Archive for May 30th, 2012
More Genes Than Humans: The Tomato Decoded
The tomato, whose genome has just now been decoded, turns out to be one well-endowed vegetable, possessing 31,760 genes. This rich legacy, possibly a reflection of the disaster that killed off the dinosaurs, is some 7,000 more than that of a person, and presents a complex puzzle to scientists who hope to understand its secrets.
A consortium of plant geneticists from 14 countries has spent nine years decoding the tomato genome in the hope of breeding better ones. The scientists sequenced the genomes of both Heinz 1706, a variety used to make ketchup, and the tomato’s closest wild relative, Solanum pimpinellifolium, which lives in the highlands of Peru, where the tomato’s ancestors originated. Their results were published online Wednesday in the journal Nature.
The tomato, though a fruit to botanists, has been decreed a vegetable by the United States Supreme Court. The verdict is not so unreasonable given that the tomato has a close cousin that is a vegetable, namely the potato. The genomes of the two plants have 92 percent of their DNA in common, the tomato researchers report. The main difference is that the potato is thought to have a handful of genes that direct the plant’s energy away from producing fruit and into the generation of tubers. But even with the genomes of the two plants deciphered, those genes have not yet been identified, said Daniel Zamir, a plant geneticist at Hebrew University in Jerusalem and one of the report’s two principal authors.
The tomato genome is both of intrinsic interest and a key to understanding the very versatile family of plants to which it belongs. Besides the potato, the Solanaceae family, as it is known, includes the tobacco plant, the pepper, the eggplant and deadly nightshade.
That the tomato and potato contain so many genes does not mean that they are more sophisticated than people but that they have chosen a different stratagem for managing their cells’ affairs. Humans make heavy use of a technique called alternative splicing, which allows the components of each gene to be assembled in many different ways, so that one gene can produce many products.
The Solanaceae family, by contrast, has developed its genetic complexity through gaining more genes. About 70 million years ago, some lucky mishap in the process of cell division led to a triplication of the Solanum genome. The two spare copies of each gene were free to change through mutation. Many were useless and got dropped from the genome, but others developed useful new functions.
The tomato genome team has been able to visualize the result of this triplication by comparing the tomato’s genome with that of the grapevine, a distant relative from which it parted company about 100 million years ago, well before the triplication event. Some of the grape’s genes have a single counterpart in the tomato genome, some have two counterparts and some have three.
Usually the triplication of a genome would be a considerable handicap, saddling a plant with three times as much DNA as it needs. But this event occurred around the time of the catastrophe in which the dinosaurs perished, and the extra genetic versatility may have been a lifesaver. “It’s easy to think that in that period, with a lot of volcanic activity and little sunlight, the reservoir of a lot of additional genes would be useful to a plant,” said Jim Giovannoni, a plant geneticist at the Boyce Thompson Institute for Plant Research in Ithaca, N.Y., who led the American contribution to the tomato genome report.
Plant breeders have had more success breeding tomatoes with features of interest to producers, like long shelf life, than with the traits that matter to consumers, like taste and quality, Dr. Giovannoni said. The tomato genome sequence may help redress the balance, since plant breeders can now rely on DNA as well as physical traits to govern their breeding programs, he said.
Price tag put on Virginia Tech’s Stadium Woods
What’s the value of an old-growth forest fragment that may be unique on the East Coast?
In a report commissioned by Virginia Tech officials, Maryland-based consulting firm Biohabitats Inc. has put the ecological value of the woods at just more than $5 million.
The report, which was dated May 2012, was obtained Tuesday by The Roanoke Times through a Virginia Freedom of Information Act request.
Now university President Charles Steger and the board of visitors — which will meet in Blacksburg on Sunday and Monday — must weigh that calculation against the value of an indoor football practice facility proposed for up to 5 acres of the woods. The report puts the total footprint of the woods at 13.75 acres.
Cutting or otherwise altering 3 acres for the facility would devalue the woods by more than $1 million, according to the report. But construction is not the only thing that could degrade the woods.
A severe gypsy moth infestation could reduce their value by about $4 million, the report stated.
No mere inventory of species or site plan assessment, the valuation is based largely on pollution management services provided by the woods and its old growth ecosystem and calculated using a model developed by the U.S. Forest Service, the report stated.
Tech paid Biohabitats $17,600 for its work, university spokesman Larry Hincker said.
But the company’s report is only one piece of information considered by a 15-member ad-hoc committee charged with studying the woods vs. practice facility issue, and recommending a course of action to Steger. The committee’s meetings, which have been ongoing since January, were closed to the public.
According to chairman John Randolph, the committee has heard presentations, received about 500 emails from the public and conducted a random survey of more than 1,000 people.
The committee’s recommendation, which is officially due Friday, was submitted over the holiday weekend, Hincker said.
He declined to release the committee’s findings, saying Steger had not had a chance to review them.
As envisioned by the athletic department, the practice facility would be about 400 feet long by 250 feet wide, and between 65 and 90 feet tall to allow punting. The department proposed siting the facility near Lane Stadium in the north end of the woods. That section is home to a Corps of Cadets rappelling tower, and is beset by invasive species, the report stated.
The better-preserved southern end of the woods behind the stadium would be retained. Still, Biohabitats’ report concluded that maintaining the highest ecological value possible in the old-growth “forest patch” requires leaving both sections intact.
The report estimates that the woods contain up to 59white oaks that may be 300 years old or older. These findings are in line with estimates of the number and age of old-growth white oaks found in the woods by retired extension specialist Jeff Kirwan, whose work touched off the debate about the future of the woods in November.
In fact, the work of Kirwan, and of Tech forestry professor John Seiler, was used as source material, the report stated.
Since November, the university Faculty Senate, the Student Government Association and the student-led Environmental Coalition have declared their support for keeping the woods intact.
Friends of Stadium Woods, a community coalition advocating preservation of the woods, has sponsored events and mounted letter writing campaigns.
Poll: Michiganders meh on tree height
Are the trees in Michigan the right height? Mitt Romney obviously thinks so, having said so back in February.
In a curious survey question, Public Policy Polling has asked Michigan voters whether they agree with the vertical quality of their trees.
The results? A collective shrug.
While 38 percent said yes when asked, “In Michigan, do you think the trees are the right height, or not?,” and 8 percent said no, 55 percent said they were “not sure.”
For those who really want to get into the weeds (or is it roots?) on this question, the crosstabs revealed that more Obama supporters believed in the perfection of Michigan trees: 44 percent of those who backed Obama in 2008 also backed the height of Michigan trees as compared to 27 percent for McCain supporters.
The poll has some other interesting results: Only 24 percent of voters think of Romney, who was raised in the state, as a Michigander, versus 65 percent who do not. And the polling firm tweeted out another tidbit (not in the poll): “Eminem has a better net favorability in Michigan than Mitt Romney.”