Physics @ Berkeley
Physics in the News
Title: Distant Relatives, Common Genes
Date: 05/29/2008
Publication: Science Matters @ Berkeley
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Distant Relatives, Common Genes

by Kathleen M. Wong

Glance through any family\'s photo album, and you\'re likely to home in on a few outstanding ancestral traits. The shape of a nose or the arch of an eyebrow can be passed down for generation after generation.

Biologists have long studied commonalities such as these to infer ancestral relationships between animals. But the more distant the relationship, such as between humans and sponges, the trickier it is to establish connections through simple comparisons of anatomy.


A Berkeley professor of both physics and cell and molecular biology, Dan Rokhsar is also a member of Berkeley\'s Center for Integrative Genomics and a faculty scientist at the Department of Energy\'s Joint Genome Institute. Photo credit: courtesy Dan Rokhsar

Dan Rokhsar, a Berkeley professor of both physics and molecular and cellular biology, and a faculty scientist at the Department of Energy\'s Joint Genome Institute, is sidestepping this problem via a different aspect of inheritance: genes. Genes shared by distantly related animals are likely to have originated in their last common ancestor. So by sequencing and comparing the genomes of creatures ranging from sea anemones to sea squirts, limpets to pufferfish, Rokhsar and his research team hope to reconstruct characteristics of the great-great grandparents to all animals.

"We\'re interested in that transition from being a unicellular organism to being multicellular-when it happened and how it happened," Rokhsar says. "The fossil record can\'t tell you much because the animals at the time were soft-bodied."

Instead, Rokhsar studies the genomes of its living descendants. His approach has already yielded many surprises. For example, sea anemones, which lack a brain or any other type of central control, have long been considered to have a correspondingly primitive nervous system. But Rokhsar has discovered genes that code for different types of neurons to grow in various regions of an anemone\'s body.

"By looking at where and when these genes are expressed, we\'re finding patterns you can\'t see just by looking at the animal," Rokhsar says.

Rokhsar\'s work is also giving scientists a broader perspective on popular model organisms such as fruit flies and nematode worms. Their genes are relatively simple in structure, with few of the intervening segments that break up human genes. Some scientists speculated that this genomic complexity is what gave humans an evolutionary edge. But Rokhsar has found that the genomes of sea anemones and limpets are equally complex.

"We\'re learning that the human genome is more typical than we thought," Rokhsar says. "It also gives us hints about why fruit flies and nematode worms have been so useful. By clearing away all that other complexity, they\'ve stripped away a lot of the stuff that makes it harder to work with vertebrate systems, and have laid bare the basic system."


Rokhsar is sequencing the genomes of organisms as diverse as the starlet sea anemone (left) and choanoflagellates (right). His work is encouraging comparative research in a broader variety of organisms and improving our understanding of animal evolution. anemone photo credit: Nicholas Putnam, UC Berkeley; choanoflagellate photo credit: Nicole King lab, UC Berkeley

By diversifying the types of organisms with available genomes, Rokhsar hopes to encourage interest in these species as laboratory models. The resulting knowledge can only improve understanding of how animals evolve and adapt to challenges such as a changing climate.

Recently, the skyrocketing price of petroleum and the threat of global climate change have turned Rokhsar\'s attention toward greener subjects: plants. Now, he is not only providing new insights into our genetic heritage but also clearing a path toward a cleaner, greener future.

"The cellulose and lignin in plant walls is where all of the carbon goes from photosynthesis. That\'s the carbon we want to convert to fuel. How do they do it? One way to find an answer is to look at genomes," Rokhsar says.

He is now working to sequence the genome of switchgrass, a native plant and strong candidate to produce biofuel. Scientists want to understand which switchgrass genes promote positive traits such as fast growth or minimal fertilizer requirements. With these in hand, they can screen sprouts for desired characteristics and hasten the development of useful varieties.

"We need to collapse the 5,000 years it took to breed maize into an edible plant into 10 years for switchgrass, because we don\'t have a lot of time to develop renewable fuels," Rokhsar says. "And we\'ll need to do this sustainably and as a solution for the long term."

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