Conserved and divergent expression patterns of markers of axial development in reptilian embryos: Chinese soft-shell turtle and Madagascar ground gecko

ETV2 induces endothelial, but not hematopoietic, lineage specification in birds

Cardiovascular system develops from the lateral plate mesoderm. Its three primary cell lineages (hematopoietic, endothelial, and muscular) are specified by the sequential actions of conserved transcriptional factors. ETV2, a master regulator of mammalian hemangioblast development, however, is absent in the chicken genome and acts downstream of NPAS4L in zebrafish. Here, we investigated the epistatic relationship between NPAS4L and ETV2 in avian hemangioblast development. We showed that ETV2 is deleted in all 363 avian genomes analyzed. Mouse ETV2 induced LMO2, but not NPAS4L or SCL, expression in chicken mesoderm. Squamate (lizards, geckos, and snakes) genomes contain both NPAS4L and ETV2 In Madagascar ground gecko, both genes were expressed in developing hemangioblasts. Gecko ETV2 induced only LMO2 in chicken mesoderm. We propose that both NPAS4L and ETV2 were present in ancestral amniote, with ETV2 acting downstream of NPAS4L in endothelial lineage specification. ETV2 may have acted as a pioneer factor by promoting chromatin accessibility of endothelial-specific genes and, in parallel with NPAS4L loss in ancestral mammals, has gained similar function in regulating blood-specific genes.

A reverse genetic approach in geckos with the CRISPR/Cas9 system by oocyte microinjection

Reptiles are important model organisms in developmental and evolutionary biology, but are used less widely than other amniotes such as mouse and chicken. One of the main reasons for this is that has proven difficult to conduct CRISPR/Cas9-mediated genome editing in many reptile species despite the widespread use of this technology in other taxa. Certain features of reptile reproductive systems make it difficult to access one-cell or early-stage zygotes, which represents a key impediment to gene editing techniques. Recently, Rasys and colleagues reported a genome editing method using oocyte microinjection that allowed them to produce genome-edited Anolis lizards. This method opened a new avenue to reverse genetics studies in reptiles. In the present article, we report the development of a related method for genome editing in the Madagascar ground gecko (Paroedura picta), a well-established experimental model, and describe the generation of Tyr and Fgf10 gene-knockout geckos in the F0 generation.

Alternative mammalian strategies leading towards gastrulation: losing polar trophoblast (Rauber's layer) or gaining an epiblast cavity

Using embryological data from 14 mammalian orders, the hypothesis is presented that in placental mammals, epiblast cavitation and polar trophoblast loss are alternative developmental solutions to shield the central epiblast from extraembryonic signalling. It is argued that such reciprocal signalling between the edge of the epiblast and the adjoining polar trophoblast or edge of the mural trophoblast or with the amniotic ectoderm is necessary for the induction of gastrulation. This article is part of the theme issue 'Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom'.

Identification of Nodal-dependent enhancer of amphioxus Chordin sufficient to drive gene expression into the chordate dorsal organizer

The core molecular mechanisms of dorsal organizer formation during gastrulation are highly conserved within the chordate lineage. One of the key characteristics is that Nodal signaling is required for the organizer-specific gene expression. This feature appears to be ancestral, as evidenced by the presence in the most basally divergent chordate amphioxus. To provide a better understanding of the evolution of organizer-specific gene regulation in chordates, we analyzed the cis-regulatory sequence of amphioxus Chordin in the context of the vertebrate embryo. First, we generated stable zebrafish transgenic lines, and by using light-sheet fluorescent microscopy, characterized in detail the expression pattern of GFP driven by the cis-regulatory sequences of amphioxus Chordin. Next, we performed a 5'deletion analysis and identified an enhancer sufficient to drive the expression of the reporter gene into a chordate dorsal organizer. Finally, we found that the identified enhancer element strongly depends on Nodal signaling, which is consistent with the well-established role of this pathway in the regulation of the expression of dorsal organizer-specific genes across chordates. The enhancer identified in our study may represent a suitable simple system to study the interplay of the evolutionarily conserved regulatory mechanisms operating during early chordate development.

