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Congenital Heart Disease (CHD) is currently the most common birth defect, affecting approximately 1% of live births. Understanding the genetic mechanisms underlying CHD is crucial for developing effective interventions. This paper explores the functional and evolutionary roles of the T-box transcription factors Tbx2a and Tbx2b in zebrafish heart development. Functional studies in zebrafish demonstrated that both homozygous and heterozygous mutations in tbx2a and tbx2b result in heart looping defects, challenging the assumption of their redundancy and indicating unique, non-overlapping functions essential for cardiac development. The observed phenotypic variability in heterozygous mutants suggests a complex interplay between these genes and highlights the sensitivity of cardiac development to precise gene dosage. Utilizing advanced bioinformatics techniques, we reconstructed the ancestral sequences of these genes to understand their evolutionary trajectory and functional divergence. Our analysis revealed strong evolutionary conservation of the T-box DNA-binding domain in Tbx2a and Tbx2b, suggesting that both proteins remain constrained to recognize the same core cis-regulatory elements. This conservation implies that their ability to bind essential cardiac target genes is functionally indispensable and under strong purifying selection. We observed unique and shared amino acid substitutions, indicating potential adaptive changes and conserved functions. Given their highly conserved DNA-binding domains, we hypothesized that Tbx2a and Tbx2b interact with different nuclear factors to regulate distinct sets of genes. Mass spectrometry-based proteomics provided insights into the unique nuclear interactions of Tbx2a and Tbx2b, supporting the hypothesis of their functional divergence. Overall, this research offers new insights into the functional and evolutionary roles of Tbx2a and Tbx2b in heart development, with implications for understanding the genetic basis of CHD.

The remarkable morphological disparity of the animal kingdom is underpinned by changes in embryonic development across the tree of life; as such, deciphering evolutionary patterns of developmental divergence depends on investigations of different species across a range of comparable developmental stages. Among the most influential ideas regarding such developmental divergences are von Baer's Laws of Development and Haeckel's Theory of Recapitulation. Here, we assess several predictions following from these ideas at the tissue-level by comparing skull osteogenesis in representatives of the bird clade Galloanserae. We investigated high-resolution µCT scans of embryonic series for four galloanseran species: chickens and quails, representing Galliformes (landfowl), and ducks and geese, representing Anseriformes (waterfowl). To compare skull osteogenesis across our taxon sample, we devised a skull-specific staging system based on ossification sequences to discretise the process into five stages. During skull osteogenesis, we found that the location of the onset of ossification within each element and the direction of ossification progression were the same in all species in our sample, implying a conserved developmental programme for induction and ossification progression across Galloanserae. Moreover, we found that the appearance of synapomorphies diagnostic of broader clades often overlapped with species-specific ones during osteogenesis. Indeed, many diagnostic features of deep clades, such as osteological synapomorphies of the phylogenetically inclusive clade Galloanserae, appear at surprisingly late stages of development. These observations fail to support several predictions of von Baer's Laws of Development and Haeckel's Theory of Recapitulation, instead suggesting what we term a 'braiding' pattern of developmental divergence in which degrees of interspecific morphological similarity wax and wane during development as a result of the interplay between developmental constraints and phyletic variation.

Hydnora (Hydnoraceae) comprises a few parasitic species exceptional among the autotrophic members of the perianth-bearing Piperales. Flowers in the genus are thick, fleshy, sapromyophilous, and develop into massive, polyspermous fruits. They are formed directly along underground rhizomes that parasitize species of Euphorbiaceae and Fabaceae. Due to its peculiar floral morphology and lack of leaves, Hydnora is often dubbed 'the strangest plant in the world'. Here we generated the first transcriptomes of Hydnora visseri from the dissected rhizome, perianth, osmophore, stamen, carpel, and fruit. Our results suggest that Hydnora possesses one of the simplest developmental genetic toolkits for flowering and floral organ identity among angiosperms, further emphasizing its uniqueness. We detected that most of the photoperiodic flowering integrators are expressed. In contrast, regulators of the autonomous pathway and circadian clock were notably absent from the transcriptomes. Conversely, we identified an intact genetic toolkit linked to floral organ identity and fruit development in Hydnora. Through positional homology and gene expression data, we inferred that the perianth of Hydnora corresponds to the calyx, and that the osmophores are late sepal elaborations. Additionally, the expression patterns of genes responsible for stamen, carpel, and ovule identity align with the canonical ABCDE model. Finally, we recorded large-scale duplications in putative perianth identity genes prior to the diversification of all perianth-bearing Piperales. This study serves as an additional comparative point for assessing the evolutionary onset of holoparasitic plants, as Hydnora and its sister genus Prosopanche are likely the earliest branching representatives of this lifestyle across angiosperms.

