Tardigrade Mystery Solved?

Tardigrades (water bears) are fascinating animals. Unlike other animals, they can survive extreme stress including high temperature or outer space.

Tardigrades are notable for being perhaps the most durable of known organisms; they are able to survive extreme conditions that would be rapidly fatal to nearly all other known life forms. They can withstand temperature ranges from ?458 F (?272.222 C) to 300 F (149 C),[7] pressures about six times greater than those found in the deepest ocean trenches, ionizing radiation at doses hundreds of times higher than the lethal dose for a human, and the vacuum of outer space.[8] They can go without food or water for more than 10 years, drying out to the point where they are 3% or less water, only to rehydrate, forage, and reproduce.[3][9][10][11]

How do they manage to do that? A new study seemed to have found the answer. They discovered that tardigrade genome went through large-scale horizontal gene transfer, and now includes many genes from bacteria. Those bacterial genes possibly help tardigrades survive extreme environment.

The work, publish today in the Proceeding of the National Academy of Sciences, not only raises the question of whether there is a connection between foreign DNA and the ability to survive extreme environments, but further stretches conventional views of how DNA is inherited.

First author Thomas Boothby, Goldstein and their collaborators revealed that tardigrades acquire about 6,000 foreign genes primarily from bacteria, but also from plants, fungi and Archaea, through a process called horizontal gene transfer the swapping of genetic material between species as opposed to inheriting DNA exclusively from mom and dad. Previously another microscopic animal called the rotifer was the record-holder for having the most foreign DNA, but it has about half as much as the tardigrade. For comparison, most animals have less than one percent of their genome from foreign DNA.

Animals that can survive extreme stresses may be particularly prone to acquiring foreign genes and bacterial genes might be better able to withstand stresses than animal ones, said Boothby, a postdoctoral fellow in Goldsteins lab. After all, bacteria have survived the Earths most extreme environments for billions of years.

Mystery solved? Not so fast. A newer study reported - “We compare our assembly to a recently published one for the same species and do not find support for massive horizontal gene transfer.”

Tardigrades are meiofaunal ecdysozoans and are key to understanding the origins of Arthropoda. We present the genome of the tardigrade Hypsibius dujardini, assembled from Illumina paired and mate-pair data. While the raw data indicated extensive contamination with bacteria, presumably from the gut or surface of the animals, careful cleaning generated a clean tardigrade dataset for assembly. We also generated an expressed sequence tag dataset, a Sanger genome survey dataset and used these and Illumina RNA-Seq data for assembly validation and gene prediction. The genome assembly is ~130 Mb in span, has an N50 length of over 50 kb, and an N90 length of 6 kb. We predict 23,031 protein-coding genes in the genome, which is available in a dedicated genome browser at http://www.tardigrades.org. We compare our assembly to a recently published one for the same species and do not find support for massive horizontal gene transfer. Additional analyses of the genome are ongoing.

Another case of “Shocking Finding that a Genome by Itself Provides Little Insight” ? Maybe two genomes together do provide some insight. The second paper wrote -

Boothby et al 6 recently published a genome assembly for H. dujardini (here called the UNC

assembly) based on a subculture of the same Sciento stock as our tardigrades. Surprisingly, the genome is very different in span and gene content (Table 3). We thus explored the differences between our nHd.2.3 assembly and the Boothby et al. one to identify likely reasons for the discrepancies. The UNC H. dujardini genome was reported to contain a surprisingly high proportion (17%) of putatively horizontally transferred protein-coding genes, and so we also compared the putative HGT gene set predictions with ours.

…

A significant proportion of the UNC scaffolds had zero or very low coverage of reads mapped in both Edinburgh and UNC raw data. These scaffolds contain matches to Bacteriodetes, spanning 27.7 Mb, that included most of the largest scaffolds in the UNC assembly. Bacterial genomes in low complexity metagenomic datasets often assemble with greater contiguity than does the target metazoan genome, because bacterial DNA usually has higher per-base complexity (i.e. does not contain so many repeats). A second group of bacterial contigs, that appeared to derive from Proteobacteria, had a wide dispersion of coverage, from ~10 fold higher than the H. dujardini nuclear mean to zero. Again these are likely to derive from one or more genomes (they span 21.5 Mb). Most of the Proteobacteria scaffolds all had distinct GC%, and grouped separately from the true H. dujardini scaffolds. Comparing coverage between read sets, it is striking that many of the putatively bacterial scaffolds had zero coverage in both UNC and Edinburgh data. We presume that these scaffolds were assembled from UNC data from other libraries (we have not yet screened their 500 and 800 base libraries) containing additional contaminants. Scaffolds with some coverage in the UNC 300 data often had zero coverage in Edinburgh data. The wide spread of proteobacterial scaffolds suggests some sharing of contaminants between the UNC and Edinburgh cultures, but it is likely that these are different taxa, as the coverages vary widely between datasets. It is thus unlikely that these are common symbionts.

….

These analyses thus positively identified much of the UNC assembly as likely derived from contaminant bacteria…

Oh well !