Left-right asymmetric expression of the Nodal-Lefty-Pitx2 module in developing turtle forebrain

The epithalamus of zebrafish shows morphological and molecular left-right (L-R) asymmetry, but such asymmetry is not apparent in tetrapods. To provide further insight into the evolutionary diversity of brain L-R asymmetry, we have now examined the developing brains of reptile embryos for expression of Nodal, Lefty, and Pitx2. Two turtle species, the Chinese softshell turtle and the red-eared slider turtle, showed left-sided expression of these three genes in the developing forebrain, with this expression occurring after Nodal expression at the lateral plate and the L-R organizer has disappeared. Nodal activity, as revealed by the detection of phosphorylated Smad2/3, was also apparent in the neural epithelium on the left side in both turtle species. In the Chinese softshell turtle, the habenula did not show apparent asymmetry in size and the parapineal organ was absent, but the expression of Kctd12 in the habenula showed a small yet reproducible asymmetry. In contrast to the turtles, L-R asymmetric expression of Nodal, Lefty, Pitx2, or Kctd12 was not detected in the developing brain of the Madagascar ground gecko. The transcriptional enhancer (ASE) responsible for the asymmetric expression of Nodal, Lefty, and Pitx2 was conserved among reptiles, including the Chinese softshell turtle and Madagascar ground gecko. Our findings suggest that Nodal, Lefty, and Pitx2 have the potential to be asymmetrically expressed in the developing brain of vertebrates, but that their expression varies even among reptiles.

Diversity of left-right symmetry breaking strategy in animals

Left-right (L-R) asymmetry of visceral organs in animals is established during embryonic development via a stepwise process. While some steps are conserved, different strategies are employed among animals for initiating the breaking of body symmetry. In zebrafish (teleost), Xenopus (amphibian), and mice (mammal), symmetry breaking is elicited by directional fluid flow at the L-R organizer, which is generated by motile cilia and sensed by mechanoresponsive cells. In contrast, birds and reptiles do not rely on the cilia-driven fluid flow. Invertebrates such as Drosophila and snails employ another distinct mechanism, where the symmetry breaking process is underpinned by cellular chirality acquired downstream of the molecular interaction of myosin and actin. Here, we highlight the convergent entry point of actomyosin interaction and planar cell polarity to the diverse L-R symmetry breaking mechanisms among animals.

Nodal paralogues underlie distinct mechanisms for visceral left-right asymmetry in reptiles and mammals

Unidirectional fluid flow generated by motile cilia at the left-right organizer (LRO) breaks left-right (L-R) symmetry during early embryogenesis in mouse, frog and zebrafish. The chick embryo, however, does not require motile cilia for L-R symmetry breaking. The diversity of mechanisms for L-R symmetry breaking among vertebrates and the trigger for such symmetry breaking in non-mammalian amniotes have remained unknown. Here we examined how L-R asymmetry is established in two reptiles, Madagascar ground gecko and Chinese softshell turtle. Both of these reptiles appear to lack motile cilia at the LRO. The expression of the Nodal gene at the LRO in the reptilian embryos was found to be asymmetric, in contrast to that in vertebrates such as mouse that are dependent on cilia for L-R patterning. Two paralogues of the Nodal gene derived from an ancient gene duplication are retained and expressed differentially in cilia-dependent and cilia-independent vertebrates. The expression of these two Nodal paralogues is similarly controlled in the lateral plate mesoderm but regulated differently at the LRO. Our in-depth analysis of reptilian embryos thus suggests that mammals and non-mammalian amniotes deploy distinct strategies dependent on different Nodal paralogues for rendering Nodal activity asymmetric at the LRO.

