Genomics and Genome Evolution
Tardigrades (Fig 1) have the remarkable ability to withstand desiccation through the process of anhydrobiosis, allowing them to live in extremely dry environments. They can survive exposure to gamma and x-rays. Tardigrades also adapted to living in other extreme environments such as freezing (Yoshida et al. 2017). Scientists continue to search for answers to how they are such resilient creatures and they believe the answers lie in the Tardigrade genome. In addition to the mystery of their resilience, there is still a debate on where tardigrades belong on the tree of life. Previous analyses have placed Tardigrades on the annelid-arthropod lineage, and others have placed it in the clade, Panarthropoda (Nichols, Nelson, and Garey 2006; Harrison, 1998).
Media Credit: Ian Woods
Among the many other unknowns, Tardigrades remain the animal holding the record for the most foreign DNA in their genome. This was initially thought to be the result of Horizontal Gene Transfer (HGT), but other more recent studies argue that tardigrades do not have extensive foreign DNA at all (Boothby et al. 2015; Koutsovoulos et al. 2016).
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Figure. 1 Visualization of vertical gene transmission from parent to offspring and horizontal gene transmission which occurs between cellular organisms
HGT, which is also known as Lateral Gene Transfer (LGT), involves the exchange of genetic information between species (Yutin 2013). Many scientists have proposed that the new genes are gained through DNA repair during rehydration, after desiccation induced breakdown of DNA. This process results in an organism gaining new genes and thus new functions, overall increasing genetic variation (Ku C, et al. 2015). In one study, they used Illumina Molecular long reads and short mate pair libraries to sequence the genome of the Tardigrade, Hypsibius dujardini (Boothby et al. 2015). Much like Caenorhabditis elegans, who’s relation to tardigrades is shown in figure 2, they found that the Tardigrade genome consisted of 95.16% of core eukaryotic genes (Parra, Bradnam, and Korf 2007). 6,663 of the genes from that sequenced genome were determined to be of foreign origin and were similar to bacteria, archaea, fungi, viruses, and plants. An HGT index was used to measure how foreign the genome was (Boschetti et al. 2012). They claimed that these results were not affected by contamination even though their solutions were not axenic, as they tried to minimize that by feeding the tardigrades algae and isolating them (Boothby et al. 2015). After testing for contamination through PacBio sequencing, PCR experiments, and gene trees they concluded that there was no significant difference.
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Figure. 2 Phylogeny with the root Panarthropoda, showing the relationship between nematodes (Caenorhabditis elegans, Caenorhabditis brenneri) and different species of eutardigrades (Milnesium tardigradum, Richtersius coronifer, Thulinius stephaniae) and a heterotardigrade (Echiniscus viridissimus)
Not everyone agrees that tardigrades do not undergo extensive HGT that has caused increased amounts of foreign genes within their genome. Another study set determined that there is no significant evidence suggesting there is extensive HGT occurring (Koutsovoulos et al. 2016). It is believed that the foreign genes found in the Tardigrade genome are mainly due to contamination. To evaluate this, they used the Illumina short-read technology to sequence the Hypsibius dujardini genome, and even after careful DNA extraction, they found significant contamination. Their experiments produced a ~120Mb shorter genome with a much lower level of HGT than that of the UNC (Boothby et al. 2015). Other studies that have sequenced Hypsibius dujardini and found strong evidence for contamination also confirm this conclusion (Bemm et al. 2016).
Evidently, it is very difficult to avoid bacterial or other organism contamination during DNA extraction and better methods need to be developed to reduce its occurrence (Bemm et al. 2016). Perhaps using antibiotic and antiviral drugs to destroy the other organisms present in the solutions to decrease the DNA contamination in results. There is still much to learn from Tardigrades and how their genome has evolved.
Media Credit: Khangelani Mhlanga
Works Cited
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Bordenstein, Sarah R., and Seth R. Bordenstein. 2016. “Eukaryotic Association Module in Phage WO Genomes from Wolbachia.” Nature Communications 7 (1): 13155. https://doi.org/10.1038/ncomms13155
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Harrison, Frederick W. n.d. “The Position of the Arthropoda in the Phylogenetic System,” 23.
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http://dx.doi.org.ezproxy.ithaca.edu:2048/10.1007/s10750-005-1414-8.
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