ArticleProceedings of the National Academy of Sciences of the United States of America2016
No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 134 papers.
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134 citing papers in PubMed, 254 citations in OpenAlex.
- At the Edge of Survival: Exploring the Frontiers of Tardigrade Extreme Stress Tolerance.Molecular ecology · 2026Review
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- A compendium of horizontal gene transfers in Metazoa.Scientific data · 2026Article
- The eukaryotic horizontal gene transfer dataset a compendium.bioRxiv : the preprint server for biology · 2025Article
- Tardigrade Dsup extendsScience advances · 2025Article
- Article
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- Horizontally acquired CSP genes contribute to wheat adaptation and improvement.Nature plants · 2025Article
- Review
- Surprising effects of differential loss in genome evolution: the last-one-out.FEMS microbiology letters · 2025Article
- Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.GigaScience · 2025Article
- Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs.Molecular ecology resources · 2025Article
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Contamination Survey of Insect Genomic and Transcriptomic Data.Animals : an open access journal from MDPI · 2024Article
- Disentangling cobionts and contamination in long-read genomic data using sequence composition.G3 (Bethesda, Md.) · 2024Article
- Antioxidant Defense in the Toughest Animals on the Earth: Its Contribution to the Extreme Resistance of Tardigrades.International journal of molecular sciences · 2024Review
- Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.G3 (Bethesda, Md.) · 2024Article
- Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes.Nature communications · 2024Article
- Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.Viruses · 2024Review
- Horizontal gene transfer in eukaryotes: aligning theory with data.Nature reviews. Genetics · 2024Review
74 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.