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Pea Aphid Genome Resources

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Acyrthosiphon pisum (pea aphid) genome view
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  BLAST search pea aphid sequences
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At present, none of the contigs from the current public WGS assembly have been placed on chromosomes so you cannot browse the sequence data by chromosome. You can find sequenced regions of interest by:

  • querying Map Viewer for a known gene name or symbol, e.g. Sxl
  • querying Map Viewer for accession numbers, e.g. XM_001950248 or NW_003383894
  • searching Gene for aphid genes that have been annotated on the genome, and using the Map Viewer link to view the Gene region.
  • searching by sequence using BLAST against the genome. Results from a BLAST sequence alignment can be displayed in Map Viewer by clicking on the Genome View button or on the accession numbers of the results.




     Lineage: Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidiformes; Aphidoidea; Aphididae; Macrosiphini; Acyrthosiphon; Acyrthosiphon pisum

In June 2010, the Human Genome Sequencing Center at Baylor College of Medicine released Acyr_2.0, a WGS assembly of the genome sequence of Acyrthosiphon pisum (pea aphid). This assembly is made from a combination of Sanger and 454 reads with a combined coverage of 15x, and assembled using a combination of Newbler and Atlas. The pea aphid genome is estimated to be 525 Mbp organized as 4 chromosomes. The genomic DNA used for library construction and sequencing was purified from a partially inbred clonal line (LSR1.AC.F1). None of the contigs have been placed on chromosomes in this version of the assembly.

The NCBI Map Viewer provides graphical displays of features on the Acyrthosiphon pisum genome sequence assembly. Map features that can be seen along the sequence include NCBI contigs (the Contig map), the WGS sequences (the Component map), and the location of aligned transcripts from Acyrthosiphon pisum (rnaAps), other aphids (rnaAph), and other insects (rnaIns). The gene on sequence map includes both known genes and putative genes based on supported Gnomon gene predictions. The complete set of Gnomon predicted gene models can be viewed on the model transcripts map. Further documentation is provided on the Aphid genome data and search tips page and through the links below to describe the resource features and methods used, tutorials, and statistics.

The Search bar or the BLAST search link above can be used to find annotation or sequence in the assembly. The sequence-based maps for any contig of interest can then be displayed. Results are indicated in a tabular format. The results table includes links to a contig graphical view where the gene or marker can be seen in the context of additional data. For genes, a particularly useful display includes the Gene, RefSeq transcript, rnaAps, and RNAseq sequence maps. Use the "Maps & Options" window to configure each display.

Other genomes can also be viewed in the NCBI Map Viewer. The Map Viewer home page provides a current list. Also consider reviewing the resources listed on the Genomic Biology site.

Available Documentation:


Last modified: May 31 2011





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