Monthly Archives: June 2017

The towering 234-year-old 'Napoleon' oak on the campus of the University of Lausanne in Switzerland has weathered storms both meteorological and political. The tree was young when Napoleons troops passed through town in 1800, and has grown into a majestic city landmark. But through it all, its genome has remained largelyand surprisinglyunchanged.

Researchers at the university discovered this unexpected stability after sequencing the genome in different branches of the tree. Their workposted on June 13 as a bioRxiv preprint, which has not been peer reviewedmeshes with a growing body of evidence that plants are able to shield their stem cells from mutations. The practice may be valuable for sustaining their health over a lifespan that can reach hundreds of years.

If you just accumulate more and more mutations, you would eventually die of mutational meltdown, says Cris Kuhlemeier, a developmental biologist at the University of Bern in Switzerland.

Each time a cell divides, mutations can arise because of errors made while copying the genome. Animals shield their reproductive cells from these mutations by isolating them early in development. These cells, called the germline, then follow a different developmental path, and typically have a low rate of cell division.

But plants do not have a dedicated germline: the cluster of stem cells that gives rise to the reproductive parts of flowers also generates plant stems and leaves. Because of this, scientists thought that the stem cells would accumulate many mutations,and that newer branches at the top of a long-lived tree would be remarkably different from the lower branches.

Plant biologist Philippe Reymond and his team at the University of Lausanne decided to test this hypothesis using the universitys prized oak tree. They sequenced the genome from leaves on lower, older branches and upper, younger ones, and tallied the number of single-letter changes they found in the tree's DNA. (Reymond declined to be interviewed byNaturebecause the paper is currently under review at a scientific journal.)

The team found that the number of mutations was much lower than would be expected based on calculations of the number of cell divisions that occurred between the lower branch and the higher one.

Its a tantalizing study, says Daniel Schoen, a plant evolutionary biologist at McGill University in Montreal, Canada. It touches on something that was simmering always, in the back of the minds of plant biologists.

It is too soon to say how general this phenomenon will be in plants, cautions Karel ha, a plant geneticist at the Central European Institute of Technology in Brno, Czech Republic. The researchers also looked only at one kind of genetic changesingle-letter changes to the sequenceand did not evaluate other kinds of mutations, such as deleted DNA.

Mao-Lun Weng, a plant evolutionary biologist at South Dakota State University in Brookings, notes that the team used a stringent filter to weed out background noise in the sequencing data, and may have inadvertently missed some mutations as a result.

This could mean that some mutations were left out of the analysis. But ha and Weng are quick to note that the results are in line with two studies published last year. In the first, led by Kuhlemeier, researchers tracked individual stem-cell divisions in the growth region of plants called the meristem. They found that in tomato and thale cress (Arabidopsis), the meristem contains a set of three or four cells that are set aside and divide much less often than the other cells in the region. The other study, led by ha, also found few mutations between old and new leaves in thale cress.

For Kuhlemeier, the results provide an answer to a question that has troubled him ever since a trip to Oregon 20 years ago. As he looked up at a soaring, 400-year-old Douglas fir, Kuhlemeier wondered how the branches towards the top of the tree would differ from those at the bottom. I had always thought of a tree not as an organism, but as a collection of organisms with different genomesmore like a colony, he says. Many ecologists shared his view, but now he has begun to question his earlier idea.

A clearer picture of plant development could help breeders as they increasingly focus on long-lived, perennial plants, says Schoen. If, as plants age, there is this mutation accumulation that could impact vigour, we would want to know about it, he says. We need more information of this type.

This article is reproduced with permission and wasfirst publishedon June 19, 2017.

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Ancient Oak's Youthful Genome Surprises Biologists - Scientific ... - Scientific American

WASHINGTON, June 19, 2017 Scientists say they are gaining a new understanding of why corn or maize as it is widely known outside the U.S. and not some other plant, is the most productive and widely grown crop in the world, after deciphering a new, much more detailed reference genome for the plant.

Among other things, according to a paper published recently in the journal Nature, the new sequence shows that that maize individuals are much, much less alike at the level of the genome than people are.

Our new genome for maize shows how incredibly flexible this plant is, a characteristic that directly follows from the way its genome is organized, says Doreen Ware, of Cold Spring Harbor Laboratory (CSHL) and the U.S. Department of Agriculture, who led scientists at seven academic institutions and several genome technology companies in the project.

