Acyrthosiphon pisum Assembly and Gene Annotation

AphidBase The Acyrthosiphon pisum data and its display on Ensembl Genomes are made possible through a joint effort by the Ensembl Genomes group and AphidBase. The source data for this genome and other resources can be accessed via the AphidBase download pages.

About Acyrthosiphon pisum

Aphids are common agricultural pests that feed on sap from the phloem vessels of a wide range of host plants. The pea aphid Acyrthosiphon pisum has co-evolved with an obligate bacterial symbiont (Buchnera aphidicola), which provides essential amino acids that are rare in phloem and would otherwise be missing from the aphids' diet. The co-evolution of the aphid and Buchnera has led to extensive gene loss from the genome, including immunity related pathways, purine salvage and the urea cycle. At the same time over 2000 gene families are duplicated, including miRNA synthesis and sugar transport.

Picture credit (Creative Commons BY 2.5): Shipher Wu (photograph) and Gee-way Lin (aphid provision), National Taiwan University 2010

Assembly

The A. pisum genome was sequenced by the Baylor College of Medicine as part of the International Aphid Genomics Consortium. The 464 Mb draft genome and annotations were published in February 2010 [1]. Ensembl Metazoa uses version 2.1 of the assembly.

Annotation

Genes were annotated with EST-based approaches and the NCBI Gnomon pipeline, and combined using GLEAN. These gene models have been refined by manual annotation, and Ensembl Metazoa uses version 2.1b of the offical gene set, imported from AphidBase [2].

BLAST hits, protein features, and cross-references have been computed by Ensembl Metazoa.

References

  1. Genome sequence of the pea aphid Acyrthosiphon pisum.
    The International Aphid Genomics Consortium. 2010. PLoS Biology. 8:e1000313.
  2. AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome.
    Legeai F, Shigenobu S, Gauthier JP, Colbourne J, Rispe C, Collin O, Richards S, Wilson AC, Murphy T, Tagu D. 2010. Insect Molecular Biology. 19 Suppl 2:5-12.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyAcyr_2.0, INSDC Assembly GCA_000142985.2, Jun 2010
Database version90.2
Base Pairs512,050,927
Golden Path Length541,675,471
Genebuild byAphidBase
Genebuild methodImport
Data sourceAphidBase

Gene counts

Coding genes36,195
Non coding genes583
Small non coding genes579
Long non coding genes4
Pseudogenes744
Gene transcripts37,522

About this species