. ”

Dr. Laxmi Parida, computational genomics manager at IBM Research

Traits of flavor and sustainability through pod color

Classification of cacao cultivars using
the IRiS algorithm, developed by
the IBM scientists

The color coding identified within these cacao candidates, as suggested by these specialized algorithms, were put through an additional vetting process of targeted sequencing, as well as RNA analysis of the relevant tissues in these target plants. The combination of these processes identified which genes expressed pod color, and where they reside within the genome.

The red pod color trait is positively correlated with an undesirable flavor characteristic in the cacao. On the other hand, the green pods taste better but have a lower yield. The ability to screen young cacao seedlings with red or green molecular markers – and then select only those carrying the alleles genes that result in green pods – would greatly reduce the population sizes required for the laborious and expensive evaluations of unlinked flavor and yield traits.

In other words, using marker assisted selection, versus naturally breeding the plants (which takes years), will greatly speed up the effort of identifying and selecting the most flavorful and sustainable cacao plants.

Analyzing any genome

IBM's work to identify the cacao’s pod color is genetic selection, not modification.

IBM conceived, designed and developed these specialized algorithms to identify candidate genes, to provide guidance for specific experiments that support Mars’ work to improve cocoa taste and sustainability. Mars hopes to use these results to rapidly accelerate breeding programs to improve the quality of chocolate produced from cacao beans. All of IBM’s algorithms are available for any research community to apply to their own plant or animal studies.
Explore other food technologies from IBM

Cacao vs. Cocoa

“Cacao” refers to the tree Theobroma cacao and its seeds (and the beans inside of the seeds). The word “cocoa” refers to the processed product of the tree, seed and bean.

This article refers to the gene sequencing of the “cacao” plant.
Meet the researcher

Laxmi Parida
Manager, Computational Genomics Group,
Thomas J. Watson Research Center


Learn more about genome sequencing
Download the algorithms used in the project
Computational genomics at IBM Research
Using genome sequencing to map humanity's family tree
Learn more about IBM Analytics

Ancestral genome reveals cotton tale

ORIGINAL: Hunt Alpha Institute

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HUNTSVILLE, Ala. -- The ability to spin a good yarn recently kept an international team of researchers focused on Gossypium raimondii, the simplest cotton genome. The researchers, including Jeremy Schmutz, faculty investigator at HudsonAlpha and head of the plant program at the U.S. Department of Energy’s Joint Genome Institute, compared the high quality draft assembly of the G. raimondii genome against other cotton species. The team’s findings are presented in the Dec. 20, 2012 edition of Nature.

“By accumulating genetic markers from a variety of species for a variety of qualities, we can facilitate better and targeted cotton strains,” said Schmutz. Textiles, biofuels production and environmental remediation are among broad categories that could benefit from specific traits, while reducing pesticide use, improving disease resistance and promoting more efficient water usage would provide across-the-board benefits.

Indigenous to the Americas, G. raimondii, while not commonly found in U.S. fields, was chosen for sequencing because it has a comparatively small genome and is less complex than most varieties. “The U.S. Department of Agriculture provided several sets of data,” said Schmutz, “and overall, more than 20 years of analysis gleaned from numerous organizations has brought us to this point.” The team of researchers representing 31 institutions traced the evolution of cotton over millions of years, from wild varieties to what is currently grown for modern production.

While much of U.S. cotton is used in textiles, the cotton data will accelerate the study of gene function in cellulose biosynthesis, a fundamental process in biofuels production. Additionally, cotton is important in bioremediation efforts. “Cotton can absorb many times its weight in oil and can be useful for cleanup efforts,” said Schmutz, referencing the Deepwater Horizon spill. “Cotton is also a metal concentrator.” The cotton plant draws metals up into its leaves, he explained, removing heavy metals from soil.

In the U.S., more than 200,000 domestic jobs are related to cotton production and processing, with an aggregate influence of $35 billion on the annual U.S. gross domestic product. The value of cotton fiber grown in the U.S. exceeds $6 billion per year. Cottonseed oil and meal byproducts add another $1 billion annually.

Top cotton-producing counties in Alabama include Limestone, Madison, Lawrence, Monroe, Colbert, Escambia, Lauderdale, Cherokee, Baldwin and Geneva. According to the Alabama Cotton Producers, the state ranks ninth in the nation in production.

Schmutz said the study is a good example of government, academic and industry resources coming together for crop improvement. In addition to DOE JGI, other key organizations include the University of Georgia, the USDA, Cotton Incorporated, Iowa State University, Mississippi State University, the Consortium for Plant Biotechnology Research and the U.S. National Science Foundation.

Hear more about this project from Jeremy Schmutz in this DOE JGI video: http://bit.ly/JGI-cotton-video or read the DOE JGI release here. 

Release Date: December 19, 2012 (All day)

Contact Name: Holly Ralston

Contact Email: hralston@hudsonalpha.org

Contact Phone: 256.508.8954

Organization Background: 

The HudsonAlpha Institute for Biotechnology in Huntsville, Ala, is the cornerstone of the Cummings Research Park Biotechnology Campus. The campus hosts a synergistic cluster of life sciences talent ‐ science, education and business professionals ‐ that promises collaborative innovation to turn knowledge and ideas into commercial products and services for improving human health and strengthening Alabama’s progressively diverse economy. The non‐profit institute is housed in a state‐of‐the‐art, 270,000-square‐ft. facility strategically located in the nation’s second largest research park. HudsonAlpha has a three‐fold mission of genomic research, economic development and educational outreach.

Tell the USDA: Say NO to Monsanto's GMO corn

ORIGINAL: CredoAction (Use this link to support this campaign and send your message)

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Monsanto has claimed for years that its GMO corn reduced the need to apply toxic pesticides to crops, like the company's own product Roundup (the brand name of the toxic pesticide glyphosate which is believed to cause birth defects in laboratory animals).(1)

Yet the sale of "Roundup Ready" GMO crops immediately increased the use of the dangerous pesticide glyphosate. And as glyphosate use skyrockets, farmers are reporting outbreaks of superweeds that can be killed with larger doses of this hazardous chemical every year. It's a vicious cycle.

Now Monsanto has applied for USDA (US department of Agriculture) approval to let yet another Roundup Ready corn variety escape regulation under rules against plant pests, in spite of evidence that some of these superweeds are the product of transgenic crossbreeding with Roundup Ready GMO crops.(2) The USDA is now accepting public comments.

Tell the USDA to start saying no to GMO crops that breed superweeds and increase hazardous pesticide use.

Monsanto can't control genetic drift from its genetically engineered crops, and farmers' continued use of Roundup gives a potential survival advantage to weed populations that absorb Roundup Ready transgenes.

What's Monsanto's solution? Buy more Roundup from Monsanto. Buy more Roundup Ready crops from Monsanto. Spray more Roundup into our environment and, when it doesn't work, do it all over again. Enough.

Tell the USDA to stop superweeds and the pesticide brew at the source by rejecting GMO corn and conducting a full environmental review.

Thank you for standing up to Monsanto.

1. Claire Robinson, "The inside story on Monsanto and the glyphosate birth defect data," The Ecologist, June 13, 2011.

2. Carol Mallory-Smith and Maria Zapiola, "Gene flow from glyphosate resistant crops," Pest Management Science, 2008.