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A Trio of New Animal Genomes Serves as Source of Information on Ancestral Bilaterians

NEW YORK (GenomeWeb News) – With three new animal genomes in hand, an international team led by investigators at Rice University, the University of California, Berkeley, and the US Department of Energy's Joint Genome Institute is getting a clearer picture of genomic features found in the earliest organisms with bilateral symmetry — findings expected to inform evolutionary studies of their own, and other animal, lineages.

"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," co-corresponding author Nicholas Putnam, an ecology and evolutionary biology researcher at Rice University, said in a statement.

As they reported online today in Nature, Putnam and his colleagues focused on three animals from annelid and mollusk phyla, generating draft genome sequences for the freshwater leech (Helobdella robusta), a marine polychaete (Capitella teleta), and the owl limpet (Lottia gigantean). Together, the two annelids and mollusk represented a group of animals known as spiralians, so classified for their spiral cleavage patterns and other features characterizing their early developmental stages.

The new genome sequences served as a source of information about the spiralian animals and their relationships to one another. But they also provided broader insights into animal evolution, study authors said, since the spiralian species in question belong to the so-called lophotrochozoan clade — one of the three main lineages thought to have stemmed from a shared ancestor with bilateral symmetry.

"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 noted.

"Sometimes the genes today might still have the same function," he added, "but other times they have evolved an entirely new function."

For the study, investigators assembled draft genomes for the leech, limpet, and polychaete using Sanger sequence data that covered each genome to a depth of around 8-fold, on average.

The team's analyses of these genomes uncovered between 23,000 and 33,000 predicted protein-coding genes apiece. And comparisons with other animal genomes pointed to at least 8,756 bilaterian gene families that apparently stem from duplications of genes present in the ancestor of all animals with bilateral symmetry.

By searching for signs of synteny between the new genomes and those of animals sequenced in the past, meanwhile, researchers went on to further define 17 sets of genes representing linkage groups believed to have been present in that ancestral bilaterian.

While rearrangements in the leech genome have obscured some of the large-scale synteny detectable in that animal's sequence, the researchers reported, gene location patterns in limpet and polychaete genomes supported the presence of the ancestral linkage groups.

In addition, many of the broader patterns in the leech, limpet, and polychaete genomes — everything from the exon and intron structures of genes to the overall organization of the genomes — were reminiscent of features found in invertebrates from the deuterostome lineage, so named because their mouth hole forms second rather than first during embryonic development.

The new genomes shared gene structure and genome organization features with other deuterostomes (a group that includes humans and other vertebrates), too, and with some non-bilaterian animals.

Such similarities may seem somewhat surprising, given that spiralians are part of the lophotrochozoan clade — one of two protostome or "mouth-first" lineages.

But those involved in the study said that these findings likely reflect features once shared amongst bilaterians and other animals that have been lost in representatives from the other protostome clade, called ecdysozoa, which includes flies, nematodes, and flatworms.

"These similarities reveal features of bilaterian and/or metazoan genomes that have been lost or diverged in many protostome genomes reported so far," they wrote, "and thus enable a more complete reconstruction of genomic features of the last common ancestors of protostomes, bilaterians, and metazoans, including gene and chromosome structure and organization."

Moreover, they showed, by getting a clearer picture of animals' shared ancestor, it becomes increasingly possible to track the changes within and between various animal lineages.

In the current study, for example, researchers identified specific gene families that have been pared back or expanded in spiralians as a group. But they also saw some changes in gene content that were specific to individual species, including larger-than-usual sensory and signaling gene families in the marine polychaete, C. teleta, and expansions to distinct sets of sensory and taste genes in the leech, H. robusta.