title: Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum.
abstract: BACKGROUND
  The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum.
  
  
  RESULTS
  We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict.
  
  
  CONCLUSIONS
  The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.
authors.affiliation: Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Sucgang
authors.forename: Alan
authors.initials: A
authors.lastname: Kuo
authors.forename: Xiangjun
authors.initials: X
authors.lastname: Tian
authors.forename: William
authors.initials: W
authors.lastname: Salerno
authors.forename: Anup
authors.initials: A
authors.lastname: Parikh
authors.forename: Christa L
authors.initials: CL
authors.lastname: Feasley
authors.forename: Eileen
authors.initials: E
authors.lastname: Dalin
authors.forename: Hank
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authors.lastname: Tu
authors.forename: Eryong
authors.initials: E
authors.lastname: Huang
authors.forename: Kerrie
authors.initials: K
authors.lastname: Barry
authors.forename: Erika
authors.initials: E
authors.lastname: Lindquist
authors.forename: Harris
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authors.lastname: Shapiro
authors.forename: David
authors.initials: D
authors.lastname: Bruce
authors.forename: Jeremy
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authors.lastname: Schmutz
authors.forename: Asaf
authors.initials: A
authors.lastname: Salamov
authors.forename: Petra
authors.initials: P
authors.lastname: Fey
authors.forename: Pascale
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authors.lastname: Gaudet
authors.forename: Christophe
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authors.lastname: Anjard
authors.forename: M Madan
authors.initials: MM
authors.lastname: Babu
authors.forename: Siddhartha
authors.initials: S
authors.lastname: Basu
authors.forename: Yulia
authors.initials: Y
authors.lastname: Bushmanova
authors.forename: Hanke
authors.initials: H
authors.lastname: van der Wel
authors.forename: Mariko
authors.initials: M
authors.lastname: Katoh-Kurasawa
authors.forename: Christopher
authors.initials: C
authors.lastname: Dinh
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Coutinho
authors.forename: Tamao
authors.initials: T
authors.lastname: Saito
authors.forename: Marek
authors.initials: M
authors.lastname: Elias
authors.forename: Pauline
authors.initials: P
authors.lastname: Schaap
authors.forename: Robert R
authors.initials: RR
authors.lastname: Kay
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.forename: Ludwig
authors.initials: L
authors.lastname: Eichinger
authors.forename: Francisco
authors.initials: F
authors.lastname: Rivero
authors.forename: Nicholas H
authors.initials: NH
authors.lastname: Putnam
authors.forename: Christopher M
authors.initials: CM
authors.lastname: West
authors.forename: William F
authors.initials: WF
authors.lastname: Loomis
authors.forename: Rex L
authors.initials: RL
authors.lastname: Chisholm
authors.forename: Gad
authors.initials: G
authors.lastname: Shaulsky
authors.forename: Joan E
authors.initials: JE
authors.lastname: Strassmann
authors.forename: David C
authors.initials: DC
authors.lastname: Queller
authors.forename: Adam
authors.initials: A
authors.lastname: Kuspa
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D017124:Conserved Sequence / Q000235:genetics; D004023:Dictyostelium / Q000235:genetics*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D049810:Genetic Speciation; D016678:Genome; D059646:Genome Size; D023281:Genomics / Q000379:methods*; D000071677:Histidine Kinase; D006801:Humans; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D010802:Phylogeny; D048630:Polyketide Synthases / Q000235:genetics; D011494:Protein Kinases / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D048630:Polyketide Synthases; D011494:Protein Kinases; D000071677:Histidine Kinase