The genome of the social amoeba Dictyostelium discoideum

I. Eichinger; J. A. Pachebat; G. Glöckner; M. A. Rajandream; R. Sucgang; M. Berriman; J. Song; R. Olsen; K. Szafranski; Q. Xu; B. Tunggal; S. Kummerfeld; M. Madera; B. A. Konfortov; F. Rivero; A. T. Bankier; R. Lehmann; N. Hamlin; R. Davies; P. Gaudet; P. Fey; K. Pilcher; G. Chen; D. Saunders; E. Sodergren; P. Davis; A. Kerhornou; X. Nie; N. Hall; C. Anjard; L. Hemphill; N. Bason; P. Farbrother; B. Desany; E. Just; T. Morio; R. Rost; C. Churcher; J. Cooper; S. Haydock; N. Van Driessche; A. Cronin; I. Goodhead; D. Muzny; T. Mourier; A. Pain; M. Lu; D. Harper; R. Lindsay; H. Hauser; K. James; M. Quiles; M. Madan Babu; T. Saito; C. Buchrieser; A. Wardroper; M. Felder; M. Thangavelu; D. Johnson; A. Knights; H. Loulseged; K. Mungall; K. Oliver; C. Price; M. A. Quail; H. Urushihara; J. Hernandez; E. Rabbinowitsch; D. Steffen; M. Sanders; J. Ma; Y. Kohara; S. Sharp; M. Simmonds; S. Spiegler; A. Tivey; S. Sugano; B. White; D. Walker; J. Woodward; T. Winckler; Y. Tanaka; G. Shaulsky; M. Schleicher; G. Weinstock; A. Rosenthal; E. C. Cox; R. L. Chisholm; R. Gibbs; W. F. Loomis; M. Platzer; R. R. Kay; J. Williams; P. H. Dear; A. A. Noegel; B. Barrell; A. Kuspa

doi:10.1038/nature03481

The genome of the social amoeba Dictyostelium discoideum

I. Eichinger, J. A. Pachebat, G. Glöckner, M. A. Rajandream, R. Sucgang, M. Berriman, J. Song, R. Olsen, K. Szafranski, Q. Xu, B. Tunggal, S. Kummerfeld, M. Madera, B. A. Konfortov, F. Rivero, A. T. Bankier, R. Lehmann, N. Hamlin, R. Davies, P. GaudetP. Fey, K. Pilcher, G. Chen, D. Saunders, E. Sodergren, P. Davis, A. Kerhornou, X. Nie, N. Hall, C. Anjard, L. Hemphill, N. Bason, P. Farbrother, B. Desany, E. Just, T. Morio, R. Rost, C. Churcher, J. Cooper, S. Haydock, N. Van Driessche, A. Cronin, I. Goodhead, D. Muzny, T. Mourier, A. Pain, M. Lu, D. Harper, R. Lindsay, H. Hauser, K. James, M. Quiles, M. Madan Babu, T. Saito, C. Buchrieser, A. Wardroper, M. Felder, M. Thangavelu, D. Johnson, A. Knights, H. Loulseged, K. Mungall, K. Oliver, C. Price, M. A. Quail, H. Urushihara, J. Hernandez, E. Rabbinowitsch, D. Steffen, M. Sanders, J. Ma, Y. Kohara, S. Sharp, M. Simmonds, S. Spiegler, A. Tivey, S. Sugano, B. White, D. Walker, J. Woodward, T. Winckler, Y. Tanaka, G. Shaulsky, M. Schleicher, G. Weinstock, A. Rosenthal, E. C. Cox, R. L. Chisholm, R. Gibbs, W. F. Loomis, M. Platzer, R. R. Kay, J. Williams, P. H. Dear^*, A. A. Noegel, B. Barrell, A. Kuspa

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

1064 Scopus citations

Abstract

The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phytogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.

Original language	English (US)
Pages (from-to)	43-57
Number of pages	15
Journal	NATURE
Volume	435
Issue number	7038
DOIs	https://doi.org/10.1038/nature03481
State	Published - May 5 2005
Externally published	Yes

Bibliographical note

Funding Information:
An international initiative to sequence the genome of Dictyostelium discoideum AX4 (refs 5, 6) was launched in 1998. The high repeat content and (AþT)-richness of the genome (the latter rendering large-insert bacterial clones unstable) posed severe challenges for sequencing and assembly. The response to these challenges was to use a whole-chromosome shotgun (WCS) strategy, partially purifying each chromosome electrophoretically and treating it as a separate project. This approach was supported by novel statistical tools to recover chromosome specificity from the impure WCS libraries, and by highly detailed HAPPY maps that provided a framework for sequence assembly. These approaches have enabled the completion of this difficult genome to a high standard, and are likely to be valuable in tackling the many other genomes that present challenges of composition and complexity.

