title: Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks.
abstract: BACKGROUND
  Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, and S. glaseri).
  
  
  RESULTS
  We used these genomes to establish phylogenetic relationships, explore gene conservation across species, and identify genes uniquely expanded in insect parasites. Protein domain analysis in Steinernema revealed a striking expansion of numerous putative parasitism genes, including certain protease and protease inhibitor families, as well as fatty acid- and retinol-binding proteins. Stage-specific gene expression of some of these expanded families further supports the notion that they are involved in insect parasitism by Steinernema. We show that sets of novel conserved non-coding regulatory motifs are associated with orthologous genes in Steinernema and Caenorhabditis.
  
  
  CONCLUSIONS
  We have identified a set of expanded gene families that are likely to be involved in parasitism. We have also identified a set of non-coding motifs associated with groups of orthologous genes in Steinernema and Caenorhabditis involved in neurogenesis and embryonic development that are likely part of conserved protein-DNA relationships shared between these two genera.
authors.affiliation: Department of Nematology, University of California, Riverside, CA, 92521, USA. adler.dillman@ucr.edu.
authors.forename: Adler R
authors.initials: AR
authors.lastname: Dillman
authors.affiliation: Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA. mmacchie@uci.edu.
authors.forename: Marissa
authors.initials: M
authors.lastname: Macchietto
authors.affiliation: Department of Biology and Evolutionary Ecology Laboratories, Brigham Young University, Provo, UT, 84602, USA. finli6@gmail.com.
authors.forename: Camille F
authors.initials: CF
authors.lastname: Porter
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA. arogers@caltech.edu.
authors.forename: Alicia
authors.initials: A
authors.lastname: Rogers
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA. bawilli@caltech.edu.
authors.forename: Brian
authors.initials: B
authors.lastname: Williams
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA. igor.antoshechkin@caltech.edu.
authors.forename: Igor
authors.initials: I
authors.lastname: Antoshechkin
authors.affiliation: Department of Entomology, University of Arizona, Tucson, AZ, 85721, USA. mingmail@email.arizona.edu.
authors.forename: Ming-Min
authors.initials: MM
authors.lastname: Lee
authors.affiliation: Division of Biology and Biomedical Sciences, Washington University, St Louis, MO, 63110, USA. gzane01@gmail.com.
authors.forename: Zane
authors.initials: Z
authors.lastname: Goodwin
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA. Luxiaojun@tsinghua.edu.cn.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Lu
authors.affiliation: Department of Entomology and Nematology, University of California, Davis, CA, 95616, USA. eelewis@ucdavis.edu.
authors.forename: Edwin E
authors.initials: EE
authors.lastname: Lewis
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA. hgblair@bact.wisc.edu.
authors.forename: Heidi
authors.initials: H
authors.lastname: Goodrich-Blair
authors.affiliation: Department of Entomology, University of Arizona, Tucson, AZ, 85721, USA. spstock@email.arizona.edu.
authors.forename: S Patricia
authors.initials: SP
authors.lastname: Stock
authors.affiliation: Department of Biology and Evolutionary Ecology Laboratories, Brigham Young University, Provo, UT, 84602, USA. byron_adams@byu.edu.
authors.forename: Byron J
authors.initials: BJ
authors.lastname: Adams
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA. pws@caltech.edu.|Howard Hughes Medical Institute, Pasadena, CA, 91125, USA. pws@caltech.edu.
authors.forename: Paul W
authors.initials: PW
authors.lastname: Sternberg
authors.affiliation: Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA. ali.mortazavi@uci.edu.
authors.forename: Ali
authors.initials: A
authors.lastname: Mortazavi
mesh_terms: D000818:Animals; D002107:Caenorhabditis / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics*; D016678:Genome; D010572:Pest Control, Biological; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D017168:Rhabditida / Q000235:genetics*; D013559:Symbiosis / Q000235:genetics