New Tardigrade Opsins and Differential Expression Analyses Show Ontogenic Variation in Light Perception

Abstract

Opsins are light-sensitive proteins involved in many photoreceptive processes, including, but not limited to, vision and regulation of circadian rhythms. Arthropod (e.g. insects, spiders, centipedes and crabs) opsins have been extensively researched, but the relationships and function of opsins found in lineages that are evolutionarily closely-related to the arthropods remains unclear. Multiple, independent, opsin duplications are known in Tardigrada (the water bears), evidencing that protostome opsin duplications are not limited to the Arthropoda. However, the relationships, function and expression of these new opsins are still unknown. Here, we use two tardigrade transcriptomes with deep coverage to greatly expand our knowledge of the diversity of tardigrade opsins. We reconstruct the phylogenetic relationships of the tardigrade opsins and investigate their ontogenetic expression. We found that while tardigrades have multiple opsins that evolved from lineage-specific duplications of well-understood arthropod opsins, their expression levels change during ontogeny such that most of these opsins are not co-temporally expressed. Co-temporal expression of multiple opsins underpins colour vision in Arthropoda and Vertebrata. Our results clearly show duplications of both rhabdomeric and ciliary opsins within Tardigrada, forming clades specific to both the Heterotardigrada and Eutardigrada in addition to multiple independent duplications within genera. However, lack of co-temporal, ontogenetic, expression suggests that while tardigrades possess multiple opsins, they are unlikely to be able to distinguish colour.

The wealth of shared resources: Improving molecular taxonomy using eDNA and public databases

“…Of particular note in this topology is the grouping of Adorybiotus with Richtersius (Figure 2, Supporting Figure S6). These affinities were presented in both Fleming et al (2021) and Guil et al (2019), but in recent studies (Guidetti et al, 2021; Stec & Morek, 2022) that propose Richtersiusidae, it comprises Richtersius and Diaforobiotus to the exclusion of Adorybiotus (which then becomes sister to the Murrayidae). Due to inadequate sampling from Diaforobiotus in this study, the five tardigrade 18S test sequences recovered as sister to Adorybiotus were instead identified as members of the Order “Parachela”, rather than attributing them to Murrayidae, Adorybiotidae or Richtersiusidae.…”

“…However, the taxonomic resolution of this data can be variable. In the last 30 years, both analytical and sequencing techniques have changed, and both the questions and answers that molecular biologists are interested in have changed in turn (Fleming et al, 2021; Lozano‐Fernandez, 2022; Przybyla & Gilbert, 2022; Varshney et al, 2021). Where previously the ability to identify an organism to phylum level purely from a molecular sequence was revolutionary (Blaxter, 2004), in the present‐day searching for a genus or species‐level understanding of the target sequence is consistently possible using DNA barcoding techniques (Hernández‐Triana et al, 2019; Li et al, 2021).…”

“…The Tardigrada are a historically undersampled and understudied taxa (Hashimoto et al, 2016; Koutsovoulos et al, 2016; Yoshida et al, 2017). In recent years, following the publication of the first tardigrade reference genomes, tardigrade genomics and proteomics has entered an exciting new era (Fleming et al, 2021; Fleming & Arakawa, 2021; Gąsiorek et al, 2021; Guil et al, 2019; Jørgensen et al, 2018; Murai et al, 2021; Yoshida et al, 2017). However, many basic questions regarding the core systematics of the group remain, including conflicts about the number and distribution of its classes, the monophyletic nature of its classes, and the assignment of species to families and genera (Fleming & Arakawa, 2021; Guidetti et al, 2021; Guil et al, 2019; Jørgensen et al, 2010.…”

High diversity of arthropod colour vision: from genes to ecology

“…Of the large family of opsin proteins, arthropods mainly express the visual Gq coupled rhabdomeric or r-opsins in the rhabdomeric photoreceptors of their eyes [22], while vertebrates express ciliary or c-opsins in their rods and cones. Whereas the common ancestor of Tardigarda is reported to only have had one visual r-opsin [23], and a similar situation is found in the Onychophora [24], the ancestral arthropod supposedly possessed five visual r-opsins, two sensitive to light of long wavelengths (green-sensitive; LWS1 and LWS2), two sensitive to light of medium wavelengths (blue-sensitive; MWS1 and MWS2) and one to light of short-wavelengths (ultraviolet-sensitive; SWS or sometimes named UVS) [25]. In addition to the visual r-opsins, arthropods have other opsins in their genomes, including pteropsin expressed in the brain [26] and some, specifically among chelicerates and possibly dragonflies, also express peropsins/retinal G-protein coupled receptors in eyes [25,27].…”

“…Different opsin genes can be expressed at different times during development (e.g. in odonates: [28]; in tardigrades, [23]), in different eye types (e.g. insect ocelli and compound eyes; see [25]) and even different regions of compound eyes (e.g.…”