ASJC Scopus subject areas

General

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10.1038/nature03481

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Eichinger, I., Pachebat, J. A., Glöckner, G., Rajandream, M. A., Sucgang, R., Berriman, M., Song, J., Olsen, R., Szafranski, K., Xu, Q., Tunggal, B., Kummerfeld, S., Madera, M., Konfortov, B. A., Rivero, F., Bankier, A. T., Lehmann, R., Hamlin, N., Davies, R., ... Kuspa, A. (2005). The genome of the social amoeba Dictyostelium discoideum. NATURE, 435(7038), 43-57. https://doi.org/10.1038/nature03481

@article{bd3fb5fbc7944ab4b52822ed04c5af9c,

title = "The genome of the social amoeba Dictyostelium discoideum",

abstract = "The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phytogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.",

author = "I. Eichinger and Pachebat, {J. A.} and G. Gl{\"o}ckner and Rajandream, {M. A.} and R. Sucgang and M. Berriman and J. Song and R. Olsen and K. Szafranski and Q. Xu and B. Tunggal and S. Kummerfeld and M. Madera and Konfortov, {B. A.} and F. Rivero and Bankier, {A. T.} and R. Lehmann and N. Hamlin and R. Davies and P. Gaudet and P. Fey and K. Pilcher and G. Chen and D. Saunders and E. Sodergren and P. Davis and A. Kerhornou and X. Nie and N. Hall and C. Anjard and L. Hemphill and N. Bason and P. Farbrother and B. Desany and E. Just and T. Morio and R. Rost and C. Churcher and J. Cooper and S. Haydock and {Van Driessche}, N. and A. Cronin and I. Goodhead and D. Muzny and T. Mourier and A. Pain and M. Lu and D. Harper and R. Lindsay and H. Hauser and K. James and M. Quiles and {Madan Babu}, M. and T. Saito and C. Buchrieser and A. Wardroper and M. Felder and M. Thangavelu and D. Johnson and A. Knights and H. Loulseged and K. Mungall and K. Oliver and C. Price and Quail, {M. A.} and H. Urushihara and J. Hernandez and E. Rabbinowitsch and D. Steffen and M. Sanders and J. Ma and Y. Kohara and S. Sharp and M. Simmonds and S. Spiegler and A. Tivey and S. Sugano and B. White and D. Walker and J. Woodward and T. Winckler and Y. Tanaka and G. Shaulsky and M. Schleicher and G. Weinstock and A. Rosenthal and Cox, {E. C.} and Chisholm, {R. L.} and R. Gibbs and Loomis, {W. F.} and M. Platzer and Kay, {R. R.} and J. Williams and Dear, {P. H.} and Noegel, {A. A.} and B. Barrell and A. Kuspa",

note = "Funding Information: An international initiative to sequence the genome of Dictyostelium discoideum AX4 (refs 5, 6) was launched in 1998. The high repeat content and (A{\th}T)-richness of the genome (the latter rendering large-insert bacterial clones unstable) posed severe challenges for sequencing and assembly. The response to these challenges was to use a whole-chromosome shotgun (WCS) strategy, partially purifying each chromosome electrophoretically and treating it as a separate project. This approach was supported by novel statistical tools to recover chromosome specificity from the impure WCS libraries, and by highly detailed HAPPY maps that provided a framework for sequence assembly. These approaches have enabled the completion of this difficult genome to a high standard, and are likely to be valuable in tackling the many other genomes that present challenges of composition and complexity.",

year = "2005",

month = may,

day = "5",

doi = "10.1038/nature03481",

language = "English (US)",

volume = "435",

pages = "43--57",

journal = "NATURE",

issn = "0028-0836",

publisher = "Nature Research",

number = "7038",

}

Eichinger, I, Pachebat, JA, Glöckner, G, Rajandream, MA, Sucgang, R, Berriman, M, Song, J, Olsen, R, Szafranski, K, Xu, Q, Tunggal, B, Kummerfeld, S, Madera, M, Konfortov, BA, Rivero, F, Bankier, AT, Lehmann, R, Hamlin, N, Davies, R, Gaudet, P, Fey, P, Pilcher, K, Chen, G, Saunders, D, Sodergren, E, Davis, P, Kerhornou, A, Nie, X, Hall, N, Anjard, C, Hemphill, L, Bason, N, Farbrother, P, Desany, B, Just, E, Morio, T, Rost, R, Churcher, C, Cooper, J, Haydock, S, Van Driessche, N, Cronin, A, Goodhead, I, Muzny, D, Mourier, T, Pain, A, Lu, M, Harper, D, Lindsay, R, Hauser, H, James, K, Quiles, M, Madan Babu, M, Saito, T, Buchrieser, C, Wardroper, A, Felder, M, Thangavelu, M, Johnson, D, Knights, A, Loulseged, H, Mungall, K, Oliver, K, Price, C, Quail, MA, Urushihara, H, Hernandez, J, Rabbinowitsch, E, Steffen, D, Sanders, M, Ma, J, Kohara, Y, Sharp, S, Simmonds, M, Spiegler, S, Tivey, A, Sugano, S, White, B, Walker, D, Woodward, J, Winckler, T, Tanaka, Y, Shaulsky, G, Schleicher, M, Weinstock, G, Rosenthal, A, Cox, EC, Chisholm, RL, Gibbs, R, Loomis, WF, Platzer, M, Kay, RR, Williams, J, Dear, PH, Noegel, AA, Barrell, B & Kuspa, A 2005, 'The genome of the social amoeba Dictyostelium discoideum', NATURE, vol. 435, no. 7038, pp. 43-57. https://doi.org/10.1038/nature03481

