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Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum.

Bloomfield G, Tanaka Y, Skelton J, Ivens A, Kay RR - Genome Biol. (2008)

Bottom Line: The expression level of many duplicated genes is increased with dosage, but for others it appears that some form of dosage compensation occurs.The genetic variation described here must underlie some of the phenotypic variation observed between strains from different laboratories.We suggest courses of action to alleviate the problem.

View Article: PubMed Central - HTML - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. garethb@mrc-lmb.cam.ac.uk

ABSTRACT

Background: Duplications of stretches of the genome are an important source of individual genetic variation, but their unrecognized presence in laboratory organisms would be a confounding variable for genetic analysis.

Results: We report here that duplications of 15 kb or more are common in the genome of the social amoeba Dictyostelium discoideum. Most stocks of the axenic 'workhorse' strains Ax2 and Ax3/4 obtained from different laboratories can be expected to carry different 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 this structure shows evidence of continuing 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 large 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.

Conclusion: The genetic variation described here must underlie some of the phenotypic variation observed between strains from different laboratories. We suggest courses of action to alleviate the problem.

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Relationships between the most commonly used Dictyostelium strains. (a) Simplified genealogical tree showing the relationships between common laboratory strains derived from NC4. The branch marked 'Ax3' is more complex than shown here: sub-lineages have been given the names KAx3 and Ax4. The auxotrophic strain DH1 was engineered in an 'Ax3' background, and JH10 from 'Ax4.' (b) Plaque morphologies. Cells were plated clonally in association with Klebsiella aerogenes on SM agar. Plaques were photographed after 4 days. Small DH1 plaques are indicated with arrowheads. Variation in diameter is a function of the rate of feeding and of the motility of the amoebae. Where the bacteria are cleared the amoebae aggregate in streams; this process had not yet begun in the slow-growing DH1 plaques. (c) Fruiting bodies. Wild type cells - in this instance NC4(Dee) - form larger, more robust fruiting bodies than axenic mutants.
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Figure 1: Relationships between the most commonly used Dictyostelium strains. (a) Simplified genealogical tree showing the relationships between common laboratory strains derived from NC4. The branch marked 'Ax3' is more complex than shown here: sub-lineages have been given the names KAx3 and Ax4. The auxotrophic strain DH1 was engineered in an 'Ax3' background, and JH10 from 'Ax4.' (b) Plaque morphologies. Cells were plated clonally in association with Klebsiella aerogenes on SM agar. Plaques were photographed after 4 days. Small DH1 plaques are indicated with arrowheads. Variation in diameter is a function of the rate of feeding and of the motility of the amoebae. Where the bacteria are cleared the amoebae aggregate in streams; this process had not yet begun in the slow-growing DH1 plaques. (c) Fruiting bodies. Wild type cells - in this instance NC4(Dee) - form larger, more robust fruiting bodies than axenic mutants.

Mentions: Virtually all laboratory strains of D. discoideum derive from the original type isolate, NC4 [34], with only limited use being made of other wild isolates, such as V12. The axenic strains Ax2 and Ax3 are the most widely used and a particular lineage of Ax3, termed Ax4, has been fully sequenced [21]. A simplified family tree of this lineage is shown in Figure 1a. Axenic strains differ substantially from their parental NC4 stock: they grow more slowly on bacteria and produce smaller fruiting bodies, as is readily apparent from their plaque morphologies (Figure 1b,c). Amplifications and deletions (copy number variation) could be one source of this between-strain variability, in addition to small-scale mutation of individual genes and promoters.


Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum.

Bloomfield G, Tanaka Y, Skelton J, Ivens A, Kay RR - Genome Biol. (2008)

Relationships between the most commonly used Dictyostelium strains. (a) Simplified genealogical tree showing the relationships between common laboratory strains derived from NC4. The branch marked 'Ax3' is more complex than shown here: sub-lineages have been given the names KAx3 and Ax4. The auxotrophic strain DH1 was engineered in an 'Ax3' background, and JH10 from 'Ax4.' (b) Plaque morphologies. Cells were plated clonally in association with Klebsiella aerogenes on SM agar. Plaques were photographed after 4 days. Small DH1 plaques are indicated with arrowheads. Variation in diameter is a function of the rate of feeding and of the motility of the amoebae. Where the bacteria are cleared the amoebae aggregate in streams; this process had not yet begun in the slow-growing DH1 plaques. (c) Fruiting bodies. Wild type cells - in this instance NC4(Dee) - form larger, more robust fruiting bodies than axenic mutants.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2643946&req=5

Figure 1: Relationships between the most commonly used Dictyostelium strains. (a) Simplified genealogical tree showing the relationships between common laboratory strains derived from NC4. The branch marked 'Ax3' is more complex than shown here: sub-lineages have been given the names KAx3 and Ax4. The auxotrophic strain DH1 was engineered in an 'Ax3' background, and JH10 from 'Ax4.' (b) Plaque morphologies. Cells were plated clonally in association with Klebsiella aerogenes on SM agar. Plaques were photographed after 4 days. Small DH1 plaques are indicated with arrowheads. Variation in diameter is a function of the rate of feeding and of the motility of the amoebae. Where the bacteria are cleared the amoebae aggregate in streams; this process had not yet begun in the slow-growing DH1 plaques. (c) Fruiting bodies. Wild type cells - in this instance NC4(Dee) - form larger, more robust fruiting bodies than axenic mutants.
Mentions: Virtually all laboratory strains of D. discoideum derive from the original type isolate, NC4 [34], with only limited use being made of other wild isolates, such as V12. The axenic strains Ax2 and Ax3 are the most widely used and a particular lineage of Ax3, termed Ax4, has been fully sequenced [21]. A simplified family tree of this lineage is shown in Figure 1a. Axenic strains differ substantially from their parental NC4 stock: they grow more slowly on bacteria and produce smaller fruiting bodies, as is readily apparent from their plaque morphologies (Figure 1b,c). Amplifications and deletions (copy number variation) could be one source of this between-strain variability, in addition to small-scale mutation of individual genes and promoters.

Bottom Line: The expression level of many duplicated genes is increased with dosage, but for others it appears that some form of dosage compensation occurs.The genetic variation described here must underlie some of the phenotypic variation observed between strains from different laboratories.We suggest courses of action to alleviate the problem.

View Article: PubMed Central - HTML - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. garethb@mrc-lmb.cam.ac.uk

ABSTRACT

Background: Duplications of stretches of the genome are an important source of individual genetic variation, but their unrecognized presence in laboratory organisms would be a confounding variable for genetic analysis.

Results: We report here that duplications of 15 kb or more are common in the genome of the social amoeba Dictyostelium discoideum. Most stocks of the axenic 'workhorse' strains Ax2 and Ax3/4 obtained from different laboratories can be expected to carry different 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 this structure shows evidence of continuing 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 large 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.

Conclusion: The genetic variation described here must underlie some of the phenotypic variation observed between strains from different laboratories. We suggest courses of action to alleviate the problem.

Show MeSH
Related in: MedlinePlus