Evo-Devo gene toolkit update: at least seven Pax transcription factor subfamilies in the last common ancestor of bilaterian animals

It takes Two: Discovery of Spider Pax2 Duplicates Indicates Prominent Role in Chelicerate Central Nervous System, Eye, as Well as External Sense Organ Precursor Formation and Diversification After Neo- and Subfunctionalization

Paired box genes are conserved across animals and encode transcription factors playing key roles in development, especially neurogenesis. Pax6 is a chief example for functional conservation required for eye development in most bilaterian lineages except chelicerates. Pax6 is ancestrally linked and was shown to have interchangeable functions with Pax2. Drosophila melanogaster Pax2 plays an important role in the development of sensory hairs across the whole body. In addition, it is required for the differentiation of compound eyes, making it a prime candidate to study the genetic basis of arthropod sense organ development and diversification, as well as the role of Pax genes in eye development. Interestingly, in previous studies identification of chelicerate Pax2 was either neglected or failed. Here we report the expression of two Pax2 orthologs in the common house spider Parasteatoda tepidariorum, a model organism for chelicerate development. The two Pax2 orthologs most likely arose as a consequence of a whole genome duplication in the last common ancestor of spiders and scorpions. Pax2.1 is expressed in the peripheral nervous system, including developing lateral eyes and external sensilla, as well as the ventral neuroectoderm of P. tepidariorum embryos. This not only hints at a conserved dual role of Pax2/5/8 orthologs in arthropod sense organ development but suggests that in chelicerates, Pax2 could have acquired the role usually played by Pax6. For the other paralog, Pt-Pax2.2, expression was detected in the brain, but not in the lateral eyes and the expression pattern associated with sensory hairs differs in timing, pattern, and strength. To achieve a broader phylogenetic sampling, we also studied the expression of both Pax2 genes in the haplogyne cellar spider Pholcus phalangioides. We found that the expression difference between paralogs is even more extreme in this species, since Pp-Pax2.2 shows an interesting expression pattern in the ventral neuroectoderm while the expression in the prosomal appendages is strictly mesodermal. This expression divergence indicates both sub- and neofunctionalization after Pax2 duplication in spiders and thus presents an opportunity to study the evolution of functional divergence after gene duplication and its impact on sense organ diversification.

Analyses of nervous system patterning genes in the tardigrade Hypsibius exemplaris illuminate the evolution of panarthropod brains

BACKGROUND

Both euarthropods and vertebrates have tripartite brains. Several orthologous genes are expressed in similar regionalized patterns during brain development in both vertebrates and euarthropods. These similarities have been used to support direct homology of the tripartite brains of vertebrates and euarthropods. If the tripartite brains of vertebrates and euarthropods are homologous, then one would expect other taxa to share this structure. More generally, examination of other taxa can help in tracing the evolutionary history of brain structures. Tardigrades are an interesting lineage on which to test this hypothesis because they are closely related to euarthropods, and whether they have a tripartite brain or unipartite brain has recently been a focus of debate.

RESULTS

We tested this hypothesis by analyzing the expression patterns of six3, orthodenticle, pax6, unplugged, and pax2/5/8 during brain development in the tardigrade Hypsibius exemplaris-formerly misidentified as Hypsibius dujardini. These genes were expressed in a staggered anteroposterior order in H. exemplaris, similar to what has been reported for mice and flies. However, only six3, orthodenticle, and pax6 were expressed in the developing brain. Unplugged was expressed broadly throughout the trunk and posterior head, before the appearance of the nervous system. Pax2/5/8 was expressed in the developing central and peripheral nervous system in the trunk.

CONCLUSION

Our results buttress the conclusion of our previous study of Hox genes-that the brain of tardigrades is only homologous to the protocerebrum of euarthropods. They support a model based on fossil evidence that the last common ancestor of tardigrades and euarthropods possessed a unipartite brain. Our results are inconsistent with the hypothesis that the tripartite brain of euarthropods is directly homologous to the tripartite brain of vertebrates.

Ancient genetic redundancy of eyeless and twin of eyeless in the arthropod ocular segment

Pax6 transcription factors are essential upstream regulators in the developing anterior brain and peripheral visual system of most bilaterian animals. While a single homolog is in charge of these functions in vertebrates, two Pax6 genes are in Drosophila: eyeless (ey) and twin of eyeless (toy). At first glance, their co-existence seems sufficiently explained by their differential involvement in the specification of two types of insect visual organs: the lateral compound eyes (ey) and the dorsal ocelli (toy). Less straightforward to understand, however, is their genetic redundancy in promoting defined early and late growth phases of the precursor tissue to these organs: the eye-antennal imaginal disc. Drawing on comparative sequence, expression, and gene function evidence, I here conclude that this gene regulatory network module dates back to the dawn of arthropod evolution, securing the embryonic development of the ocular head segment. Thus, ey and toy constitute a paradigm to explore the organization and functional significance of longterm conserved genetic redundancy of duplicated genes. Indeed, as first steps in this direction, recent studies uncovered the shared use of binding sites in shared enhancers of target genes that are under redundant (string) and, strikingly, even subfunctionalized control by ey and toy (atonal). Equally significant, the evolutionarily recent and paralog-specific function of ey to repress the transcription of the antenna fate regulator Distal-less offers a functionally and phylogenetically well-defined opportunity to study the reconciliation of shared, partitioned, and newly acquired functions in a duplicated developmental gene pair.

