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

• Published in: Evolutionary bioinformatics online Vol. 18; p. 11769343221140277
• Main Authors: Metivier, Jean-Christophe, Chain, Frédéric J J
• Format: Journal Article
• Language: English
• Published: London, England SAGE Publications 01-01-2022; Sage Publications Ltd; SAGE Publishing
• Subjects: Adaptation; Adults; Developmental stages; Embryogenesis; Evolutionary genetics; Gene expression; Genes; Genetic diversity; Genetics; Microorganisms; Original Research; Species; Tardigrada; Transcriptomes; Ramazzottius varieornatus; expression specificity; cryptobiosis; lineage-specific genes; Expression bias; tardigrade; gene duplication; Hypsibius dujardini; comparative transcriptomics; Hypsibius examplaris
• ISSN: 1176-9343; 1176-9343
• DOI: 10.1177/11769343221140277

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.