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The Tardigrade Genome (Ramazzottius varieornatus)

Full Title: The Tardigrade Genome (Ramazzottius varieornatus) – Identifying Genes Associated with Survival in Extreme Environments


Author: Cheryl Mazzeo


Institutional Affiliation: University of Maine


Location of Work: United States


Year Completed: 2023


Not Submitted for Publications Because: Never Planned to Publish


Topic: Biology


Keywords: Tardigrades, Bioinformatics, Genes



Dataset: GSE212632 was initially developed using Illumina NextSeq 500 to identify the gene expression patterns of the two tardigrade species Ramazzottius varieornatus and Hypsibius exemplaris. Tardigrades contain characteristic free-floating body cavity cells that are also called storage cells. To investigate the cell-specific expression patterns of tardigrade-unique genes, the expression levels of genes from dissected storage cells are compared to those of the whole body. The original researchers performed RNA-Seq on the active whole body of the organisms (n=3) and extracted storage cells (n=5) for sequencing.

However, the present research will use GSE212632 to focus on the differences in expression between the active and inactive forms of only Ramazzottius varieornatus. The exploration of this genome will focus on the identification of differentially expressed genes in the active and inactive forms that are most likely to be associated with the ability for Tardigrade to survive in extreme environments. Ramazzottius varieornatus was selected because its genome has been less explored in the literature compared to the more commonly encountered Hypsibius exemplaris. The present publication using this dataset by Tanaka et al. 2023 focuses on the anhydrobiosis features of the genome, but it is likely that additional genes are upregulated and downregulated to achieve resistance in this state, and it is possible that additional features of survival in extreme environments could be detected using this dataset.


Publication Associated with GSE212632:

Tanaka S, Aoki K, Arakawa K. In vivo expression vector derived from anhydrobiotic tardigrade genome enables live imaging in Eutardigrada. Proc Natl Acad Sci U S A 2023 Jan 31;120(5):e2216739120. PMID: 36693101


Expected Results: Tardigrades are known to survive in extreme environments, primarily in their inactive forms. Survival in extremities for tardigrades is often related to radiotolerance, stress-resistance, resistance to desiccation, their ability to enter a state of anhydrobiosis, and resist extreme heat, UV radiation, and competition with microbes. It is expected that a majority of these traits will be observed for Ramazzottius varieornatus in the inactive state, reflected by the gene expression observed in the storage cells. However, it is possible that Ramazzottius varieornatus will retain some of its protective abilities in the active state.


Abstract

The original authors generated dataset GSE212632 to identify the gene expression patterns of the two tardigrade species Ramazzottius varieornatus and Hypsibius exemplaris (Tanaka et al. 2023). Tardigrades contain characteristic free-floating body cavity cells that are also called storage cells. To investigate the cell-specific expression patterns of tardigrade-unique genes, the expression levels of dissected storage cells are compared to those of the whole body. The researchers performed RNA-Seq on the active whole body of the organisms (n=3) and extracted storage cells (n=5) for sequencing.


However, the current research will use GSE212632 to examine the differences in expression between the active and inactive forms of Ramazzottius varieornatus. The exploration of this genome will focus on the exploration of highly expressed genes in the active and inactive forms that are most likely to be associated with the ability for the tardigrades to survive in extreme environments. Ramazzottius varieornatus was selected because its genome has been less explored in the literature compared to the more commonly encountered Hypsibius exemplaris. The present publication using this dataset by Tanaka et al. 2023 focuses on the anhydrobiosis features of the genome, but it is likely that additional genes are upregulated and downregulated to achieve resistance in this state, and it is possible that additional features of survival in extreme environments could be detected using this dataset.

Tardigrades are known to survive in extreme environments, primarily in their inactive forms. Survival in extremities for tardigrades is often related to radiotolerance, stress-resistance, resistance to desiccation, their ability to enter a state of anhydrobiosis, and resist extreme heat, UV radiation, and competition with microbes. It is expected that a majority of these traits will be observed for Ramazzottius varieornatus in the inactive state, reflected by the gene expression observed in the storage cells. However, it is possible that Ramazzottius varieornatus will retain some of its protective abilities in the active state. The top 20 differentially expressed genes from the active cellular state and the inactive cellular state will be examined using bioinformatic methods.


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