Sonic hedgehog specifies flight feather positional information in avian wings

The feather's multi-functional structure across nano to macro scales inspires hierarchical design

Bird feathers are finely tuned structures with key features at every length scale, from nanometre to metre, furnishing a unique multi-functional hierarchical design that can inspire material scientists, biologists and designers alike. Feathers are not only a crucial component in equipping birds with flight, but are also responsible for thermoregulation, coloration and crypsis, water repellency, silencing and sound production, sensing, directional fastening and even self-healing. Despite this broad multifunctionality, all feathers are formed from the same basic template using a universal building block: the feather keratin protein. Consequently, feather diversity across approximately 10 000 bird species arises from subtle differences in architecture rather than variations in chemical composition. To understand these underlying hierarchical mechanisms, we systematically review feather properties across all length scales, connecting development and morphogenesis to biomechanics and integrated structure-property-function relationships. This systematic distillation of the feather's complex design into comprehensive principles will enkindle new biohybrid, biomimetic and bioinspired material solutions.

In vivo sonic hedgehog pathway antagonism temporarily results in ancestral proto-feather-like structures in the chicken

The morphological intricacies of avian feathers make them an ideal model for investigating embryonic patterning and morphogenesis. In particular, the sonic hedgehog (Shh) pathway is an important mediator of feather outgrowth and branching. However, functional in vivo evidence regarding its role during feather development remains limited. Here, we demonstrate that an intravenous injection of sonidegib, a potent Shh pathway inhibitor, at embryonic day 9 (E9) temporarily produces striped domains (instead of spots) of Shh expression in the skin, arrests morphogenesis, and results in unbranched and non-invaginated feather buds-akin to proto-feathers-in embryos until E14. Although feather morphogenesis partially recovers, hatched treated chickens exhibit naked skin regions with perturbed follicles. Remarkably, these follicles are subsequently reactivated by seven weeks post-hatching. Our RNA-sequencing data and rescue experiment using Shh-agonism confirm that sonidegib specifically down-regulates Shh pathway activity. Overall, we provide functional evidence for the role of the Shh pathway in mediating feather morphogenesis and confirm its role in the evolutionary emergence and diversification of feathers.

Chromosome-level genome sequencing and multi-omics of the Hungarian White Goose (Anser anser domesticus) reveals novel miRNA-mRNA regulation mechanism of waterfowl feather follicle development

The Hungarian White Goose (Anser anser domesticus) is an excellent European goose breed, with high feather and meat production. Despite its importance in the poultry industry, no available genome assembly information has been published. This study aimed to present Chromosome-level and functional genome sequencing of the Hungarian White Goose. The results showed that the genome assembly has a total length of 1115.82 Mb, 39 pairs of chromosomes, 92.98% of the BUSCO index, and contig N50 and scaffold N50 were up to 2.32 Mb and 60.69 Mb, respectively. Annotation of the genome assembly revealed 19550 genes, 286 miRNAs, etc. We identified 235 expanded and 1,167 contracted gene families in this breed compared with the other 16 species. We performed a positive selection analysis between this breed and four species of Anatidae to uncover the genetic information underlying feather follicle development. Further, we detected the function of miR-199-x, miR-143-y, and miR-23-z on goose embryonic skin fibroblast. In summary, we have successfully generated a highly complete genome sequence of the Hungarian white goose, which will provide a great resource to improve our understanding of gene functions and enhance the studies on feather follicle development at the genomic level.

Parsing patterns: Emerging roles of tissue self-organization in health and disease

Patterned morphologies, such as segments, spirals, stripes, and spots, frequently emerge during embryogenesis through self-organized coordination between cells. Yet, complex patterns also emerge in adults, suggesting that the capacity for spontaneous self-organization is a ubiquitous property of biological tissues. We review current knowledge on the principles and mechanisms of self-organized patterning in embryonic tissues and explore how these principles and mechanisms apply to adult tissues that exhibit features of patterning. We discuss how and why spontaneous pattern generation is integral to homeostasis and healing of tissues, illustrating it with examples from regenerative biology. We examine how aberrant self-organization underlies diverse pathological states, including inflammatory skin disorders and tumors. Lastly, we posit that based on such blueprints, targeted engineering of pattern-driving molecular circuits can be leveraged for synthetic biology and the generation of organoids with intricate patterns.

Genetics and Evolution of Bird Migration

Bird migration has long been a subject of fascination for humankind and is a behavior that is both intricate and multifaceted. In recent years, advances in technology, particularly in the fields of genomics and animal tracking, have enabled significant progress in our understanding of this phenomenon. In this review, we provide an overview of the latest advancements in the genetics of bird migration, with a particular focus on genomics, and examine various factors that contribute to the evolution of this behavior, including climate change. Integration of research from the fields of genomics, ecology, and evolution can enhance our comprehension of the complex mechanisms involved in bird migration and inform conservation efforts in a rapidly changing world.