Ware says this flexibility not only helps explain why maize has been so successful since its adaptation by primitive farmers thousands of years ago, but also bodes well for its ability to grow in new places as the earths climate changes, and for increasing the plants productivity and environmental sustainability in the U.S. and abroad.

The maize genome is large, but its size is not really what is responsible for what scientists call the plants phenotypic plasticity, that is the potential range in its ability to adapt. In trying to determine what possibilities are available to a plant when adapting to new or changing conditions, it is just as much the context in which genes are activated or silenced as the identity of the genes themselves that determines what the total set of genes enables a plant to do, Ware explains.

It is precisely this context of gene activity variations in way the plants genes are regulated in different individuals across the species that the new genome is bringing to light, the researchers said in a release. By assembling a highly accurate and very detailed reference genome for an important maize line called B73, and then comparing it with genome maps for maize individuals from two other lines (W22 and Ki11), grown in different climates, the sequencing team arrived at an astonishing realization.

Maize individuals are much, much less alike at the level of the genome than people are, for one thing, Ware says. The genome maps of two people will each match the reference human genome at around 98 percent of genome positions. Humans are virtually identical, in genome terms. But weve found that two maize individuals from the W22 and Ki11 lines each align with our new reference genome for B73 maize only 35 percent, on average. Their genome organization is incredibly different, she says.

Yinping Jiao, a postdoctoral researcher in the Ware lab and first author of the paper announcing the new genome, said this difference between maize individuals is a reflection not only of changes in the sequence of the genes themselves, but also where and when genes are expressed, and at what levels.

It is possible to home in on these variabilities in gene expression in unprecedented detail in the new reference genome sequence. The first reference genome for maize, completed in 2009, was a major milestone, but owing to now outdated technology, it yielded a final genome text more akin to a speed-reading version than one fit for close reading, says Ware.

The 2009 sequence tended to miss two things. So-called first-generation sequencing technology could not solve the great number of repetitive sequences in the maize genome, and tended to miss a significant number of spaces between genes. Because so many tiny pieces had to be stitched together to form a whole, it was particularly hard to accurately capture the many places in maize where DNA letters form long repeating sequences. Repeat sequences are especially important in maize, owing to the particular way its genome evolved over millions of years.

The new sequence makes use of what biologists call long-read sequencing, which, as the name suggests, assembles a complete genome from many fewer pieces about 3,000 as opposed to the over 100,000 smaller pieces it took to build the 2009 reference genome. The new technology is also much cheaper; the just completed effort cost around $150,000, compared with more than $35 million for its predecessor.

Long-read technology, by giving scientists a granular view of the space between genes in maize, sheds revealing light on how those genes are regulated, since regulatory elements are often physically situated in regions just up- or downstream from genes.

Because of its amazing phenotypic plasticity, concludes Ware, so many more combinations are available to this plant. What does this mean to breeding? It means we have a very large variation in the regulatory component of most of the plants genes. They have lots of adaptability beyond what we see them doing now. That has huge implications for growing maize as the population increases and climate undergoes major change in the period immediately ahead of us.

The new genomes resolution of spaces between genes -- intergenic regions -- also makes it possible to read detailed histories from the texts of genomes from different maize individuals. We want to understand how the maize genome evolved, Ware says, to be able to look at the genome in an individual and have it tell us a story. Why does the expression of a given gene change, and under what circumstances?

Consider, for instance, the impact of transposons bits of DNA that jump around in genomes. This can now be assessed with specificity not previously possible. Transposons, which are present in all genomes, were first seen and described in maize in the 1940s by CSHL Nobel laureate Barbara McClintock.

The new reference genome helps scientists understand how the history and structure of the maize genome has been determined by the action of transposons more than in most plants. When they jump into a position within a gene, the gene can be compromised entirely. Other times, whether a transposon has hopped into a position just before or after a gene can determine when and how much it is expressed.

While the phenomenon of jumping genes has been understood for decades, its impact in different individuals in various maize lines provides precisely the kind of information that can help explain the plants evolutionary success.

The plants genomic plasticity is also a boon to breeders. Diversity in maize is the resource base for breeding, says Jiao. Its the key to making better maize, and more of it, in the future.