Background: Within the symbiont-hosting Siboglinidae (Annelida), Osedax stands out as the sole genus capable of degrading bones and displaying pronounced sexual dimorphism (except O. priapus). While macroscopic, gutless females feed on whale falls with their symbiont-housing "roots", males are microscopic and non-feeding. Yet, embryos and larvae look identical, and sex is suggested to be environmentally determined, i.e., larvae metamorphose into females on bare bone or into males when finding an adult female.

Results: However, we here describe a transient gut present in half of the late larvae and in juvenile females of O. japonicus. We confirm the gut-carrying larvae as being females from sex-specific in situ gene expression. Moreover, morphological evidence coupled with differential gene expression indicate that the 'non-feeding' transient gut may pattern the vascular system and/or act as a gas-exchange surface in juvenile females, before their branchial appendages develop.

Conclusions: The transient gut of O. japonicus females reveals a genetic sex determination. Proposedly homologous across siboglinids, this vestigial gut is suggested to function in organ patterning and/or for gas-exchange during development of the gutless adult.

Some aspects of the life cycle of the scyphozoan jellyfish Cassiopea xamachana have been described in detail. Investigations of C. xamachana have largely focused on strobilation and the unusual pattern of planuloid budding at the polyp stage, in which the body wall of the polyp forms a swimming planuloid bud that shows morphological and behavioral similarities to the planula. Here, we fill gaps in our understanding of C. xamachana life history by characterizing embryonic development and planula settlement and metamorphosis. These processes happen in a manner similar to other scyphozoans studied. Gastrulation occurs by invagination, as in many other scyphozoans. Morphological observations of planula settlement and metamorphosis resemble observations of the process in Aurelia, the other well-studied scyphozoan, though some details about germ layer fates remain unclear. We also show that homeobox genes expressed during planula development are redeployed in a similar pattern in the planuloid bud. In the newly settled polyp, one of these genes is expressed in a pattern that breaks radial symmetry, extremely unusual in a scyphozoan. Our results set the stage for more detailed molecular dissections of morphogenesis in organisms with metagenic life cycles.

Background: Lineage-specific adult structures form through modifications of pre-existing juvenile body parts during postembryonic development in insects. It remains unclear how these novel traits originate from ancestral structures within the constrained body plan. In the coffin-headed cricket Loxoblemmus equestris, an ancestral rounded head shape directly transforms into a flattened derived form in a sex-specific manner. To understand the origin of novel traits, we investigated the development of the adult head in L. equestris as a model of lineage-specific novelty.

Results: We found that head morphologies remained sexually monomorphic until the final molt, and the male-specific head shape emerged in the frons region during the transition to adulthood in L. equestris. Two- and three-dimensional morphological analyses revealed that the sexual dimorphism in the frons epithelial folding patterns appeared in the late final nymphal instar. These results suggest that the male-specific novel head development is linked to the final molt in L. equestris. We tested this hypothesis by knocking down the metamorphic gene network (MGN) comprised of Krüppel-homolog 1 (Kr-h1), broad (br), and Ecdysone induced protein 93F (E93). Despite the timing shifts of the nymph-to-adult transition caused by knockdown of the MGN, male-specific head structures are formed only after the final molt.

Conclusions: These results demonstrate that the novel male head structures are formed during the final molt through the formation of sex-specific epithelial patterns in L. equestris. This highlights the unique metamorphic lifecycle with the final molt as a driver that has created lineage- and sex-specific adult forms in insects.

Background: Evidence suggests that Pax6 genes are necessary for the specification of eyes in a variety of metazoans, including mandibulate arthropods. In these arthropods, Pax6 genes usually interact with a conserved set of genes, collectively called the retinal determination gene network (RDGN), to specify eye cells. However, recent data have argued that Pax6 genes lack a role in the development of the eyes in Chelicerata (= arachnids, horseshoe crabs, and sea spiders). A genome sequence of the eyeless mite Archegozetes longisetosus revealed that it retains two Pax6 paralogs, as well as singleton orthologs of all RDGN genes. We hypothesized that the retention of these two Pax6 paralogs could be due to their non-eye determining roles, and/or their expression in vestigial eye primordia. We therefore used hybridization chain reactions (HCRs) to follow the embryonic expression of these genes.

