Epidermal Differentiation Genes of the Common Wall Lizard Encode Proteins with Extremely Biased Amino Acid Contents

The epidermal differentiation complex (EDC) is a cluster of genes that code for protein components of cornified cells on the skin surface of amniotes. Squamates are the most species-rich clade of reptiles with skin adaptations to many different environments. As the genetic regulation of the skin epidermis and its evolution has been characterized for only a few species so far, we aimed to determine the organization of the EDC in a model species of squamates, the common wall lizard (Podarcis muralis). By comparative genomics, we identified EDC genes of the wall lizard and compared them with homologs in other amniotes. We found that the EDC of the wall lizard has undergone a major rearrangement leading to a unique order of three ancestral EDC segments. Several subfamilies of EDC genes, such as those encoding epidermal differentiation proteins containing PCCC motifs (EDPCCC) and loricrins, have expanded by gene duplications. Most of the EDPCCC proteins have cysteine contents higher than 50%, whereas glycine constitutes more than 50% of the amino acid residues of loricrin 1. The extremely biased amino acid compositions indicate unique structural properties of these EDC proteins. This study demonstrates that cornification proteins of the common wall lizard differ from homologous proteins of other reptiles, illustrating the evolutionary dynamics of diversifying evolution in squamates.

Insights into the adaptive evolution of chromosome and essential traits through chromosome-level genome assembly of Gekko japonicus

Gekko japonicus possesses flexible climbing and detoxification abilities under insectivorous habits. Still, the evolutionary mechanisms behind these traits remain unclarified. This study presents a chromosome-level G. japonicus genome, revealing that its evolutionary breakpoint regions were enriched with specific repetitive elements and defense response genes. Gene families unique to G. japonicus and positively selected genes are mainly enriched in immune, sensory, and nervous pathways. Expansion of bitter taste receptor type 2 primarily in insectivorous species could be associated with toxin clearance. Detox cytochrome P450 in G. japonicus has undergone more birth and death processes than biosynthesis-type P450 genes. Proline, cysteine, glycine, and serine in corneous beta proteins of G. japonicus might influence flexibility and setae adhesiveness. Certain thermosensitive transient receptor potential channels under relaxed purifying selection or positive selection in G. japonicus might enhance adaptation to climate change. This genome assembly offers insights into the adaptive evolution of gekkotans.

Micro-ornamentation patterns in different areas of the epidermis in the gecko Tarentola mauritanica reflect variations in the accumulation of corneous material in Oberhautchen cells

Micro-ornamentations characterize the surface of scales in lepidosaurians and are summarized in four main patterns, i.e., spinulated, lamellated, lamellate-dentate, and honeycomb, although variations of these patterns are present in different species. Although geckos are known to possess a spinulated pattern derived from the Oberhautchen layer, also other pattern variations of the spinulated micro-ornamentation are present such as those indicated as dendritic ramification, corneous belts, and small bare patches. The present study mainly describes the variation of micro-ornamentations present in scales of different skin regions in the Mediterranean gecko Tarentula mauritanica using scannig and transmission electron microscopy. The study reports that the accumulation of corneous material in Oberhautchen cells is not homogenous in different areas of body scales and, when mature, this process gives rise to different sculpturing on the epidermal surface generating not only spinulae but also transitional zones leading to the other main patterns. It is hypothesized that spinulae formation derives from the vertical and lateral symmetric growth of tubercolate, non-overlapped scales of geckos. Sparse areas also result smooth or with serpentine-ridges likely revealing the beta-layer located underneath and merged with the Oberhautchen. The eco-functional role of this variable micro-ornamentation in the skin of lizards however remains largely speculative.

The revised reference genome of the leopard gecko (Eublepharis macularius) provides insight into the considerations of genome phasing and assembly

Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest-quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified 9 of the 19 chromosomal scaffolds were assembled as a near-single contig, whereas the other 10 chromosomes were each scaffolded together from multiple contigs. We qualitatively identified that the percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction of previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000.

