No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini

<p><strong>No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini</strong></p> <p>These files accompany the peer-reviewed version of http://dx.doi.org/10.1101/033464</p> <p>A previous dataset&nbsp;https://zenodo.org/record/45162 accompanied the version of this manuscript at BioRxiv -&nbsp;biorxiv.org/content/early/2015/12/13/033464</p> <p>This dataset includes all files from&nbsp;https://zenodo.org/record/45162 plus all&nbsp;the Supplemental files, and one additional file&nbsp;HGT_phylogenetic_files.tgz. All files are described in Hypsibius_dujardini_files_README.md</p> <p><strong>Abstract</strong></p> <p>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 <em>et al </em>(2015) Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. <em>Proc Natl Acad Sci USA</em> 112:15976-15981) the authors concluded that the tardigrade <em>Hypsibius dujardini </em>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 <em>H. dujardini</em>. As expected from whole-organism DNA sampling, our raw data contained reads from non-target genomes. Filtering using metagenomics approaches generated a draft <em>H. dujardini</em> 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 non-metazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby <em>et al.</em> genome derived from contaminants. We conclude that fHGT into <em>H. dujardini </em>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 artefact of undetected contamination.</p> <p>&nbsp;</p>