On 2016 Jul 29, Sujai Kumar commented:

The peer-reviewed version of the biorxiv paper showing that the extensive HGT was an artefact of bacterial contamination is now available at

• Koutsovoulos G, 2016 No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini

The supplementary info section of that paper systematically refutes each of the lines of evidence for HGT presented in this paper (PCR, PacBio sequencing, coverage, and phylogenetic trees).

Since then, three more peer-reviewed papers have independently shown extensive contamination rather than extensive HGT:

• Delmont TO, 2016 Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies
• Arakawa K, 2016 No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade
• Bemm F, 2016 Genome of a tardigrade: Horizontal gene transfer or bacterial contamination?

See also #tardigate and Mark Blaxter's blog post Eight things I learned from tardigate

On 2016 Jan 12, Sujai Kumar commented:

Disclaimer: I'm an author on the biorxiv preprint below that conclusively (in our opinion) demonstrates that the "extensive HGT" is almost entirely bacterial contamination that was not identified by Boothby et al.

We'd be happy to answer any questions about our rebuttal here or on http://twitter.com/sujaik #tardigate

The genome of the tardigrade Hypsibius dujardini

Abstract

Background: Tardigrades are meiofaunal ecdysozoans that may be key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through adoption of a cryptobiotic state. A recent high profile paper suggested that the genome of a model tardigrade, Hypsibius dujardini, has been shaped by unprecedented levels of horizontal gene transfer (HGT) encompassing 17% of protein coding genes, and speculated that this was likely formative in the evolution of stress resistance. We tested these findings using an independently sequenced and assembled genome of H. dujardini, derived from the same original culture isolate.

Results: Whole-organism sampling of meiofaunal species will perforce include gut and surface microbiotal contamination, and our raw data contained bacterial and algal sequences. Careful filtering generated a cleaned H. dujardini genome assembly, validated and annotated with GSSs, ESTs and RNA-Seq data, with superior assembly metrics compared to the published, HGT-rich assembly. A small amount of additional microbial contamination likely remains in our 135 Mb assembly. Our assembly length fits well with multiple empirical measurements of H. dujardini genome size, and is 120 Mb shorter than the HGT-rich version. Among 23,021 protein coding gene predictions we found 216 genes (0.9%) with similarity to prokaryotes, 196 of which were expressed, suggestive of HGT. We also identified ~400 genes (<2%) that could be HGT from other non-metazoan eukaryotes. Cross-comparison of the assemblies, using raw read and RNA-Seq data, confirmed that the overwhelming majority of the putative HGT candidates in the previous genome were predicted from scaffolds at very low coverage and were not transcribed. Crucially much of the natural contamination in both projects was non-overlapping, confirming it as foreign to the shared target animal genome.

Conclusions: We find no support for massive horizontal gene transfer into the genome of H. dujardini. Many of the bacterial sequences in the previously published genome were not present in our raw reads. In construction of our assembly we removed most, but still not all, contamination with approaches derived from metagenomics, which we show are very appropriate for meiofaunal species. We conclude that HGT into H. dujardini accounts for 1-2% of genes and that the proposal that 17% of tardigrade genes originate from HGT events is an artefact of undetected contamination.

On 2016 Jan 12, Sujai Kumar commented:

Disclaimer: I'm an author on the biorxiv preprint below that conclusively (in our opinion) demonstrates that the "extensive HGT" is almost entirely bacterial contamination that was not identified by Boothby et al.

We'd be happy to answer any questions about our rebuttal here or on http://twitter.com/sujaik #tardigate

The genome of the tardigrade Hypsibius dujardini

Abstract

Background: Tardigrades are meiofaunal ecdysozoans that may be key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through adoption of a cryptobiotic state. A recent high profile paper suggested that the genome of a model tardigrade, Hypsibius dujardini, has been shaped by unprecedented levels of horizontal gene transfer (HGT) encompassing 17% of protein coding genes, and speculated that this was likely formative in the evolution of stress resistance. We tested these findings using an independently sequenced and assembled genome of H. dujardini, derived from the same original culture isolate.

Results: Whole-organism sampling of meiofaunal species will perforce include gut and surface microbiotal contamination, and our raw data contained bacterial and algal sequences. Careful filtering generated a cleaned H. dujardini genome assembly, validated and annotated with GSSs, ESTs and RNA-Seq data, with superior assembly metrics compared to the published, HGT-rich assembly. A small amount of additional microbial contamination likely remains in our 135 Mb assembly. Our assembly length fits well with multiple empirical measurements of H. dujardini genome size, and is 120 Mb shorter than the HGT-rich version. Among 23,021 protein coding gene predictions we found 216 genes (0.9%) with similarity to prokaryotes, 196 of which were expressed, suggestive of HGT. We also identified ~400 genes (<2%) that could be HGT from other non-metazoan eukaryotes. Cross-comparison of the assemblies, using raw read and RNA-Seq data, confirmed that the overwhelming majority of the putative HGT candidates in the previous genome were predicted from scaffolds at very low coverage and were not transcribed. Crucially much of the natural contamination in both projects was non-overlapping, confirming it as foreign to the shared target animal genome.

Conclusions: We find no support for massive horizontal gene transfer into the genome of H. dujardini. Many of the bacterial sequences in the previously published genome were not present in our raw reads. In construction of our assembly we removed most, but still not all, contamination with approaches derived from metagenomics, which we show are very appropriate for meiofaunal species. We conclude that HGT into H. dujardini accounts for 1-2% of genes and that the proposal that 17% of tardigrade genes originate from HGT events is an artefact of undetected contamination.

On 2016 Jul 29, Sujai Kumar commented:

The peer-reviewed version of the biorxiv paper showing that the extensive HGT was an artefact of bacterial contamination is now available at

• Koutsovoulos G, 2016 No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini

The supplementary info section of that paper systematically refutes each of the lines of evidence for HGT presented in this paper (PCR, PacBio sequencing, coverage, and phylogenetic trees).

Since then, three more peer-reviewed papers have independently shown extensive contamination rather than extensive HGT:

• Delmont TO, 2016 Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies
• Arakawa K, 2016 No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade
• Bemm F, 2016 Genome of a tardigrade: Horizontal gene transfer or bacterial contamination?

See also #tardigate and Mark Blaxter's blog post Eight things I learned from tardigate