Tuesday, May 17, 2016

Academic Bun Fight Over an Extraordinary Claim: do Tardigrades Have Extensive Horizontal Gene Transfer Like Bacteria?!

Original Paper:

Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade


Boothby et al


Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes.

No!  They don't!
Genome of a tardigrade: Horizontal gene transfer or bacterial contamination?


Bemm et al


We have read the article “Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade” (1) with interest and were astonished by the high number of genes horizontally transferred into the tardigrade genome. Still, we were surprised by the reported genome size of greate than 200 Mbp, which is in stark contrast to a previously published size of ∼78 Mbp determined by the same group (2).
Seriously!  You guys screwed up!

No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade




Through a draft genome sequencing of a tardigrade Hypsibius dujardini, Boothby et al. (1) report that “Approximately one-sixth of the genes in the tardigrade genome were found to have been acquired through horizontal transfer, a proportion nearly double the proportion of previous known cases of extreme horizontal gene transfer (HGT) in animals.” However, the authors also state that the “cultures are not axenic,” which means that they are highly prone to contamination.

Damnit! yes! It Does!

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


Boothyby et al


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⇓⇓–5). Bemm et al. (2) now report filtering our data for likely contaminants, resulting in a new, prefiltered genome assembly. 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.

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