A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information

Some computational methods have been given for small molecule-RNA binding site identification due to that it plays a significant role in revealing biology function researches. However, it is still challenging to design an accurate model, especially for MCC. We designed a feature extraction technology from two aspects (position specificity and complex network information). Specifically, complex network was employed to express the space topological structure and sequence position information for improving prediction effect. Then, the features fused position specificity and complex network information were input into random forest classifier for model construction. The AUC of 88.22%, 77.92% and 81.46% were obtained on three independent datasets (RB19, CS71, RB78). Compared with the existing method, the best MCC were obtained on three datasets, which were 8.19%, 0.59% and 4.35% higher than the state-of-the-art prediction methods, respectively. The outstanding performances show that our method is a powerful tool to identify RNA binding sites, helping to the design RNA-targeting small molecule drugs. The data and resource codes are available at https://github.com/Kangxiaoneuq/PCN_RNAsite.

Transient agonism of the sonic hedgehog pathway triggers a permanent transition of skin appendage fate in the chicken embryo

Vertebrate skin appendage early development is mediated by conserved molecular signaling composing a dynamical reaction-diffusion-like system. Variations to such systems contribute to the remarkable diversity of skin appendage forms within and among species. Here, we demonstrate that stage-specific transient agonism of sonic hedgehog (Shh) pathway signaling in chicken triggers a complete and permanent transition from reticulate scales to feathers on the ventral surfaces of the foot and digits. Resulting ectopic feathers are developmentally comparable to feathers adorning the body, with down-type feathers transitioning into regenerative, bilaterally symmetric contour feathers in adult chickens. Crucially, this spectacular transition of skin appendage fate (from nodular reticulate scales to bona fide adult feathers) does not require sustained treatment. Our RNA sequencing analyses confirm that smoothened agonist treatment specifically promotes the expression of key Shh pathway-associated genes. These results indicate that variations in Shh pathway signaling likely contribute to the natural diversity and regionalization of avian integumentary appendages.

Genetic and ecological drivers of molt in a migratory bird

The ability of animals to sync the timing and location of molting (the replacement of hair, skin, exoskeletons or feathers) with peaks in resource availability has important implications for their ecology and evolution. In migratory birds, the timing and location of pre-migratory feather molting, a period when feathers are shed and replaced with newer, more aerodynamic feathers, can vary within and between species. While hypotheses to explain the evolution of intraspecific variation in the timing and location of molt have been proposed, little is known about the genetic basis of this trait or the specific environmental drivers that may result in natural selection for distinct molting phenotypes. Here we take advantage of intraspecific variation in the timing and location of molt in the iconic songbird, the Painted Bunting (Passerina ciris) to investigate the genetic and ecological drivers of distinct molting phenotypes. Specifically, we use genome-wide genetic sequencing in combination with stable isotope analysis to determine population genetic structure and molting phenotype across thirteen breeding sites. We then use genome-wide association analysis (GWAS) to identify a suite of genes associated with molting and pair this with gene-environment association analysis (GEA) to investigate potential environmental drivers of genetic variation in this trait. Associations between genetic variation in molt-linked genes and the environment are further tested via targeted SNP genotyping in 25 additional breeding populations across the range. Together, our integrative analysis suggests that molting is in part regulated by genes linked to feather development and structure (GLI2 and CSPG4) and that genetic variation in these genes is associated with seasonal variation in precipitation and aridity. Overall, this work provides important insights into the genetic basis and potential selective forces behind phenotypic variation in what is arguably one of the most important fitness-linked traits in a migratory bird.

Teeth outside the mouth: The evolution and development of shark denticles

Vertebrate skin appendages are incredibly diverse. This diversity, which includes structures such as scales, feathers, and hair, likely evolved from a shared anatomical placode, suggesting broad conservation of the early development of these organs. Some of the earliest known skin appendages are dentine and enamel-rich tooth-like structures, collectively known as odontodes. These appendages evolved over 450 million years ago. Elasmobranchs (sharks, skates, and rays) have retained these ancient skin appendages in the form of both dermal denticles (scales) and oral teeth. Despite our knowledge of denticle function in adult sharks, our understanding of their development and morphogenesis is less advanced. Even though denticles in sharks appear structurally similar to oral teeth, there has been limited data directly comparing the molecular development of these distinct elements. Here, we chart the development of denticles in the embryonic small-spotted catshark (Scyliorhinus canicula) and characterize the expression of conserved genes known to mediate dental development. We find that shark denticle development shares a vast gene expression signature with developing teeth. However, denticles have restricted regenerative potential, as they lack a sox2+ stem cell niche associated with the maintenance of a dental lamina, an essential requirement for continuous tooth replacement. We compare developing denticles to other skin appendages, including both sensory skin appendages and avian feathers. This reveals that denticles are not only tooth-like in structure, but that they also share an ancient developmental gene set that is likely common to all epidermal appendages.

