No evidence for extensive horizontal gene transfer in the genome of the tardigradeHypsibius 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) Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci USA 112:15976-15981) 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 non-target 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 non-metazoan 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 artefact of undetected contamination.

Reply to Bemm et al. and Arakawa: Identifying foreign genes in independent Hypsibius dujardini genome assemblies

“…This assembly was 252 Mb, larger than the 212.3-Mb assembly that we had used in our report (1), as pointed out correctly by others (5). The 212.3-Mb assembly used in our report is available at the link provided below.…”

“…Our report (1) describing the discovery of extensive horizontal gene transfer in a tardigrade genome has raised questions from other groups who were sequencing the Hypsibius dujardini genome in parallel or who have done new experiments and analyses since our report (2)(3)(4)(5). Bemm et al (2) now report filtering our data for likely contaminants, resulting in a new, prefiltered genome assembly.…”

“…A central finding of our original report (1) is a high rate of foreign genes in the H. dujardini genome, which has been argued by others (2)(3)(4)(5) to be an artifact of incomplete filtering of contaminating microbial sequences. The availability of these other groups' independent assemblies and multiple filtering approaches [via k-mer selection (2) or GC% and coverage (5)] allows us to test the robustness of our conclusions.…”

“…It has been suggested that many foreign genes in the H. dujardini genome might not be functional or might be contaminants because RNAseq reads do not map to some of these genes (3,5). However, it is well documented in the literature that many HGT genes are expressed at low levels or, in some cases, are not expressed at all.…”

“…Arakawa (3) has sequenced genomes of starved, washed, individual animals that had been treated with antibiotics for 48 h, and used this genomic sequence and RNA-Seq data to identify likely bona fide tardigrade contigs. Two other reports have contributed data and analysis: Delmont and Eren (4) used a newly published analysis and visualization platform, Anvi'o (6), to identify likely contaminants in our genome assembly, and Koutsovoulos et al (5) applied useful taxon-annotated GC coverage plots (Blobplots) (7) to our data and reported an independent genome assembly.…”