Results: To provide a basis for understanding RDGN expression patterns, we developed a staging system for A. longisetosus head development. This showed the presence of structures that in other arachnids form neural components of all eye types. We then showed that two genes in the RDGN of eyed arachnids, i.e., sine oculis and atonal, are expressed in a manner that are suggestive of vestigial eye primordia. We also found that the expression of the Pax6 paralogs was consistent with their roles in the development of the central nervous system. By co-staining for these genes with the conserved head-patterning gene orthodenticle, we observed early expression patterns of these genes in the brains of early A. longisetosus embryos that are comparable to those arachnids with embryonic eyes.

Conclusions: Our data provide support for the hypothesis that the retention of Pax6 genes in A. longisetosus is due to their non-eye patterning roles. Furthermore, our survey of RDGN gene expression also provides support that A. longisetosus patterns vestigial eye primordia. Lastly, our data suggest that the Pax6 genes, with orthodenticle, acts to specify the ancestral arachnid brain. We then discuss our results considering eye loss in other arachnids.

Background: The development of the digits (fingers/toes) provides an excellent model for analyzing the molecular regulation of skeletal morphogenesis in vertebrates. Digits develop in the autopod as radial chondrogenic condensations separated by interdigital spaces containing undifferentiated skeletal progenitors destined to die by apoptosis. In avian species, leg digits are characterized by a differential size, with the first digit being short and the fourth largest.

Results: In vitro experiments using micromass cultures of digit progenitors demonstrated that RA controls the balance between cell death, cell proliferation, and cell differentiation in a dose-dependent fashion. In vivo, qPCR analysis revealed that the RA-synthesizing enzyme Raldh2 and the RA-degrading enzyme Cyp26a1 are expressed in the interdigits in an inverse gradient that correlates with the size of the digit adjacent to each interdigit. RA gain- and loss-of-function experiments via pharmacological approaches confirmed a close correlation between interdigital RA and digit size. A low concentration of RA applied to the first interdigits, when the phalanxes of the first digit are being formed, promoted mesodermal cell proliferation and caused elongation of digit 1, while blocking RA synthesis into the third interdigit inhibited cell proliferation, followed by a reduction in the size of digits 3 and 4.

Conclusions: This study reveals a potential role for Retinoic Acid (RA) expressed in the interdigits in the regulation of the differential digit size. The morphological similarity of the digit patterns obtained in our experimental assays with those of other tetrapods suggests an evolutionary role of RA in determining digit morphology.

Background: Phagocytosis is a universal physiological process in eukaryotes with many important biological functions. In nudibranch gastropods, a novel form of phagocytosis called nematocyst sequestration is specialized for the uptake of venomous stinging organelles stolen from their cnidarian prey. This process is highly selective. Here we use the emerging model nudibranch species Berghia stephanieae and Hermissenda opalescens to identify genes enriched within the body regions where nematocyst sequestration occurs, and investigate how the expression profile of phagocytosis, immune, and digestive genes differs between nematocyst-sequestering regions relative to those where other phagocytic functions occur.

Results: We identified 166 genes with significantly higher expression in sequestering regions in B. stephanieae, including genes associated with development, membrane transport, and metabolism. Of these, at least 31 overlap with transcripts upregulated in H. opalescens sequestering tissues. Using hybridization chain reaction in situs, we show that at least two of these genes were localized to sequestering cells in B. stephanieae, including a putative C-type lectin receptor and a collagen. Genes annotated with phagocytosis, digestion, or immunity GO terms were often expressed in both sequestering and non-sequestering tissues, suggesting that they may also play a role in sequestration processes.

Conclusion: Our results suggest that phagocytosis genes likely play a role in the sequestration phenotype, and that a small subset of genes (e.g., collagen) may play unique functions yet to be uncovered. We also show that genes categorized as functioning in endocytosis, immunity, and digestion have lower overall expression in sequestering tissues, supporting the hypothesis that sequestering tissues show a narrowing of function compared to digestive tissues. This study lays the foundation for further inquiry into mechanisms of organelle sequestration in nudibranchs and other organisms.