Computational Biology & Evolution

Archive for the ‘functional annotation’ tag

The pea aphid genome and phylome

without comments

With the sequencing of the Acyrthosiphon pisum genome [1], aphid research enters the genome era. The reconstruction of the complete collection of evolutionary histories of aphid  genes and their homologues in other sequenced arthropods [2] has not only helped in the annotation of the genome sequence but has also already provided important insights into the evolution of this specialized hemipteran. In particular, we undertook a phylogenetic analysis for every protein of this species in a context 13 other fully-sequenced arthropods and three out-group species. Subsequent analyses have revealed multiple gene expansions that are specific to aphids and have served to transfer functional annotations to 4058 pea aphid genes that display one-to-one orthology relationships with Drosophila melanogaster annotated genes. To our knowledge, this is the first time that such a reliable methodology has been applied in the annotation pipeline of a newly sequenced genome.

  1. Genome sequence of the pea aphid Acyrthosiphon pisum. International Aphid Genomics Consortium. PLoS Biol. 2010 Feb 23;8(2):e1000313.
  2. The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes. J. Huerta-Cepas, M. Marcet-Houben, M. Pignatelli, A. Moya and T. Gabaldón

Written by jaime

March 17th, 2010 at 11:20 am