New genomes hint at evolution’s slimy past

RICE/ UC BERKELEY (US) — Scientists have unveiled the genomes of a leech, an ocean-dwelling worm, and a limpet, more than doubling the number of genomes from a vast, under-studied swath of the animal kingdom.

Lophotrochozoans, (pronounced “LOH-foh-troh-coh-zoh-uhns”), are a diverse group of animals that includes mollusks—such as snails, clams, and octopuses—and annelids—such as leeches and earthworms. This group includes as many as one-quarter of Earth’s marine species.

This scanning electron microscope image shows an 18-hour-old trochophore of the owl limpet, Lottia gigantea. (Credit: Eric Edsinger-Gonzales, UC Berkeley)


“Through comparison of these diverse genomes with each other, we can learn what animals have in common with each other, which in turn tells us about the features that their common ancestors had,” says Daniel Rokhsar, University of California, Berkeley, professor of molecular and cell biology and of physics.

“That is a big driver for comparative genome sequencing—it is one of the few ways we have of looking back in deep time.”

For these organisms, deep time means more than 500 million years ago, toward the end of the Precambrian era, when they split off from animals that eventually evolved to become vertebrates (animals with backbones), such as humans.

Most animals, including people, have body plans with bilateral symmetry, which means they have left and right sides that are mirror images of one other,” says co-author Nicholas Putnam, assistant professor of ecology and evolutionary biology at Rice University. “When you look at all bilaterian species, you can divide them into three big groups that biologists call clades.

“Lophotrochozoans are one of these clades, and when we looked at all of the genomes that had been sequenced, we found that only two were lophotrochozoans,” he says. “That left a big hole in the genetic record, and our goal with this study was to fill in some of the gaps in that blank space.”

Genome sequencing for the new study was performed at the Department of Energy’s Joint Genome Institute in Walnut Creek, California, where Rokhsar is program lead for eukaryotic genomics. As reported in Nature, the three newly sequenced species are Capitella teleta, an ocean-dwelling worm; Helobdella robusta, a freshwater leech; and Lottia gigantean, a large marine mollusk.

One of the latest three sequenced genomes belongs to the ocean-dwelling worm Capitella teleta, seen here. View larger. (Credit: E. Seaver/University of Hawaii)

Finding ancestors

“At Rice, we work on comparative genomics,” Putnam says. “We look for recognizable similarities across genomes, and we are interested in similarities among the genes themselves and also among the patterns of genetic organization. These structural similarities can tell us a lot about the evolution of individual genes and functional gene groups, like chromosomes.”

In examining the lophotrochozoan genomes, Putnam’s group developed new computational tools to examine and compare the differences among the three new genomes and hundreds of known genomes, including those for humans and oft-studied model organisms like the fruit fly.

The tools streamlined the search for similarities among the genomes and also helped the researchers trace evolutionary changes that occurred in specific groups of genes.

“Using these tools, we focus on the part of the evolutionary tree where specific mutations took place,” Putnam says. “For example, we can say, ‘A mutation occurred here that moved a big chunk of this chromosome, and it must have happened after lophotrochozoans diverged from deuterostomes but before the split between mollusks and annelids.'”

So far, Putnam’s group has traced 17 “ancestral linkage groups,” large groups of genes that are similar in structure to chromosomes, to the last common ancestor of all the bilaterians.

Genes today

“For us, the interesting thing is finding genes that exist today in different species, tracing those to a single gene in a common ancestor and then using the patterns we find to test hypotheses about evolutionary processes,” Putnam says. “Sometimes the genes today might still have the same function, but other times they have evolved an entirely new function.”

Putnam says the team has been able to trace the lineage of almost half of the genes in the three new genomes, and the work continues.

“These studies teach us important lessons about ourselves and other vertebrates,” Putnam says. “Looking across the animal kingdom gives us more resolution and clarity about what in our genome is new and what has been preserved from our ancient ancestors.”

Additional co-authors contributed from Rice, UC Berkeley, the European Molecular Biology Laboratory, JGI, Williams College, Children’s Hospital Oakland Research Institute, Hudson Alpha Institute for Biotechnology, and the University of Hawaii.

The DOE, the Gordon and Betty Moore Foundation, R. Melmon, the National Science Foundation, the National Institutes of Health, the Boehringer Ingelheim Fonds, and the National Human Genome Research Institute supported the research.

Sources: Rice, UC Berkeley