E-TABM-394 - Comparative genomic hybridization of laboratory strains of the social amoeba Dictyostelium discoideum shows extensive and gratuitous duplications

Status
Released on 21 April 2008, last updated on 2 May 2014
Organism
Dictyostelium discoideum
Samples (40)
Array (1)
Protocols (10)
Description
We report here that duplications of 15 kb or more are common in the genome of the social amoeba Dictyostelium discoideum. Most of the axenic "workhorse" strains Ax2 and Ax3/4 obtained from different laboratories can be expected to carry new duplications. The auxotrophic strains DH1 and JH10 also bear previously unreported duplications. Strain Ax3/4 is known to carry a large duplication on chromosome 2 and the domain boundary of this structure shows evidence of further instability; we find a further variable duplication on chromosome 5. These duplications are lacking in Ax2, which has instead a small duplication on chromosome 1. Stocks of the type isolate NC4 are similarly variable, though we have identified some approximating the assumed ancestral genotype. More recent wild-type isolates are almost without duplications, but we can identify small deletions or regions of high divergence, possibly reflecting responses to local selective pressures. Duplications are scattered through most of the genome, and can be stable enough to reconstruct genealogies spanning decades of the history of the NC4 lineage. The expression level of many duplicated genes is increased with dosage, but for others it appears that some form of dosage compensation occurs.
Experiment types
comparative genomic hybridization by array, co-expression, comparative genome hybridization, strain or line
Contact
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-TABM-394.idf.txt
Sample and data relationshipE-TABM-394.sdrf.txt
Raw data (2)E-TABM-394.raw.1.zip, E-TABM-394.raw.2.zip
Processed data (1)E-TABM-394.processed.1.zip
Array designA-SGRP-3.adf.txt
R ExpressionSetE-TABM-394.eSet.r
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