A lizard is never late: Squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution

In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the "genomics age" was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012 and 2017. However, since 2018, an exponential increase in high-quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa.

A lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution

In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the "genomics age" was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012-2017. However, since 2018, an exponential increase in high-quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa.

The revised reference genome of the leopard gecko ( Eublepharis macularius ) provides insight into the considerations of genome phasing and assembly

Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified that 9 of the 19 chromosomes were assembled as single contigs, while the other 10 chromosomes were each scaffolded together from two or more contigs. We qualitatively identified that percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000. The genome version and its associated annotations are also available via this Figshare repository https://doi.org/10.6084/m9.figshare.20069273 .

Can extreme climatic events induce shifts in adaptive potential? A conceptual framework and empirical test with Anolis lizards

Multivariate adaptation to climatic shifts may be limited by trait integration that causes genetic variation to be low in the direction of selection. However, strong episodes of selection induced by extreme climatic pressures may facilitate future population-wide responses if selection reduces trait integration and increases adaptive potential (i.e., evolvability). We explain this counter-intuitive framework for extreme climatic events in which directional selection leads to increased evolvability and exemplify its use in a case study. We tested this hypothesis in two populations of the lizard Anolis scriptus that experienced hurricane-induced selection on limb traits. We surveyed populations immediately before and after the hurricane as well as the offspring of post-hurricane survivors, allowing us to estimate both selection and response to selection on key functional traits: forelimb length, hindlimb length, and toepad area. The direct selection was parallel in both islands and strong in several limb traits. Even though overall limb integration did not change after the hurricane, both populations showed a non-significant tendency toward increased evolvability after the hurricane despite the direction of selection not being aligned with the axis of most variance (i.e., body size). The population with comparably lower between-limb integration showed a less constrained response to selection. Hurricane-induced selection, not aligned with the pattern of high trait correlations, likely conflicts with selection occurring during normal ecological conditions that favours functional coordination between limb traits, and would likely need to be very strong and more persistent to elicit a greater change in trait integration and evolvability. Future tests of this hypothesis should use G-matrices in a variety of wild organisms experiencing selection due to extreme climatic events.

Evidence that gecko setae are coated with an ordered nanometre-thin lipid film

The fascinating adhesion of gecko to virtually any material has been related to surface interactions of myriads of spatula at the tips of gecko feet. Surprisingly, the molecular details of the surface chemistry of gecko adhesion are still largely unknown. Lipids have been identified within gecko adhesive pads. However, the location of the lipids, the extent to which spatula are coated with lipids, and how the lipids are structured are still open questions. Lipids can modulate adhesion properties and surface hydrophobicity and may play an important role in adhesion. We have therefore studied the molecular structure of lipids at spatula surfaces using near-edge X-ray absorption fine structure imaging. We provide evidence that a nanometre-thin layer of lipids is present at the spatula surfaces of the tokay gecko (Gekko gecko) and that the lipids form ordered, densely packed layers. Such dense, thin lipid layers can effectively protect the spatula proteins from dehydration by forming a barrier against water evaporation. Lipids can also render surfaces hydrophobic and thereby support the gecko adhesive system by enhancement of hydrophobic-hydrophobic interactions with surfaces.

Immunolocalization of corneous proteins including a serine-tyrosine-rich beta-protein in the adhesive pads in the tokay gecko