Morphogenetic mechanism of the acquisition of the dinosaur-type acetabulum

Understanding morphological evolution in dinosaurs from a mechanistic viewpoint requires the elucidation of the morphogenesis that gave rise to derived dinosaurian traits, such as the perforated acetabulum. In the current study, we used embryos of extant animals with ancestral- and dinosaur-type acetabula, namely, geckos and turtles (with unperforated acetabulum), and birds (with perforated acetabulum). We performed comparative and experimental analyses, focusing on inter-tissue interaction during embryogenesis, and found that the avian perforated acetabulum develops via a secondary loss of cartilaginous tissue in the acetabular region. This cartilage loss might be mediated by inter-tissue interaction with the hip interzone, a mesenchymal tissue that exists in the embryonic joint structure. Furthermore, the data indicate that avian pelvic anlagen is more susceptible to paracrine molecules, e.g. Wnt ligand, secreted by the hip interzone than 'reptilian' anlagen. We hypothesize that during the emergence of dinosaurs, the pelvic anlagen became susceptible to the Wnt ligand, which led to the loss of the cartilaginous tissue and to the perforation in the acetabular region. Thus, the current evolutionary-developmental biology study deepens our understanding of morphological evolution in dinosaurs and provides it with a novel perspective.

Building Principles for Constructing a Mammalian Blastocyst Embryo

The self-organisation of a fertilised egg to form a blastocyst structure, which consists of three distinct cell lineages (trophoblast, epiblast and hypoblast) arranged around an off-centre cavity, is unique to mammals. While the starting point (the zygote) and endpoint (the blastocyst) are similar in all mammals, the intervening events have diverged. This review examines and compares the descriptive and functional data surrounding embryonic gene activation, symmetry-breaking, first and second lineage establishment, and fate commitment in a wide range of mammalian orders. The exquisite detail known from mouse embryogenesis, embryonic stem cell studies and the wealth of recent single cell transcriptomic experiments are used to highlight the building principles underlying early mammalian embryonic development.

Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes

Background

Conventionally, comparison among amniotes – birds, mammals, and reptiles – has often been approached through analyses of mammals and, for comparison, birds. However, birds are morphologically and physiologically derived and, moreover, some parts of their genomes are recognized as difficult to sequence and/or assemble and are thus missing in genome assemblies. Therefore, sequencing the genomes of reptiles would aid comparative studies on amniotes by providing more comprehensive coverage to help understand the molecular mechanisms underpinning evolutionary changes.

Results

Herein, we present the whole genome sequences of the Madagascar ground gecko (Paroedura picta), a promising study system especially in developmental biology, and used it to identify changes in gene repertoire across amniotes. The genome-wide analysis of the Madagascar ground gecko allowed us to reconstruct a comprehensive set of gene phylogenies comprising 13,043 ortholog groups from diverse amniotes. Our study revealed 469 genes retained by some reptiles but absent from available genome-wide sequence data of both mammals and birds. Importantly, these genes, herein collectively designated as ‘elusive’ genes, exhibited high nucleotide substitution rates and uneven intra-genomic distribution. Furthermore, the genomic regions flanking these elusive genes exhibited distinct characteristics that tended to be associated with increased gene density, repeat element density, and GC content.

Conclusion

This highly continuous and nearly complete genome assembly of the Madagascar ground gecko will facilitate the use of this species as an experimental animal in diverse fields of biology. Gene repertoire comparisons across amniotes further demonstrated that the fate of a duplicated gene can be affected by the intrinsic properties of its genomic location, which can persist for hundreds of millions of years.

Electronic supplementary material

The online version of this article (10.1186/s12915-018-0509-4) contains supplementary material, which is available to authorized users.

A Sensitive and Versatile In Situ Hybridization Protocol for Gene Expression Analysis in Developing Amniote Brains

The detection of specific RNA molecules in embryonic tissues has wide research applications including studying gene expression dynamics in brain development and evolution. Recent advances in sequencing technologies have introduced new animal models to explore the molecular principles underlying the assembly and diversification of brain circuits between different amniote species. Here, we provide a step-by-step protocol for a versatile in situ hybridization method that is immediately applicable to a range of amniote embryos including zebra finch and Madagascar ground gecko, two new model organisms that have rapidly emerged for comparative brain studies over recent years. The sensitive detection of transcripts from low to high abundance expression range using the same platform enables direct comparison of gene of interest among different amniotes, providing high-resolution spatiotemporal information of gene expression to dissect the molecular principles underlying brain evolution.