title: Comparative genomics of flatworms (platyhelminthes) reveals shared genomic features of ecto- and endoparastic neodermata.
abstract: The ectoparasitic Monogenea comprise a major part of the obligate parasitic flatworm diversity. Although genomic adaptations to parasitism have been studied in the endoparasitic tapeworms (Cestoda) and flukes (Trematoda), no representative of the Monogenea has been investigated yet. We present the high-quality draft genome of Gyrodactylus salaris, an economically important monogenean ectoparasite of wild Atlantic salmon (Salmo salar). A total of 15,488 gene models were identified, of which 7,102 were functionally annotated. The controversial phylogenetic relationships within the obligate parasitic Neodermata were resolved in a phylogenomic analysis using 1,719 gene models (alignment length of >500,000 amino acids) for a set of 16 metazoan taxa. The Monogenea were found basal to the Cestoda and Trematoda, which implies ectoparasitism being plesiomorphic within the Neodermata and strongly supports a common origin of complex life cycles. Comparative analysis of seven parasitic flatworm genomes identified shared genomic features for the ecto- and endoparasitic lineages, such as a substantial reduction of the core bilaterian gene complement, including the homeodomain-containing genes, and a loss of the piwi and vasa genes, which are considered essential for animal development. Furthermore, the shared loss of functional fatty acid biosynthesis pathways and the absence of peroxisomes, the latter organelles presumed ubiquitous in eukaryotes except for parasitic protozoans, were inferred. The draft genome of G. salaris opens for future in-depth analyses of pathogenicity and host specificity of poorly characterized G. salaris strains, and will enhance studies addressing the genomics of host-parasite interactions and speciation in the highly diverse monogenean flatworms.
authors.affiliation: Department for Research and Collections, Natural History Museum, University of Oslo, Oslo, Norway.
authors.forename: Christoph
authors.initials: C
authors.lastname: Hahn
authors.forename: Bastian
authors.initials: B
authors.lastname: Fromm
authors.forename: Lutz
authors.initials: L
authors.lastname: Bachmann
mesh_terms: D000818:Animals; D016678:Genome; D018840:HSP70 Heat-Shock Proteins / Q000235:genetics; D006790:Host-Parasite Interactions / Q000235:genetics; D008018:Life Cycle Stages / Q000235:genetics; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D020675:Peroxisomes / Q000235:genetics; D010802:Phylogeny; D010986:Platyhelminths / Q000235:genetics; D017422:Sequence Analysis, DNA; D014200:Trematoda / Q000235:genetics*
chemical_list: D018840:HSP70 Heat-Shock Proteins
keywords: Gyrodactylus salaris; draft genome; flatworms; genomic adaptations; parasitism; phylogenomics
references.citation: Genome Biol. 2007;8(2):R21
references.pmid: 17309804
references.citation: Mol Syst Biol. 2011 Oct 11;7:539
references.pmid: 21988835
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14
references.pmid: 22080510
references.citation: Genome Biol. 2010;11(9):403
references.pmid: 20887641
references.citation: BMC Evol Biol. 2007 Feb 02;7:11
references.pmid: 17270057
references.citation: Genome Res. 2009 Jun;19(6):1117-23
references.pmid: 19251739
references.citation: Bioinformatics. 2009 Jul 15;25(14):1754-60
references.pmid: 19451168
references.citation: Adv Parasitol. 2005;60:165-243
references.pmid: 16230104
references.citation: Nature. 2008 Apr 10;452(7188):745-9
references.pmid: 18322464
references.citation: Nature. 2013 Apr 04;496(7443):57-63
references.pmid: 23485966
references.citation: Trends Parasitol. 2014 Mar;30(3):123-9
references.pmid: 24485046
references.citation: PLoS Pathog. 2006 Apr;2(4):e29
references.pmid: 16617374
references.citation: Mol Biol Evol. 2006 Apr;23(4):838-45
references.pmid: 16452116
references.citation: Gigascience. 2012 Dec 27;1(1):18
references.pmid: 23587118
references.citation: Int J Parasitol. 1998 Oct;28(10):1653-7
references.pmid: 9801923
references.citation: Nature. 2009 Jul 16;460(7253):345-51
references.pmid: 19606140
references.citation: Genome Biol Evol. 2012;4(10):1033-43
references.pmid: 22930760
references.citation: BMC Bioinformatics. 2011 Dec 22;12:491
references.pmid: 22192575
references.citation: Int J Parasitol. 2010 Sep;40(11):1237-45
references.pmid: 20493870
references.citation: Int J Parasitol. 2003 Nov;33(13):1471-8
references.pmid: 14572510
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W116-20
references.pmid: 15980438
references.citation: Nucleic Acids Res. 2008 Jun;36(10):3420-35
references.pmid: 18445632
references.citation: Syst Biol. 2009 Feb;58(1):21-34
references.pmid: 20525566
references.citation: Genome Biol. 2011 Oct 24;12(10):R107
references.pmid: 22023798
references.citation: Acta Trop. 2003 May;86(2-3):125-39
references.pmid: 12745133
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Genome Biol. 2005;6(8):R67
references.pmid: 16086849
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D599-606
references.pmid: 17881371
references.citation: Nucleic Acids Res. 2005 Nov 28;33(20):6494-506
references.pmid: 16314312
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D815-22
references.pmid: 17135190
references.citation: Mol Biol Evol. 2004 Jun;21(6):1095-109
references.pmid: 15014145
references.citation: Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25
references.pmid: 14534192
references.citation: Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13272-7
references.pmid: 22847406
references.citation: Syst Biol. 2013 Jul;62(4):611-5
references.pmid: 23564032
references.citation: Mol Biochem Parasitol. 1997 Dec 15;90(2):433-8
references.pmid: 9476791
references.citation: Genome Res. 2008 May;18(5):821-9
references.pmid: 18349386
references.citation: Nature. 2013 May 16;497(7449):327-31
references.pmid: 23657258
references.citation: Bioinformatics. 2007 May 1;23(9):1061-7
references.pmid: 17332020
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D1295-300
references.pmid: 22058131
references.citation: Nature. 2011 Oct 26;480(7377):364-7
references.pmid: 22031330
references.citation: Nature. 2010 Jan 21;463(7279):311-7
references.pmid: 20010809
references.citation: Nature. 2011 Feb 10;470(7333):255-8
references.pmid: 21307940
references.citation: Nat Rev Genet. 2004 Feb;5(2):114-22
references.pmid: 14735122
references.citation: Genome Res. 2010 Feb;20(2):265-72
references.pmid: 20019144
references.citation: Curr Protoc Bioinformatics. 2011 Sep;Chapter 6:Unit 6.12.1-19
references.pmid: 21901743
references.citation: Bioinformatics. 2011 Aug 1;27(15):2156-8
references.pmid: 21653522
references.citation: Nature. 2005 Sep 15;437(7057):376-80
references.pmid: 16056220
references.citation: PLoS One. 2009 Sep 02;4(9):e6864
references.pmid: 19724646
references.citation: Nucleic Acids Res. 2009 Jan;37(1):289-97
references.pmid: 19042974
references.citation: Symbiosis. 2011 Nov;55(3):119-126
references.pmid: 22448083
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: Trends Parasitol. 2007 Aug;23(8):363-7
references.pmid: 17602869
references.citation: Int J Parasitol. 2004 Mar 29;34(4):515-26
references.pmid: 15013741
references.citation: Int J Parasitol. 2007 Apr;37(5):515-23
references.pmid: 17188275
references.citation: Mol Phylogenet Evol. 2010 Sep;56(3):1115-8
references.pmid: 20416383
references.citation: Nature. 2013 Jan 24;493(7433):526-31
references.pmid: 23254933
references.citation: Adv Parasitol. 2007;64:161-376
references.pmid: 17499102
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: Proc Biol Sci. 2009 Dec 22;276(1677):4261-70
references.pmid: 19759036
references.citation: Nat Genet. 2013 Oct;45(10):1168-75
references.pmid: 24013640
references.citation: Bioinformatics. 2006 Nov 1;22(21):2688-90
references.pmid: 16928733
references.citation: Mol Biol Evol. 2013 Dec;30(12):2619-28
references.pmid: 24025793
references.citation: Nature. 2003 Aug 21;424(6951):928-31
references.pmid: 12931185
references.citation: Genetics. 2005 May;170(1):481-5
references.pmid: 15781704
references.citation: Parasitology. 2002 Jan;124(Pt 1):53-68
references.pmid: 11811803
references.citation: Annu Rev Cell Biol. 1985;1:489-530
references.pmid: 3916321
references.citation: Nucleic Acids Res. 2013 Jul;41(13):e129
references.pmid: 23661685
references.citation: Nature. 2009 Jul 16;460(7253):352-8
references.pmid: 19606141
references.citation: Dis Model Mech. 2011 Jan;4(1):12-9
references.pmid: 21135057
references.citation: Mol Phylogenet Evol. 2013 Mar;66(3):1050-4
references.pmid: 23211720
references.citation: Syst Biol. 2005 Oct;54(5):710-8
references.pmid: 16195215
references.citation: Science. 2000 Mar 24;287(5461):2196-204
references.pmid: 10731133
references.citation: BMC Bioinformatics. 2004 May 14;5:59
references.pmid: 15144565
references.citation: Nat Rev Genet. 2012 Apr 18;13(5):329-42
references.pmid: 22510764
references.citation: Genome Res. 2002 Aug;12(8):1185-9
references.pmid: 12176926