Regional specific differentiation of integumentary organs: SATB2 is involved in α- and β-keratin gene cluster switching in the chicken

BACKGROUND

Animals develop skin regional specificities to best adapt to their environments. Birds are excellent models in which to study the epigenetic mechanisms that facilitate these adaptions. Patients suffering from SATB2 mutations exhibit multiple defects including ectodermal dysplasia-like changes. The preferential expression of SATB2, a chromatin regulator, in feather-forming compared to scale-forming regions, suggests it functions in regional specification of chicken skin appendages by acting on either differentiation or morphogenesis.

RESULTS

Retrovirus mediated SATB2 misexpression in developing feathers, beaks, and claws causes epidermal differentiation abnormalities (e.g. knobs, plaques) with few organ morphology alterations. Chicken β-keratins are encoded in 5 sub-clusters (Claw, Feather, Feather-like, Scale, and Keratinocyte) on Chromosome 25 and a large Feather keratin cluster on Chromosome 27. Type I and II α-keratin clusters are located on Chromosomes 27 and 33, respectively. Transcriptome analyses showed these keratins (1) are often tuned up or down collectively as a sub-cluster, and (2) these changes occur in a temporo-spatial specific manner.

CONCLUSIONS

These results suggest an organizing role of SATB2 in cluster-level gene co-regulation during skin regional specification.

THE FORELIMBS OF ALVAREZSAUROIDEA (DINOSAURIA: THEROPODA): INSIGHT FROM EVOLUTIONARY TERATOLOGY

Alvarezsauroidea (Tetanurae) are non-avian theropod dinosaurs whose forelimb evolution is characterised by overdevelopment of digit I, at the expense of the other two digits, complemented by a drastic forelimb shortening in derived species (Parvicursorinae). These variations are recognised as evolutionary developmental anomalies. Evolutionary teratology hence leads to a double diagnosis with 1) macrodactyly of digit I and microdactyly of digits II and III, plus 2) anterior micromelia. The teratological macrodactyly/microdactyly coupling evolved first. Developmental mechanisms disturbing limb proportion are thought to be convergent with those of other Tetanurae (Tyrannosauridae, Carcharodontosauridae). As for the manual anomalies, both are specific to Alvarezsauroidea (macrodactyly/microdactyly) and inherited (digit loss/reduction). While considering the frame-shift theory, posterior digits develop before the most anterior one. There would therefore be a decrease in the area devoted to digits II (condensation 3) and III (condensation 4), in connection with the Shh signalling pathway, interacting with other molecular players such as the GLI 3 protein and the Hox system. Developmental independence of digit I (condensation 2) would contribute to generate a particular morphology. Macrodactyly would be linked to a variation in Hoxd-13, impacting Gli3 activity, increasing cell proliferation. The loss/reduction of digital ray/phalanges (digits II and III), would be associated to Shh activity, a mechanism inherited from the theropodan ancestry. The macrodactyly/macrodactyly coupling, and then anterior micromelia, fundamentally changed the forelimb mechanical function, compared to the 'classical' grasping structure of basal representatives and other theropods. The distal ossification of the macrodactylian digit has been identified as physiological, implying the use of the structure. However, the debate of a particular 'adaptive' use is pointless since the ecology of an organism is interactively complex, being both at the scale of the individual and dependent on circumstances. Other anatomical features also allow for compensation and a different predation (cursorial hindlimbs). This article is protected by copyright. All rights reserved.

Assessing evolutionary and developmental transcriptome dynamics in homologous cell types

Background

During development, complex organ patterns emerge through the precise temporal and spatial specification of different cell types. On an evolutionary timescale, these patterns can change, resulting in morphological diversification. It is generally believed that homologous anatomical structures are built—largely—by homologous cell types. However, whether a common evolutionary origin of such cell types is always reflected in the conservation of their intrinsic transcriptional specification programs is less clear.

Results

Here, we developed a user‐friendly bioinformatics workflow to detect gene co‐expression modules and test for their conservation across developmental stages and species boundaries. Using a paradigm of morphological diversification, the tetrapod limb, and single‐cell RNA‐sequencing data from two distantly related species, chicken and mouse, we assessed the transcriptional dynamics of homologous cell types during embryonic patterning. With mouse limb data as reference, we identified 19 gene co‐expression modules with varying tissue or cell type‐restricted activities. Testing for co‐expression conservation revealed modules with high evolutionary turnover, while others seemed maintained—to different degrees, in module make‐up, density or connectivity—over developmental and evolutionary timescales.

Conclusions

We present an approach to identify evolutionary and developmental dynamics in gene co‐expression modules during patterning‐relevant stages of homologous cell type specification using single‐cell RNA‐sequencing data.

We present an approach to identify evolutionary and developmental dynamics in gene co‐expression modules during patterning‐relevant stages of homologous cell type specification using single‐cell RNA‐sequencing data.