Diversity in Expression Biases of Lineage-Specific Genes During Development and Anhydrobiosis Among Tardigrade Species

Abstract

Lineage-specific genes can contribute to the emergence and evolution of novel traits and adaptations. Tardigrades are animals that have adapted to tolerate extreme conditions by undergoing a form of cryptobiosis called anhydrobiosis, a physical transformation to an inactive desiccated state. While studies to understand the genetics underlying the interspecies diversity in anhydrobiotic transitions have identified tardigrade-specific genes and family expansions involved in this process, the contributions of species-specific genes to the variation in tardigrade development and cryptobiosis are less clear. We used previously published transcriptomes throughout development and anhydrobiosis (5 embryonic stages, 7 juvenile stages, active adults, and tun adults) to assess the transcriptional biases of different classes of genes between 2 tardigrade species, Hypsibius exemplaris and Ramazzottius varieornatus. We also used the transcriptomes of 2 other tardigrades, Echiniscoides sigismundi and Richtersius coronifer, and data from 3 non-tardigrade species ( Adenita vaga, Drosophila melanogaster, and Caenorhabditis elegans) to help identify lineage-specific genes. We found that lineage-specific genes have generally low and narrow expression but are enriched among biased genes in different stages of development depending on the species. Biased genes tend to be specific to early and late development, but there is little overlap in functional enrichment of biased genes between species. Gene expansions in the 2 tardigrades also involve families with different functions despite homologous genes being expressed during anhydrobiosis in both species. Our results demonstrate the interspecific variation in transcriptional contributions and biases of lineage-specific genes during development and anhydrobiosis in 2 tardigrades.

The major inducible small heat shock protein HSP20-3 in the tardigrade Ramazzottius varieornatus forms filament-like structures and is an active chaperone

“…The RNA-seq data sets for R. varieornatus that included the small heat shock protein expression after heat shock 29 , 30 , cold shock 40 and the different life stages 21 were downloaded from the European Nucleotide Archive 52 at EMBL-EBI under accession number PRJEB49649 for heat shock and PRJEB47628 for cold shock, PRJNA369262 and PRJNA533981 for the different life-cycle stages and states including the tun as the anhydrobiotic stage 53 . Ramazzottius varieornatus reference genome Rvar_4.0 data set 54 , including the genome sequences and general feature format file, was downloaded from the NCBI genome database 54 .…”

“…This is accompanied by a reduction in both cell and mitochondrial size 17 and most noticeably by the appearance of two types of secretory active cells, one with a large number of vesicles and the other rough endoplasmic reticulum 18 , 19 as water and solutes levels are regulated 16 , 20 . Comparison of the molecular adaptions across Eutardigrada ( Hypsibius exemplaris, R. varieornatus , Richtersius coronifer ) and Heterotardigrada 21 with two other related invertebrates, the arthropod, Drosophila melanogaster and the nematode, Caenorhabditis elegans and various vertebrates and yeast 7 established that proteins in addition to the tardigrade specific proteins (CAHS, MAHS, SAHS) are necessary for the unique molecular adaptions that supports cryptogenic responses to extreme stresses 7 , 21 . With this in mind, we investigated the small heat shock protein (sHSP) family present in R. varieornatus because sHSPs have properties in common with CAHS and SAHS proteins, such as their ability to prevent protein aggregation and precipitation 22 , 23 , 24 , 25 , form biomolecular condensates 26 , 27 , 28 and to be upregulated in response to cold and heat shock of R. varieornatus 29 , 30 .…”

“…Using publicly available expression datasets 21 , 28 , 29 , 40 we have characterised the sHSP expression profile in response to a 35 0 C heat shock for R. varieornatus . A previous transcriptomic study had identified that four sHSPs were upregulated, 29 , 30 , but their relative upregulation as well as their structural-functional capabilities were not characterised.…”