title: Comparative genome and transcriptome analyses of the social amoeba Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation.
abstract: BACKGROUND
  Social amoebae are lower eukaryotes that inhabit the soil. They are characterized by the construction of a starvation-induced multicellular fruiting body with a spore ball and supportive stalk. In most species, the stalk is filled with motile stalk cells, as represented by the model organism Dictyostelium discoideum, whose developmental mechanisms have been well characterized. However, in the genus Acytostelium, the stalk is acellular and all aggregated cells become spores. Phylogenetic analyses have shown that it is not an ancestral genus but has lost the ability to undergo cell differentiation.
  
  
  RESULTS
  We performed genome and transcriptome analyses of Acytostelium subglobosum and compared our findings to other available dictyostelid genome data. Although A. subglobosum adopts a qualitatively different developmental program from other dictyostelids, its gene repertoire was largely conserved. Yet, families of polyketide synthase and extracellular matrix proteins have not expanded and a serine protease and ABC transporter B family gene, tagA, and a few other developmental genes are missing in the A. subglobosum lineage. Temporal gene expression patterns are astonishingly dissimilar from those of D. discoideum, and only a limited fraction of the ortholog pairs shared the same expression patterns, so that some signaling cascades for development seem to be disabled in A. subglobosum.
  
  
  CONCLUSIONS
  The absence of the ability to undergo cell differentiation in Acytostelium is accompanied by a small change in coding potential and extensive alterations in gene expression patterns.
authors.affiliation: Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan. hideko@biol.tsukuba.ac.jp.
authors.forename: Hideko
authors.initials: H
authors.lastname: Urushihara
authors.affiliation: Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan. hidekuwayama@biol.tsukuba.ac.jp.
authors.forename: Hidekazu
authors.initials: H
authors.lastname: Kuwayama
authors.affiliation: Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan. kufuhara@gmail.com.
authors.forename: Kensuke
authors.initials: K
authors.lastname: Fukuhara
authors.affiliation: Tokyo Institute of Technology, Yokohama, Japan. takehiko@bio.titech.ac.jp.
authors.forename: Takehiko
authors.initials: T
authors.lastname: Itoh
authors.affiliation: National Institute of Genetics, Mishima, Japan. hkagoshi@lab.nig.ac.jp.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kagoshima
authors.affiliation: National Institute of Genetics, Mishima, Japan. tshini@genes.nig.ac.jp.
authors.forename: Tadasu
authors.initials: T
authors.lastname: Shin-I
authors.affiliation: National Institute of Genetics, Mishima, Japan. atoyoda@lab.nig.ac.jp.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.affiliation: National Institute of Genetics, Mishima, Japan. kohishi@lab.nig.ac.jp.
authors.forename: Kazuyo
authors.initials: K
authors.lastname: Ohishi
authors.affiliation: Mitsubishi Research Institute, Tokyo, Japan. tany@mri.co.jp.
authors.forename: Tateaki
authors.initials: T
authors.lastname: Taniguchi
authors.affiliation: Tokyo Institute of Technology, Yokohama, Japan. hnoguchi@nig.ac.jp.
authors.forename: Hideki
authors.initials: H
authors.lastname: Noguchi
authors.affiliation: RIKEN Advanced Science Institute, Yokohama, Japan. kuroki@megabank.tohoku.ac.jp.
authors.forename: Yoko
authors.initials: Y
authors.lastname: Kuroki
authors.affiliation: Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan. hatatakashi7@gmail.com.
authors.forename: Takashi
authors.initials: T
authors.lastname: Hata
authors.affiliation: Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan. imori.k@gmail.com.
authors.forename: Kyoko
authors.initials: K
authors.lastname: Uchi
authors.affiliation: Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan. mori.kurato.fw@un.tsukuba.ac.jp.
authors.forename: Kurato
authors.initials: K
authors.lastname: Mohri
authors.affiliation: Beatson Institute for Cancer Research, Glasgow, UK. jason.king@sheffield.ac.uk.
authors.forename: Jason S
authors.initials: JS
authors.lastname: King
authors.affiliation: Beatson Institute for Cancer Research, Glasgow, UK. r.insall@beatson.gla.ac.uk.
authors.forename: Robert H
authors.initials: RH
authors.lastname: Insall
authors.affiliation: National Institute of Genetics, Mishima, Japan. ykohara@lab.nig.ac.jp.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Kohara
authors.affiliation: National Institute of Genetics, Mishima, Japan. afujiyam@nii.ac.jp.|National Institute of Informatics, Tokyo, Japan. afujiyam@nii.ac.jp.
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
mesh_terms: D000656:Amoeba / Q000235:genetics* / Q000254:growth & development; D002454:Cell Differentiation / Q000235:genetics; D015870:Gene Expression; D020869:Gene Expression Profiling; D018503:Genome, Protozoan; D010802:Phylogeny; D059467:Transcriptome / Q000235:genetics*