Daily Archives: April 15, 2013

The extraordinary level of conservation of the tulip tree (Liriodendron tulipifera) mitochondrial genome has redefined our interpretation of evolution of the angiosperms (flowering plants), finds research in biomed Central's open access journal BMC Biology. Credit: Gary Cot

The extraordinary level of conservation of the tulip tree (Liriodendron tulipifera) mitochondrial genome has redefined our interpretation of evolution of the angiosperms (flowering plants), finds research in biomed Central's open access journal BMC Biology. This beautiful 'molecular fossil' has a remarkably slow mutation rate meaning that its mitochondrial genome has remained largely unchanged since the dinosaurs were roaming the earth.

Evolutionary studies make used of mitochondrial (powerhouse) genomes to identify maternal lineages, for example the human mitochondrial Eve. Among plants, the lack of genomic data from lineages which split away from the main evolutionary branch early on has prevented researchers from reconstructing patterns of genome evolution.

L. tulipifera is native to North America. It belongs to a more unusual group of dicotyledons (plants with two seed leaves) known as magnoliids, which are thought to have diverged early in the evolution of flowing plants.

By sequencing the mitochondrial genome of L. tulipifera, researchers from Indiana University and University of Arkansas discovered that its mitochondrial genome has one of the slowest silent mutation rates (ones which do not affect gene function) of any known genome. Compared to humans the rate is 2000 times slower the amount of genomic change in a single human generation would take 50,000 years for the tulip tree. The rate is even slower for magnolia trees, taking 130,000 years for the same amount of mitochondrial genomic change.

Ancestral gene clusters and tRNA genes have been preserved and L. tulipifera still contains many genes lost during the subsequent 200 million years of evolution of flowering plants. In fact one tRNA gene is no longer present in any other sequenced angiosperm.

Prof Jeffrey Palmer who led this study explained, "By using the tulip tree as a guide we are able to estimate that the ancestral angiosperm mitochondrial genome contained 41 protein genes, 14 tRNA genes, seven tRNA genes sequestered from chloroplasts, and more than 700 sites of protein editing. Based on this, it appears that the genome has been more-or-less frozen in time for millions and millions of years."

More information: The "fossilized" mitochondrial genome of Liriodendron tulipifera: Ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate, Aaron O Richardson, Danny W Rice, Gregory J Young, Andrew J Alverson and Jeffrey D Palmer, BMC Biology 2013, 11:29 doi:10.1186/1741-7007-11-29

Commentary: Mitochondrial genomes as living 'fossils', Ian Small, BMC Biology 2013, 11:30 doi:10.1186/1741-7007-11-30

Provided by BioMed Central

Link:
The tulip tree reveals mitochondrial genome of ancestral flowering plant

Ion Torrent via YouTube

A researcher initializes an Ion Proton system at the Baylor College of Medicine Human Genome Sequencing Center in Houston. Ion Torrent says the benchtop device is designed to sequence a human genome in a day for less than $1,000.

By Tanya Lewis, LiveScience

This month marks the 10-year anniversary of the Human Genome Project, a 13-year international effort to determine the sequence of the 3 billion "letters" in a human being's DNA.

The $3 billion project, led by the U.S. Department of Energy and the National Institutes of Health, began in 1990 and was completed on April 14, 2003. In the decade since then, scientists have achieved many important milestones in using genomic discoveries to advance medical knowledge.

Sequencing technology has vastly improved in recent years. Sequencing the first human genome cost about $1 billion and took 13 years to complete; today it costs about $3,000 to $5,000 and takes just one to two days.

But just knowing the sequence would be meaningless without a way to interpret it. So researchers found ways to study the genomes function, by sequencing the genomes of 135 other organisms and surveying the global variation among human genomes. [Unraveling the Human Genome: 6 Molecular Milestones]

Researchers compared the genome sequences of other animals, such as chimpanzees and platypuses, as well as other eurkaryotic organisms (those whose cells have a nucleus), such as yeast and flat worms. From this comparison, scientists could identify stretches of DNA that have remained largely unchanged over the course of evolution. Five to 8 percent of the human genome has been unchanged for thousands of years.

One of the more surprising findings is how little of the human genome (only 1.5 percent) actually encodes proteins, the molecular building blocks that perform most of the critical functions inside cells.

To probe this mystery, more than 400 researchers from 32 labs worldwide created the ENCyclopedia Of DNA Elements (ENCODE) consortium. In 2012, they published many important findings about how the human genome functions. These include locations in the genome that may be genetic "switches" to turn genes on and off, as well as demonstrating that more than 80 percent of the genome that was once called "junk DNA" actually does serve a function.

Here is the original post:
Human Genome Project marks 10 years

This month marks the 10-year anniversary of the Human Genome Project, a 13-year international effort to determine the sequence of the 3 billion "letters" in a human being's DNA.

The $3 billion project, led by the U.S. Department of Energy and the National Institutes of Health, began in 1990 and was completed on April 14, 2003. In the decade since then, scientists have achieved many important milestones in using genomic discoveries to advance medical knowledge.

Sequencing technology has vastly improved in recent years. Sequencing the first human genome cost about $1 billion and took 13 years to complete; today it costs about $3,000 to $5000 and takes just one to two days.

Probing genome function

But just knowing the sequence would be meaningless without a way to interpret it. So researchers found ways to study the genomes function, by sequencing the genomes of 135 other organisms and surveying the global variation among human genomes. [Unraveling the Human Genome: 6 Molecular Milestones]

Researchers compared the genome sequences of other animals, such as chimpanzees and platypuses, as well as other eurkaryotic organisms (those whose cells have a nucleus), such as yeast and flat worms. From this comparison, scientists could identify stretches of DNA that have remained largely unchanged over the course of evolution. Five to 8 percent of the human genome has been unchanged for thousands of years.

One of the more surprising findings is how little of the human genome (only 1.5 percent) actually encodes proteins, the molecular building blocks that perform most of the critical functions inside cells.

To probe this mystery, more than 400 researchers from 32 labs worldwide created the ENCyclopedia Of DNA Element (ENCODE) consortium. In 2012, they published many important findings about how the human genome functions. These include locations in the genome that may be genetic "switches" to turn genes on and off, as well as demonstrating that more than 80 percent of the genome that was once called "junk DNA" actually does serve a function.

Other research has focused on measuring the variation among human genomes. Preliminary studies during the Human Genome Project indicated that human genomes differ by just one-tenth of a percent. Investigating the limited variation that does exist is key to understanding human health and disease.

In sickness and in health

Link:
Human Genome Project Marks 10th Anniversary