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

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 tar...

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Published in:Proceedings of the National Academy of Sciences - PNAS 2016-05, Vol.113 (18), p.5053-5058
Main Authors: Koutsovoulos, Georgios, Kumar, Sujai, Laetsch, Dominik R., Stevens, Lewis, Daub, Jennifer, Conlon, Claire, Maroon, Habib, Thomas, Fran, Aboobaker, Aziz A., Blaxter, Mark
Format: Article
Language:English
Subjects:
Animals
Arthropoda
Arthropods - genetics
Biological Sciences
Deoxyribonucleic acid
DNA
Eukaryotes
Gene Transfer, Horizontal
Genes
Genome
Genomes
Hypsibius dujardini
Molecular Sequence Data
Phylogeny
Sampling
Tardigrada
Tardigrada - genetics
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Summary: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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1600338113