Characterizing Hox genes in mayflies (Ephemeroptera), with Hexagenia limbata as a new mayfly model

BACKGROUND

Hox genes are key regulators of appendage development in the insect body plan. The body plan of mayfly (Ephemeroptera) nymphs differs due to the presence of abdominal appendages called gills. Despite mayflies' phylogenetic position in Paleoptera and novel morphology amongst insects, little is known of their developmental genetics, such as the appendage-regulating Hox genes. To address this issue we present an annotated, early instar transcriptome and embryonic expression profiles for Antennapedia, Ultrabithorax, and Abdominal A proteins in the mayfly Hexagenia limbata, identify putative Hox protein sequences in the mayflies H. limbata, Cloeon dipterum, and Ephemera danica, and describe the genomic organization of the Hox gene cluster in E. danica.

RESULTS

Transcriptomic sequencing of early instar H. limbata nymphs yielded a high-quality assembly of 83,795 contigs, of which 22,975 were annotated against Folsomia candida, Nilaparvata lugens, Zootermopsis nevadensis and UniRef90 protein databases. Homeodomain protein phylogeny and peptide annotations identified coding sequences for eight of the ten canonical Hox genes (excluding zerknüllt/Hox3 and fushi tarazu) in H. limbata and C. dipterum, and all ten in E. danica. Mayfly Hox protein sequences and embryonic expression patterns of Antp, Ubx, and Abd-A appear highly conserved with those seen in other non-holometabolan insects. Similarly, the genomic organization of the Hox cluster in E. danica resembles that seen in most insects.

CONCLUSIONS

We present evidence that mayfly Hox peptide sequences and the embryonic expression patterns for Antp, Ubx, and Abd-A are extensively conserved with other insects, as is organization of the mayfly Hox gene cluster. The protein data suggest mayfly Antp, Ubx, and Abd-A play appendage promoting and repressing roles during embryogenesis in the thorax and abdomen, respectively, as in other insects. The identified expression of eight Hox genes, including Ubx and abd-A, in early instar nymphs further indicates a post-embryonic role, possibly in gill development. These data provide a basis for H. limbata as a complementary Ephemeridae model to the growing repertoire of mayfly model species and molecular techniques.

Molecular insights into deuterostome evolution from hemichordate developmental biology

Hemichordates, along with echinoderms and chordates, belong to the lineage of bilaterians called the deuterostomes. Their phylogenetic position as an outgroup to chordates provides an opportunity to investigate the evolutionary origins of the chordate body plan and reconstruct ancestral deuterostome characters. The body plans of the hemichordates and chordates are organizationally divergent making anatomical comparisons very challenging. The developmental underpinnings of animal body plans are often more conservative than the body plans they regulate, and offer a novel data set for making comparisons between morphologically divergent body architectures. Here I review the hemichordate developmental data generated over the past 20 years that further test hypotheses of proposed morphological affinities between the two taxa, but also compare the conserved anteroposterior, dorsoventral axial patterning programs and germ layer specification programs. These data provide an opportunity to determine which developmental programs are ancestral deuterostome or bilaterian innovations, and which ones occurred in stem chordates or vertebrates representing developmental novelties of the chordate body plan.

сWnt signaling modulation results in a change of the colony architecture in a hydrozoan

At the polyp stage, most hydrozoan cnidarians form highly elaborate colonies with a variety of branching patterns, which makes them excellent models for studying the evolutionary mechanisms of body plan diversification. At the same time, molecular mechanisms underlying the robust patterning of the architecturally complex hydrozoan colonies remain unexplored. Using non-model hydrozoan Dynamena pumila we showed that the key components of the Wnt/β-catenin (cWnt) pathway (β-catenin, TCF) and the cWnt-responsive gene, brachyury 2, are involved in specification and patterning of the developing colony shoots. Strikingly, pharmacological modulation of the cWnt pathway leads to radical modification of the monopodially branching colony of Dynamena which acquire branching patterns typical for colonies of other hydrozoan species. Our results suggest that modulation of the cWnt signaling is the driving force promoting the evolution of the vast variety of the body plans in hydrozoan colonies and offer an intriguing possibility that the involvement of the cWnt pathway in the regulation of branching morphogenesis might represent an ancestral feature predating the cnidarian-bilaterian split.

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.

Adoption of conserved developmental genes in development and origin of the medusa body plan

BACKGROUND

The metagenesis of sessile polyps into pelagic medusae in cnidarians represents one of the most ancient complex life cycles in animals. Interestingly, scyphozoans and hydrozoans generate medusae by apparently fundamentally different processes. It is therefore unclear whether medusa formation has evolved independently in different medusozoans. To this end, a thorough understanding of the correspondence of polyp and medusa is required.

RESULTS

We monitored the expression patterns of conserved developmental genes in developing medusae of Clytia hemisphaerica (Hydrozoa) and Aurelia aurita (Scyphozoa) and found that developing medusae and polyps share similarities in their morphology and developmental gene expression. Unexpectedly, however, polyp tentacle marker genes were consistently expressed in the developing medusa bell, suggesting that the bell of medusae corresponds to modified and fused polyp tentacle anlagen.

CONCLUSIONS

Our data represent the first comparative gene expression analysis of developing medusae in two representatives of Scyphozoa and Hydrozoa. The results challenge prevailing views about polyp medusa body plan homology. We propose that the evolution of a new life stage may be facilitated by the adoption of existing developmental genes.

A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems

BACKGROUND

The de novo assembly of transcriptomes from short shotgun sequences raises challenges due to random and non-random sequencing biases and inherent transcript complexity. We sought to define a pipeline for de novo transcriptome assembly to aid researchers working with emerging model systems where well annotated genome assemblies are not available as a reference. To detail this experimental and computational method, we used early embryos of the sea anemone, Nematostella vectensis, an emerging model system for studies of animal body plan evolution. We performed RNA-seq on embryos up to 24 h of development using Illumina HiSeq technology and evaluated independent de novo assembly methods. The resulting reads were assembled using either the Trinity assembler on all quality controlled reads or both the Velvet and Oases assemblers on reads passing a stringent digital normalization filter. A control set of mRNA standards from the National Institute of Standards and Technology (NIST) was included in our experimental pipeline to invest our transcriptome with quantitative information on absolute transcript levels and to provide additional quality control.

RESULTS

We generated >200 million paired-end reads from directional cDNA libraries representing well over 20 Gb of sequence. The Trinity assembler pipeline, including preliminary quality control steps, resulted in more than 86% of reads aligning with the reference transcriptome thus generated. Nevertheless, digital normalization combined with assembly by Velvet and Oases required far less computing power and decreased processing time while still mapping 82% of reads. We have made the raw sequencing reads and assembled transcriptome publically available.

CONCLUSIONS

Nematostella vectensis was chosen for its strategic position in the tree of life for studies into the origins of the animal body plan, however, the challenge of reference-free transcriptome assembly is relevant to all systems for which well annotated gene models and independently verified genome assembly may not be available. To navigate this new territory, we have constructed a pipeline for library preparation and computational analysis for de novo transcriptome assembly. The gene models defined by this reference transcriptome define the set of genes transcribed in early Nematostella development and will provide a valuable dataset for further gene regulatory network investigations.