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International Consortium Sequences Pea Aphid Genome

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Members of the International Aphid Genomics Consortium reported today in PLoS Biology that they have sequenced the genome of the pea aphid, Acyrthosiphon pisum.

The team used Sanger sequencing to come up with a draft version of the pea aphid genome — and in their subsequent scrutiny identified some 35,000 high confidence or suspected pea aphid genes. The large number of genes seems to be partly owing to extensive gene duplications, they found, which affect almost 2,500 aphid gene families. Still, the new findings show that the pea aphid genome is also missing certain conserved genes, including some involved in immune function.

"This genome has generated far more exciting questions than we could have anticipated," Princeton University ecologist and evolutionary biologist David Stern, one of the project leaders, said in a statement. "There is more mystery in this genome than anyone would have expected."

In general, aphids feed on phloem, plant tissue that transports sugars and amino acids. Of the roughly 5,000 aphid species found so far, those attacking crop plants are among the most commercially important, contributing to crop losses and agricultural expenses estimated at hundreds of millions of dollars each year.

To begin genetically characterizing the pea aphid, which feeds on field peas, sweet peas, and other plants such as alfalfa, the researchers sequenced the genome of an aphid clone called LSR1.AC.G1. The parental line for this inbred clone was collected from an alfalfa field in upstate New York.

The team generated sequence covering 464 million bases of the A. pisum genome to about 6.2 times coverage using Sanger 3730 sequencing.

During their subsequent analyses, they pinned down a core set of 10,249 high-quality protein-coding gene models, along with 24,355 suspected genes. A definitive count for the number of authentic pea aphid genes awaits improved assembly and functional annotation of the genome, the researchers noted.

Gene duplications were widespread in the pea aphid, with 2,459 gene families — including genes contributing to processes such as sugar transport, chromatin modification, and microRNA production — showing aphid-specific duplications.

While the precise function of these duplications is still a matter of some speculation, the team suspects they may relate to the aphid's development patterns.

"One hypothesis is that one copy of this back-up is kept unchanged and used for the functioning of the cells and the organism, and that the second set can allow modifications by mutations," project co-leader Denis Tagu, senior scientist at the French National Institute for Agricultural Research (INRA), said in a statement.

For his part, Princeton's Stern noted that the gene duplications detected in aphids may reflect their complex life cycles. For instance he noted, not only are A. pisum capable of both various forms of sexual and asexual reproduction, they may also be winged or wingless.

Along with the duplications, though, the pea aphid genome is missing some conserved genes. Among them: genes involved in immune function — particularly components of the immunodeficiency pathway.

This diminished collection of immune genes could be related to the fact that the aphids typically carry the symbiotic bacteria Buchnera aphidicola, which live in the cytoplasm of so-called bacteriocyte cells in the aphid.

As a byproduct of the pea aphid sequencing project, the team also obtained roughly 20 times coverage of the B. aphidicola genome.

When they compared the newly sequenced symbiont genome to a B. aphidicola genome sequence published by Japanese researchers in Nature in 2000 and several North American Buchnera strains sequenced by American and Israeli researchers last year, the team found that the new genome was nearly identical to the genomes of five of the North American strains. In contrast, it showed 1,500 mismatches and two large inserts when compared to the Japanese strain.

With the pea aphid and additional Buchnera genome sequences now available, investigators are starting to apply the data to explore a range of research problems — from how pea aphids adapt to different environments to how they interact with plants and B. aphidicola symbionts. They also hope to nail down genetic traits contributing to insecticide resistance.

"Our analysis of the pea aphid genome has begun to reveal the genetic underpinnings of this animal's complex ecology — including its capacity to parasitize agricultural crops, its association with microbial symbionts, and its developmental patterning," the researchers concluded.

Companion papers describing specific aspects of the work are also being published in PLoS Genetics, Genome Biology, and a special issue of the journal Insect Molecular Biology.

Data from the pea aphid genome sequencing project was released before the publication of these papers under the Fort Lauderdale agreement guidelines. Information on manually curated genes and other findings from the genome are available through the AphidBase web site.