Navigation Links
One species, many genomes

Faster growth, darker leaves, a different way of branching - wild varieties of the plant Arabidopsis thaliana are often substantially different from the laboratory strain of this small mustard plant, a favorite of many plant biologists. Which detailed differences distinguish the genomes of strains from the polar circle or the subtropics, from America, Africa or Asia has been investigated for the first time by research teams from Tübingen, Germany, and California led by Detlef Weigel from the Max Planck Institute for Developmental Biology. The results were surprising: The extent of the genetic differences far exceeds the expectations for such a streamlined genome, as the scientists write in this week’s edition of Science magazine.
Arabidopsis plants from different geographical origins differ in many traits (the background shows schematically sequence variation in the DNA of these plants).


To track down the variation in the genome of the different Arabidopsis strains, the researchers compared the genetic material of 19 wild strains with that of the genome of the lab strain, which was sequenced in the year 2000. Using a very elaborate procedure, they examined every one of the roughly 120 million building blocks of the genome. For their molecular sleuthing they used almost one billion specially designed DNA probes. "All together, these probes would have seven times the length of human genome," illustrates Weigel the extent of the project. The data were evaluated with several specially designed statistical methods, including a variant of machine learning.

The result of this painstaking analysis: on average, every 180th DNA building block is variable. And about four percent of the reference genome either looks very different in the wild varieties, or cannot be found at all. Almost every tenth gene was so defective that it could not fulfill its normal function anymore!

Results such as these raise fundamental questions. For one, they qualify the value of the model genomes sequenced so far. "There isn’t such a thing as the genome of a species," says Weigel. He adds "The insight that the DNA sequence of a single individual is by far not sufficient to understand the genetic potential of a species also fuels current efforts in human genetics."

Still, it is surprising that Arabidopsis has such a plastic genome. In contrast to the genome of humans or many crop plants such as corn, that of Arabidopsis is very much streamlined, and its size is less than a twentieth of that of humans or corn—even though it has about the same number of genes. In contrast to these other genomes, there are few repeats or seemingly irrelevant filler sequences. "That even in a minimal genome every tenth gene is dispensable, has been a great surprise," admits Weigel.

Detailed analyses showed that genes for basic cellular functions such as protein production or gene regulation rarely suffer knockout hits. Genes that are important for the interaction with other organisms, on the other hand, such as those responsible for defense against pathogens or infections, are much more variable than the average gene. "The genetic variability appears to reflect adaptation of local circumstances," says Weigel. It is likely that such variable genes allow plants to withstand dry or wet, hot or cold conditions, or make use of short and long growing seasons.

Such genome analyses of unprecedented details will allow a much better understanding of local adaptation, and this was indeed one of the main reasons for conduction the study. "By extending these types of studies to other species we hope to help breeders to produce varieties that are optimally adapted to rapidly changing environmental conditions," explains Weigel. He is already collaborating with the International Rice Research Institute (IRRI) in the Philippines to apply the methods and experience gathered with Arabidopsis to twenty different rice varieties.

How environment and genome interact is also the goal of new, even more powerful methods. While the technology used so far can only identify genes that have changed or are lost relative to the reference genome, direct sequencing of the genome of wild strains will allow the detection of new genes. The plan is to decipher the genomes of at least 1001 Arabidopsis varieties. A new instrument, with which the entire genome of a plant can be read in just a few days, is already available. Still missing are the computational algorithms to interpret the anticipated flood of data.


'"/>

Source:Max-Planck-Gesellschaft


Related biology news :

1. Same mutation aided evolution in many fish species, Stanford study finds
2. Reservoirs may accelerate the spread of invasive aquatic species, researchers say
3. First surveys of Tanzanian mountains reveal 160+ animal species, including new & endemic
4. Multiple Campylobacter Genomes Sequenced
5. Big differences in duplicated DNA distinguish chimp and human genomes
6. Double trouble: Cells with duplicate genomes can trigger tumors
7. Three deadly parasite genomes sequenced
8. Researchers predict infinite genomes
9. Breaking the mold: Research teams sequence three fungus genomes
10. DOE JGI releases IMG 1.5 with curated archaeal genomes
11. Whats shaped like a pear and has 2 genomes? Check the pond
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:4/15/2016)... DUBLIN , April 15, 2016 ... of the,  "Global Gait Biometrics Market 2016-2020,"  report ... http://photos.prnewswire.com/prnh/20160330/349511LOGO ) , ,The global gait ... CAGR of 13.98% during the period 2016-2020. ... movement angles, which can be used to compute ...
(Date:4/13/2016)... , April 13, 2016  IMPOWER physicians supporting Medicaid ... setting a new clinical standard in telehealth thanks to ... leveraging the higi platform, IMPOWER patients can routinely track ... and body mass index, and, when they opt in, ... convenient visit to a local retail location at no ...
(Date:3/31/2016)... -- Genomics firm Nabsys has completed a financial  restructuring under ... M.D., who returned to the company in October 2015. ... including Chief Technology Officer, John Oliver , Ph.D., ... Vice President of Software and Informatics, Michael Kaiser ... Bready served as CEO of Nabsys from 2005-2014 and ...
Breaking Biology News(10 mins):
(Date:6/23/2016)... , June, 23, 2016  The Biodesign Challenge ... envision new ways to harness living systems and biotechnology, ... Art (MoMA) in New York City ... 130 participating students, showcased projects at MoMA,s Celeste Bartos ... Paola Antonelli , MoMA,s senior curator of architecture and ...
(Date:6/23/2016)... NC (PRWEB) , ... June 23, 2016 , ... In ... University Hospital in Denmark detail how a patient who developed lymphedema after being treated ... tissue. The results could change the paradigm for dealing with this debilitating, frequent side ...
(Date:6/23/2016)... , June 23, 2016 On ... session at 4,833.32, down 0.22%; the Dow Jones Industrial Average ... 500 closed at 2,085.45, down 0.17%. Stock-Callers.com has initiated coverage ... INFI ), Nektar Therapeutics (NASDAQ: NKTR ), Aralez ... Inc. (NASDAQ: BIND ). Learn more about these ...
(Date:6/23/2016)... , June 22, 2016  Amgen (NASDAQ: ... the QB3@953 life sciences incubator to accelerate ... The shared laboratory space at QB3@953 was created to ... key obstacle for many early stage organizations - access ... the sponsorship, Amgen launched two "Amgen Golden Ticket" awards, ...
Breaking Biology Technology: