title: No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini.
abstract: Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976-15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1-2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination.
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
authors.forename: Georgios
authors.initials: G
authors.lastname: Koutsovoulos
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
authors.forename: Sujai
authors.identifier: 0000-0001-5902-6641
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom; The James Hutton Institute, Dundee DD2 5DA, United Kingdom;
authors.forename: Dominik R
authors.initials: DR
authors.lastname: Laetsch
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
authors.forename: Lewis
authors.initials: L
authors.lastname: Stevens
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
authors.forename: Jennifer
authors.initials: J
authors.lastname: Daub
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
authors.forename: Claire
authors.initials: C
authors.lastname: Conlon
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
authors.forename: Habib
authors.initials: H
authors.lastname: Maroon
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
authors.forename: Fran
authors.initials: F
authors.lastname: Thomas
authors.affiliation: Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom.
authors.forename: Aziz A
authors.initials: AA
authors.lastname: Aboobaker
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom; mark.blaxter@ed.ac.uk.
authors.forename: Mark
authors.identifier: 0000-0003-2861-949X
authors.initials: M
authors.lastname: Blaxter
mesh_terms: D000818:Animals; D001181:Arthropods / Q000235:genetics; D022761:Gene Transfer, Horizontal; D016678:Genome; D008969:Molecular Sequence Data; D010802:Phylogeny; D058467:Tardigrada / Q000235:genetics*
keywords: blobtools; contamination; horizontal gene transfer; metagenomics; tardigrade