(Employees of two companies were involved in the research and co-authored the paper: Pacific Biosciences of Menlo Park (sequencing); and BioNano Genomics of San Diego (optical mapping). The paper, titled Improved maize reference genome with single molecule technologies, can be accessed by clicking here.)

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Corn genome research bodes well for plant's adaptation to climate change - Agri-Pulse

Our knowledge of our genomes is accelerating rapidly, associate professor Marcel Dinger

The traditional annual health check for executives is changing. While all the usual tests are still being used, for the first time there will be an option for whole genome sequencing too.

This new generation testing began in Sydney this week and, though it has the potential to add tremendous value and can already add some value it is early days and there are issues for participants to consider.

The service, called GoNavigate, is a private partnership operating from the St Vincent's campus in Sydney. It checks people from their diet to their DNA.

It combines the genomics expertise of the Garvan Institute for Medical Research and that of Executive Health Solutions, which has provided health checks for corporates in Australia for more than 30 years.

Although anyone who is curious about their health can use the service, at a cost of $6400 (excluding GST), with no Medicare rebate, it is likely to be used mostly by corporates.

It's predicted that one day whole genome sequencing will be routine and babies will have it done at birth. But getting there is complicated and costly.

A few years ago the Mayo Clinic in the US identified executives as the ideal population group to lead the rest of us into the new world of genomic medicine.

Executives were the perfect pioneers; they could afford it, they were already on health check programs and as "early adapters" they were willing to embrace the new culture of genomics.

And they would be attracted by the double benefit: the immediate benefits for their own health and the "heritage" benefits for their children and grandchildren.

While many places in Australia offer some genetic testing to patients, the Garvan is the only place that can sequence the entire genome in a clinical setting.

Now through a commercial partnership between its own company, Genome.One and Executive Health Solutions' corporate clinic, Life First, whole genome sequencing is available to the public.

Their joint service, GoNavigate, is the first attempt in Australia to embed whole genome sequencing in a comprehensive medical check. It's ambitious because genomic knowledge is still limited, although it is evolving fast.

While GoNavigate will sequence a person's whole genome and screen all 20,000 genes, presently it can only interpret 230 of them.

But the sequencing creates a lasting resource that can be mined repeatedly as knowledge grows. This means when the person returns a year or two later, more interpretations may be possible. This and subsequent checks will be far cheaper because the sequencing is already done.

From the current 230 genes this service can detect increased genetic risk for more than 49 conditions which include 31 types of cancer and 13 heart conditions where monitoring and intervention can be of benefit.

It can also predict the person's response to more than 220 medications.

While only 5 to 10 per cent of participants are expected to discover a genetic variation that increases their health risk, almost all will receive some information that can help to refine their choice of medications.

"Genetic information provides an entirely new dimension to understand your health but its value is best realised in the context of other health data," says Marcel Dinger, associate professor at the Garvan and CEO of Genome.One.

The next generation of healthcare is about prevention. He says it is about knowing what you are facing and then trying to prevent it. Genomics is a crucial part of this.

But do people want to know what is lurking in their genes? If something untoward is found, under what conditions would they be obliged to disclose it to their employer or insurance company?

These are complex issues which the service can help answer. Dinger says all information will remain strictly confidential between the service and the participant.

In addition, the service will not provide genetic information where no evidence-based lifestyle change or treatment is possible. A genetic counsellor makes this clear to participants at the outset.

While the sequencing can't diagnose cancer, it can tell if a person has a predisposition to a cancer and alert them to the value of possible precautionary action to prevent or detect it as early as possible.

A common example would involve cholesterol. A person with fluctuating high cholesterol on blood tests may be undecided about whether to try to control it with a statin. These drugs are taken over the long term and have side effects.

In recent times people have begun questioning whether they really need them. If the genetic test shows they have familial high cholesterol, then the case for taking these drugs is stronger.

"The extra genetic layer provides a more certain diagnosis of particular conditions that otherwise wouldn't be available. It allows people to have more confidence in the result," says Dinger. "And as new treatments grow for existing diseases and as we get better at identifying new diseases, so the importance of that genetic layer will increase."

Five per cent of Genome.One's revenue from this service will be dedicated to iHope, which is for families with rare and genetic conditions who can't afford genomic diagnosis.

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Health checks for executives leap into the genomic future - The Australian Financial Review