title: HOX gene complement and expression in the planarian Schmidtea mediterranea.
abstract: BACKGROUND
  Freshwater planarians are well known for their regenerative abilities. Less well known is how planarians maintain spatial patterning in long-lived adult animals or how they re-pattern tissues during regeneration. HOX genes are good candidates to regulate planarian spatial patterning, yet the full complement or genomic clustering of planarian HOX genes has not yet been described, primarily because only a few have been detectable by in situ hybridization, and none have given morphological phenotypes when knocked down by RNAi.
  
  
  RESULTS
  Because the planarian Schmidtea mediterranea (S. mediterranea) is unsegmented, appendage less, and morphologically simple, it has been proposed that it may have a simplified HOX gene complement. Here, we argue against this hypothesis and show that S. mediterranea has a total of 13 HOX genes, which represent homologs to all major axial categories, and can be detected by whole-mount in situ hybridization using a highly sensitive method. In addition, we show that planarian HOX genes do not cluster in the genome, yet 5/13 have retained aspects of axially restricted expression. Finally, we confirm HOX gene axial expression by RNA deep-sequencing 6 anterior-posterior "zones" of the animal, which we provide as a dataset to the community to discover other axially restricted transcripts.
  
  
  CONCLUSIONS
  Freshwater planarians have an unappreciated HOX gene complexity, with all major axial categories represented. However, we conclude based on adult expression patterns that planarians have a derived body plan and their asexual lifestyle may have allowed for large changes in HOX expression from the last common ancestor between arthropods, flatworms, and vertebrates. Using our in situ method and axial zone RNAseq data, it should be possible to further understand the pathways that pattern the anterior-posterior axis of adult planarians.
authors.affiliation: Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G10A4 Canada ; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G10A4 Canada.
authors.forename: Ko W
authors.initials: KW
authors.lastname: Currie
authors.affiliation: Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G10A4 Canada ; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G10A4 Canada.
authors.forename: David D R
authors.initials: DD
authors.lastname: Brown
authors.affiliation: Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G10A4 Canada ; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G10A4 Canada.
authors.forename: Shujun
authors.initials: S
authors.lastname: Zhu
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5G10A4 Canada.
authors.forename: ChangJiang
authors.initials: C
authors.lastname: Xu
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5G10A4 Canada.
authors.forename: Veronique
authors.initials: V
authors.lastname: Voisin
authors.affiliation: Department of Molecular Genetics, University of Toronto, Toronto, ON M5G10A4 Canada ; Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5G10A4 Canada.
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
authors.affiliation: Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G10A4 Canada ; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G10A4 Canada ; Ontario Institute for Cancer Research, Toronto, ON M5G10A4 Canada.
authors.forename: Bret J
authors.initials: BJ
authors.lastname: Pearson
keywords: Body plan; Flatworm; HOX; Homeotic; In situ hybridization; Lophotrochozoan; Planarians; Schmidtea mediterranea