Adhesive pads of geckos contain many thousands of nanoscale spatulae for the adhesion and movement along vertical or inverted surfaces. Setae are composed of interlaced corneous bundles made of small cysteine-glycine-rich corneous beta proteins (CBPs, formerly indicated as beta-keratins), embedded in a matrix material composed of cytoskeletal proteins and lipids. Negatively charged intermediate filament keratins (IFKs) and positively charged CBPs likely interact within setae, aside disulphide bonds, giving rise to a flexible and resistant corneous material. Using differernt antibodies against CBPs and IFKs an updated model of the composition of setae and spatulae is presented. Immunofluorescence and ultrastructural immunogold labeling reveal that one type of neutral serine-tyrosine-rich CBP is weakly localized in the setae while it is absent from the spatula. This uncharged protein is mainly present in the thin Oberhautchen layer sustaining the setae, although with a much lower intensity with respect to the cysteine-rich CBPs. These proteins in the spatula likely originate a positively charged or neutral contact surface with the substrate but the influence of lipids and cytoskeletal proteins present in setae on the mechanism of adhesion is not known. In the spatula, protein-lipid complexes may impart the pliability for the attachment and adapt to irregular surfaces. The presence of cysteine-glycine medium rich CBPs and softer IFKs in alpha-layers sustaining the setae forms a flexible base for compliance of the setae to substrate and improved adhesion.

Attachment Beyond the Adhesive System: The Contribution of Claws to Gecko Clinging and Locomotion

Attachment is imperative for many biological functions, such as holding position and climbing, but can be challenged by natural conditions. Adhesive toe pads and claws have evolved in multiple terrestrial lineages as important dynamic attachment mechanisms, and some clades (e.g., geckos) exhibit both features. The functional relationship of these features that comprise a complex attachment system is not well-understood, particularly within lizards (i.e., if pads and claws are redundant or multifunctional). Geckos exhibit highly adept frictional adhesive toe pads that continue to fuel biological inquiry and inspiration. However, gecko claws (the ancestral lizard clinging condition) have received little attention in terms of their functional or evolutionary significance. We assessed claw function in Thecadactylus rapicauda using assays of clinging performance and locomotor trials on different surfaces (artificial and natural) and inclines with claws intact, then partially removed. Area root mean square height (Sq), a metric of 3D surface roughness, was later quantified for all test surfaces, including acrylic, sandpaper, and two types of leaves (smooth and hairy). Maximum clinging force significantly declined on all non-acrylic surfaces after claw removal, indicating a substantial contribution to static clinging on rough and soft surfaces. With and without claws, clinging force exhibited a negative relationship with Sq. However, claw removal had relatively little impact on locomotor function on surfaces of different roughness at low inclines (≤30°). High static and dynamic safety factor estimates support these observations and demonstrate the species’ robust frictional adhesive system. However, maximum station-holding capacity significantly declined on the rough test surface after partial claw removal, showing that geckos rely on their claws to maintain purchase on rough, steeply inclined surfaces. Our results point to a context-dependent complex attachment system within geckos, in which pads dominate on relatively smooth surfaces and claws on relatively rough surfaces, but also that these features function redundantly, possibly synergistically, on surfaces that allow attachment of both the setae and the claw (as in some insects). Our study provides important novel perspectives on gecko attachment, which we hope will spur future functional studies, new evolutionary hypotheses, and biomimetic innovation, along with collaboration and integration of perspectives across disciplines.

The Integrative Biology of Gecko Adhesion: Historical Review, Current Understanding, and Grand Challenges

Geckos are remarkable in their ability to reversibly adhere to smooth vertical, and even inverted surfaces. However, unraveling the precise mechanisms by which geckos do this has been a long process, involving various approaches over the last two centuries. Our understanding of the principles by which gecko adhesion operates has advanced rapidly over the past 20 years and, with this knowledge, material scientists have attempted to mimic the system to create artificial adhesives. From a biological perspective, recent studies have examined the diversity in morphology, performance, and real-world use of the adhesive apparatus. However, the lack of multidisciplinarity is likely a key roadblock to gaining new insights. Our goals in this paper are to 1) present a historical review of gecko adhesion research, 2) discuss the mechanisms and morphology of the adhesive apparatus, 3) discuss the origin and performance of the system in real-world contexts, 4) discuss advancement in bio-inspired design, and 5) present grand challenges in gecko adhesion research. To continue to improve our understanding, and to more effectively employ the principles of gecko adhesion for human applications, greater intensity and scope of interdisciplinary research are necessary.