Lineage-specific expansions of the Dicer gene family in tardigrades

RNA interference (RNAi) is an important pathway for gene regulation and immunity. Dicer is a conserved RNAi pathway protein that is found in eukaryotes, with many species expressing multiple dicer gene copies. However, there remains entire lineages such as the phylum Tardigrada with little information about the presence and diversity of dicer genes, limiting our understanding of the evolution and diverse functions of dicer. Our study sought to understand dicer evolution in tardigrades and its phylogenetic relationship to other invertebrate dicers, including the dicer gene duplication in arthropods.

Comparative genomic analyses with ten tardigrade species revealed an expansion of dicer genes in tardigrades. The eight Eutardigrades investigated - Hypsibius exemplaris, Ramazzottius varieornatus, Paramacrobiotus metropolitanus, P. fairbanksi, P. richtersi, Richtersius cf. coronifer, Acutuncus antarcticus and Milnesium tardigradum - and two Heterotardigrades Echiniscoides cf. sigismundi and Echiniscus testudo each contain two to four copies of dicer in their genome. Our results are consistent with a Dicer duplication in the common ancestor of Tardigrada and Arthropoda, followed by lineage-specific duplications that form a sister clade to the arthropod Dicer-2. The tardigrade Dicers contain canonical conserved domains including helicase, PAZ, and RNase III, and their domain-specific phylogenetic diversification suggests functional differentiation after duplication, especially for helicase.

Our study identified multiple distinct tardigrade-specific dicer duplications following an ancient duplication that is shared in both Eutardigrades and Heterotardigrades. Phylogenetic analyses are consistent with a Dicer duplication before the split of Tardigrada and Arthropoda that led to Dicer-2, which also groups with duplications found in Kinorhyncha and Platyhelminthes. Our study provides insights into Dicer evolution in Tardigrada by characterizing dicer duplications and divergence across various lineages.