Ancestral and novel roles of Pax family genes in mollusks

Background

Pax genes are transcription factors with significant roles in cell fate specification and tissue differentiation during animal ontogeny. Most information on their tempo-spatial mode of expression is available from well-studied model organisms where the Pax-subfamilies Pax2/5/8, Pax6, and Paxα/β are mainly involved in the development of the central nervous system (CNS), the eyes, and other sensory organs. In certain taxa, Pax2/5/8 seems to be additionally involved in the development of excretion organs. Data on expression patterns in lophotrochozoans, and in particular in mollusks, are very scarce for all the above-mentioned Pax-subfamilies, which hampers reconstruction of their putative ancestral roles in bilaterian animals. Thus, we studied the developmental expression of Pax2/5/8, Pax6, and the lophotrochozoan-specific Paxβ in the worm-shaped mollusk Wirenia argentea, a member of Aplacophora that together with Polyplacophora forms the Aculifera, the proposed sister taxon to all primarily single-shelled mollusks (Conchifera).

Results

All investigated Pax genes are expressed in the developing cerebral ganglia and in the ventral nerve cords, but not in the lateral nerve cords of the tetraneural nervous system. Additionally, Pax2/5/8 is expressed in epidermal spicule-secreting or associated cells of the larval trunk and in the region of the developing protonephridia. We found no indication for an involvement of the investigated Pax genes in the development of larval or adult sensory organs of Wirenia argentea.

Conclusions

Pax2/5/8 seems to have a conserved role in the development of the CNS, whereas expression in the spicule-secreting tissues of aplacophorans and polyplacophorans suggests co-option in aculiferan skeletogenesis. The Pax6 expression pattern in Aculifera largely resembles the common bilaterian expression during CNS development. All data available on Paxβ expression argue for a common role in lophotrochozoan neurogenesis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0919-x) contains supplementary material, which is available to authorized users.

The Pax gene family: Highlights from cephalopods

Pax genes play important roles in Metazoan development. Their evolution has been extensively studied but Lophotrochozoa are usually omitted. We addressed the question of Pax paralog diversity in Lophotrochozoa by a thorough review of available databases. The existence of six Pax families (Pax1/9, Pax2/5/8, Pax3/7, Pax4/6, Paxβ, PoxNeuro) was confirmed and the lophotrochozoan Paxβ subfamily was further characterized. Contrary to the pattern reported in chordates, the Pax2/5/8 family is devoid of homeodomain in Lophotrochozoa. Expression patterns of the three main pax classes (pax2/5/8, pax3/7, pax4/6) during Sepia officinalis development showed that Pax roles taken as ancestral and common in metazoans are modified in S. officinalis, most likely due to either the morphological specificities of cephalopods or to their direct development. Some expected expression patterns were missing (e.g. pax6 in the developing retina), and some expressions in unexpected tissues have been found (e.g. pax2/5/8 in dermal tissue and in gills). This study underlines the diversity and functional plasticity of Pax genes and illustrates the difficulty of using probable gene homology as strict indicator of homology between biological structures.

Dermestes maculatus: an intermediate-germ beetle model system for evo-devo

BACKGROUND

Understanding how genes change during evolution to direct the development of diverse body plans is a major goal of the evo-devo field. Achieving this will require the establishment of new model systems that represent key points in phylogeny. These new model systems must be amenable to laboratory culture, and molecular and functional approaches should be feasible. To date, studies of insects have been best represented by the model system Drosophila melanogaster. Given the enormous diversity represented by insect taxa, comparative studies within this clade will provide a wealth of information about the evolutionary potential and trajectories of alternative developmental strategies.

RESULTS

Here we established the beetle Dermestes maculatus, a member of the speciose clade Coleoptera, as a new insect model system. We have maintained a continuously breeding culture in the lab and documented Dermestes maculatus embryogenesis using nuclear and phalloidin staining. Anterior segments are specified during the blastoderm stage before gastrulation, and posterior segments are added sequentially during germ band elongation. We isolated and studied the expression and function of the pair-rule segmentation gene paired in Dermestes maculatus. In this species, paired is expressed in stripes during both blastoderm and germ band stages: four primary stripes arise prior to gastrulation, confirming an intermediate-germ mode of development for this species. As in other insects, these primary stripes then split into secondary stripes. To study gene function, we established both embryonic and parental RNAi. Knockdown of Dmac-paired with either method resulted in pair-rule-like segmentation defects, including loss of Engrailed expression in alternate stripes.

CONCLUSIONS

These studies establish basic approaches necessary to use Dermestes maculatus as a model system. Methods are now available for use of this intermediate-germ insect for future studies of the evolution of regulatory networks controlling insect segmentation, as well as of other processes in development and homeostasis. Consistent with the role of paired in long-germ Drosophila and shorter-germ Tribolium, paired functions as a pair-rule segmentation gene in Dermestes maculatus. Thus, paired retains pair-rule function in insects with different modes of segment addition.