A new report in the journal Nature unveils three of the first genomes from a vast, understudied swath of the animal kingdom that includes as many as one-quarter of Earth's marine species. By publishing the genomes of a leech, an ocean-dwelling worm and a kind of sea snail creature called a limpet, scientists from Rice University, the University of California-Berkeley and the Department of Energy's Joint Genome Institute (JGI) have more than doubled the number of genomes from a diverse group of animals called lophotrochozoans (pronounced: LOH-foh-troh-coh-zoh-uhns).
Lophotrochozoans are a diverse group of animals that includes mollusks – such as snails, clams and octopuses -- and annelids -- such as leeches and earthworms. Like humans and all other animals, lophotrochozoans can trace their evolutionary history to the earliest multicellular creatures. But the lophotrochozoan branch of the evolutionary tree diverged more than 500 million years ago from the branch that produced 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," said co-author Nicholas Putnam, assistant professor of ecology and evolutionary biology at Rice. "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 said. "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 JGI in Walnut Creek, Calif. The three newly sequenced species are Capitella teleta, an ocean-dwelling worm; Helobdella robusta, a freshwater leech; and Lottia gigantean, a large marine mollusk.
Putnam's co-investigators included Daniel Rokhsar, of both Berkeley and JGI; David Weisblat and Eric Edsinger-Gonzales, both of Berkeley; Elaine Seaver of the University of Hawaii; and Oleg Simakov of the European Molecular Biology Laboratory at Heidelberg, Germany. Putnam's group, which included Rice graduate student Jie Lv and scientific programmer Paul Havlak, focused on genomic analysis.
"At Rice, we work on comparative genomics," Putnam said. "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."
Almost all published genomes are from the animal kingdom's most-studied clades: deuterostomes, which includes humans and other vertebrates, and ecdysozoans, which includes insects. Only two lophotrochozoan genomes have been previously mapped, and both are for parasitic worms, which aren't representative of most species in the clade, Putnam said.
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 said. "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.
"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 said. "Sometimes the genes today might still have the same function, but other times they have evolved an entirely new function."
Putnam said 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 said. "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."
Rice University: http://media.rice.edu
This press release was posted to serve as a topic for discussion. Please comment below. We try our best to only post press releases that are associated with peer reviewed scientific literature. Critical discussions of the research are appreciated. If you need help finding a link to the original article, please contact us on twitter or via e-mail.
South Africa has begun testing a humane way to make its beaches safer
There used to be rhinos in North America. In fact, they originated on the continent. The earliest ones …
James Watson is to sell the Nobel Prize medal he won for the discovery of the structure of DNA.
An international team of more than 100 researchers has mapped the genome of the centipede and found that, while it easily outpaces humans on number of legs, it falls short when it comes to genes.
The tech giant has created a utensil to make mealtime easier for people with Parkinson's disease and essential tremors
The brain has a weak spot for Alzheimer's disease and schizophrenia, according to experts who have pinpointed the region using scans.
Scientists in California have captured the elusive anglerfish on film in its natural habitat, 1,900 feet below sea level
Researchers were shocked to discover multiple instances of seal-on-penguin rape
The tiny shrimp survive without sunlight and crawl within an inch of boiling hot waters
Birds are one of the most widely studied forms of life on the planet. And, there are still new species out there to discover — as one young researcher found recently in a forest in Indonesia.