TY - JOUR

T1 - The genome of the social amoeba Dictyostelium discoideum

AU - Eichinger, I.

AU - Pachebat, J. A.

AU - Glöckner, G.

AU - Rajandream, M. A.

AU - Sucgang, R.

AU - Berriman, M.

AU - Song, J.

AU - Olsen, R.

AU - Szafranski, K.

AU - Xu, Q.

AU - Tunggal, B.

AU - Kummerfeld, S.

AU - Madera, M.

AU - Konfortov, B. A.

AU - Rivero, F.

AU - Bankier, A. T.

AU - Lehmann, R.

AU - Hamlin, N.

AU - Davies, R.

AU - Gaudet, P.

AU - Fey, P.

AU - Pilcher, K.

AU - Chen, G.

AU - Saunders, D.

AU - Sodergren, E.

AU - Davis, P.

AU - Kerhornou, A.

AU - Nie, X.

AU - Hall, N.

AU - Anjard, C.

AU - Hemphill, L.

AU - Bason, N.

AU - Farbrother, P.

AU - Desany, B.

AU - Just, E.

AU - Morio, T.

AU - Rost, R.

AU - Churcher, C.

AU - Cooper, J.

AU - Haydock, S.

AU - Van Driessche, N.

AU - Cronin, A.

AU - Goodhead, I.

AU - Muzny, D.

AU - Mourier, T.

AU - Pain, A.

AU - Lu, M.

AU - Harper, D.

AU - Lindsay, R.

AU - Hauser, H.

AU - James, K.

AU - Quiles, M.

AU - Madan Babu, M.

AU - Saito, T.

AU - Buchrieser, C.

AU - Wardroper, A.

AU - Felder, M.

AU - Thangavelu, M.

AU - Johnson, D.

AU - Knights, A.

AU - Loulseged, H.

AU - Mungall, K.

AU - Oliver, K.

AU - Price, C.

AU - Quail, M. A.

AU - Urushihara, H.

AU - Hernandez, J.

AU - Rabbinowitsch, E.

AU - Steffen, D.

AU - Sanders, M.

AU - Ma, J.

AU - Kohara, Y.

AU - Sharp, S.

AU - Simmonds, M.

AU - Spiegler, S.

AU - Tivey, A.

AU - Sugano, S.

AU - White, B.

AU - Walker, D.

AU - Woodward, J.

AU - Winckler, T.

AU - Tanaka, Y.

AU - Shaulsky, G.

AU - Schleicher, M.

AU - Weinstock, G.

AU - Rosenthal, A.

AU - Cox, E. C.

AU - Chisholm, R. L.

AU - Gibbs, R.

AU - Loomis, W. F.

AU - Platzer, M.

AU - Kay, R. R.

AU - Williams, J.

AU - Dear, P. H.

AU - Noegel, A. A.

AU - Barrell, B.

AU - Kuspa, A.

N1 - Funding Information: An international initiative to sequence the genome of Dictyostelium discoideum AX4 (refs 5, 6) was launched in 1998. The high repeat content and (AþT)-richness of the genome (the latter rendering large-insert bacterial clones unstable) posed severe challenges for sequencing and assembly. The response to these challenges was to use a whole-chromosome shotgun (WCS) strategy, partially purifying each chromosome electrophoretically and treating it as a separate project. This approach was supported by novel statistical tools to recover chromosome specificity from the impure WCS libraries, and by highly detailed HAPPY maps that provided a framework for sequence assembly. These approaches have enabled the completion of this difficult genome to a high standard, and are likely to be valuable in tackling the many other genomes that present challenges of composition and complexity.

PY - 2005/5/5

Y1 - 2005/5/5

N2 - The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phytogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.

AB - The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phytogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.

UR - http://www.scopus.com/inward/record.url?scp=18344395923&partnerID=8YFLogxK

U2 - 10.1038/nature03481

DO - 10.1038/nature03481

M3 - Article

C2 - 15875012

AN - SCOPUS:18344395923

SN - 0028-0836

VL - 435

SP - 43

EP - 57

JO - NATURE

JF - NATURE

IS - 7038

ER -

The genome of the social amoeba Dictyostelium discoideum

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