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Encyclop'APHID

Genomics

Aphids and ‘omics development

The aphid international community has developed high throughput approaches of aphid genomes to give bases to the study of adaptation mechanisms of these insects to their environment.
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The International Aphid Genomics Consortium (IAGC) was launched in 2003. Its first contribution was to post a white paper describing the advantage and the necessity to give access for the community to an aphid genome in order to get bases and to allow future analyses by structural, functional and evolutionary genomics.

After nearly 7 years, the pea aphid genome (Acyrthosiphon pisum) has been sequenced [1], assembled [2] and annotated [3] and published (refer to Tagu et al. 2010 for a summary, and IAGC 2010 for the initial publication). This work was the result of a large community effort of more than 100 collaborators worldwide, and was completed by several other publications focused on specific gene families. The principal highlights are as follows.

 

Many predicted genes in the A. pisum genome are duplicated or even belong to multigene families. This is the case of the protein genes encoding the machinery for microRNAs (small non coding regulatory RNAs): Dicer1, Argonaute1 and Pasha genes are duplicated or expanded (4 copies for instance for Pasha). In all cases, one of the copies is homolog to similar genes in other insect species, and one copy diverges, sometimes at a high level, with indication that the new protein sequences have been selected by evolution and might acquire a new function. Despite the gene duplication event on many families, there are some pathways that are missing in the pea aphid genome such as the immune pathway (IMD/JNK) involved in bacteria recognition. Aphids have a long history of 150 million years of co-evolution with their obligate bacterial symbionts Buchnera aphidicola. The genome of this symbiont has been strongly reduced during evolution, but surprisingly, no gene transfer from Buchnera to the pea aphid genome has been detected. However, a transfer of fungal genes has been characterized, involved in carotenoid synthesis and responsible – in part - for the body color of the pea aphid individuals.

Since the description of the pea aphid genome, other aphid genomes have been sequenced and are all accessible at AphidBase. The sequence of species belonging to other sub-families than Aphidinae (such as Cinara cedri for the Lachninae, or phylloxera for the family of Phylloxeridae) is an important resource, mainly for phylogenetic studies and for evolutionary history of species and genes.

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[1] This means to characterize the nature and order of the nucleotides from the DNA of an organism. This DNA is clustered into chromosomes, and the genome is composed of all the chromosomes.

[2]  Sequencing a genome requires to cut its DNA into pieces. The result of the sequencing is thus a large quantity of small DNA fragments that are no more arranged. The assembly consists in a bioinformatic reconstruction of the initial DNA molecule by aligning those small sequenced fragments.

[3]  Genome annotation is the step where genes are identified within the assembled genome. For eukaryotes, the genes represent only a few percentage of the whole genome (e. g. 5%). The major part of the DNA consists in repeats or unknown pieces of DNA.

See also

Tagu et al. The anatomy of an aphid genome : from sequence to biology, Comptes Rendus Biologiques 333 (2010) 464–473 pour un résumé de cette étape http://dx.doi.org/10.1016/j.crvi.2010.03.006

IAGC Genome Sequence of the Pea Aphid Acyrthosiphon pisum, PLoS Biology 8(2): e1000313 pour la publication du génome http://dx.doi.org/10.1371%2Fjournal.pbio.1000313