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Fly Study Suggests New Genes Can Be Essential

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Genes that have sprung up relatively recently in the genome are just as likely to be essential as ancient, well-conserved genes, according to a new online study in Science today.

"A new gene is as essential as any other gene," senior author Manyuan Long, an ecology and evolution researcher at the University of Chicago, said in a statement. "The importance of a gene is independent of its age."

Long and his co-workers first compared the genomes of a dozen Drosophila species, narrowing in on several hundred genes that appear to have arisen relatively recently in fly evolution. They then used RNA interference to systematically block 195 different genes that have been added to the Drosophila genomes over the past 35 million years, showing that nearly a third of these new genes tested are essential.

The findings hint that it will likely be important to understand the functions of genes that have arisen recently in specific lineages as well as more ancient, conserved genes that are shared across many species, according to those involved in the study.

"Each species has a different species-specific developmental program shaped by natural selection, and we can no longer say that from Drosophila to humans the development of different organisms is just encoded by the same genetic program," Long said. "The story is much more complicated than what we used to believe."

To begin exploring the process through which genes become essential in the genome, Long and his co-workers first compared the genomes of 12 Drosophila species, identifying 566 genes that have arisen in the fly genome since a species called D. willistoni diverged from the lineage some 35 million years.

They then looked at the consequences of removing 195 of these genes individually using a set of Drosophila lines containing interfering RNA that knocked down each gene.

Of the 195 young genes tested, the researchers found that 59 genes — more than 30 percent — are required for Drosophila viability. Almost all of these genes are located on autosomal chromosomes, they noted, and roughly 95 percent appear to have arisen through gene duplication and divergence, in some cases accompanied by retrotransposition.

And, they noted, these new and essential genes don't seem to cluster at any particular point in the fly phylogenetic tree and include genes that arose as recently as three million years ago.

Similarly, when they tested the effects of knocking down 245 more ancient, conserved genes selected at random, the team found that 86 of these genes — about 35 percent — were essential.

"The proportion of genes that are essential is similar in every evolutionary age group that we examined," the researchers wrote, arguing that their findings indicate that "new genes frequently and rapidly evolve essential functions and participate in development."

Even so, when they assessed gene expression in the fruit fly, D. melanogaster, at various stages of development, the researchers did find that many of essential new genes identified in the first phase of the study tended to show elevated expression during late larval or metamorphosis stages of development.

By knocking down the same genes at different stages of fly development, they also found that nearly 80 percent of the young essential genes have their crucial role during pupation, with a handful of the genes acting during larval development or during both the pupal and larval stages.

Based on these and other findings, the team concluded that new genes may be particularly prone to becoming essential if they contribute to these larval and/or pupal processes — and if they interact with more ancestral genes.

"New genes come in and quickly interact with older genes, and if that interaction is favorable by helping the organism survive or reproduce better, it is favored by natural selection and stays in the genome," lead author Sidi Chen, a graduate student in Long's University of Chicago lab, said in a statement. "After a while, it becomes essential, and the organism literally cannot live without the gene any more."

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