The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order

Current Technologies in Snake Venom Analysis and Applications

This comprehensive review explores the cutting-edge advancements in snake venom research, focusing on the integration of proteomics, genomics, transcriptomics, and bioinformatics. Highlighting the transformative impact of these technologies, the review delves into the genetic and ecological factors driving venom evolution, the complex molecular composition of venoms, and the regulatory mechanisms underlying toxin production. The application of synthetic biology and multi-omics approaches, collectively known as venomics, has revolutionized the field, providing deeper insights into venom function and its therapeutic potential. Despite significant progress, challenges such as the functional characterization of toxins and the development of cost-effective antivenoms remain. This review also discusses the future directions of venom research, emphasizing the need for interdisciplinary collaborations and new technologies (mRNAs, cryo-electron microscopy for structural determinations of toxin complexes, synthetic biology, and other technologies) to fully harness the biomedical potential of venoms and toxins from snakes and other animals.

Understanding vertebrate immunity through comparative immunology

Evolutionary immunology has entered a new era. Classical studies, using just a handful of model animal species, combined with clinical observations, provided an outline of how innate and adaptive immunity work together to ensure tissue homeostasis and to coordinate the fight against infections. However, revolutionary advances in cellular and molecular biology, genomics and methods of genetic modification now offer unprecedented opportunities. They provide immunologists with the possibility to consider, at unprecedented scale, the impact of the astounding phenotypic diversity of vertebrates on immune system function. This Perspective is intended to highlight some of the many interesting, but largely unexplored, biological phenomena that are related to immune function among the roughly 60,000 existing vertebrate species. Importantly, hypotheses arising from such wide-ranging comparative studies can be tested in representative and genetically tractable species. The emerging general principles and the discovery of their evolutionarily selected variations may inspire the future development of novel therapeutic strategies for human immune disorders.

Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics

We present genome assemblies for 18 snake species representing 18 families (Serpentes: Caenophidia): Acrochordus granulatus, Aparallactus werneri, Boaedon fuliginosus, Calamaria suluensis, Cerberus rynchops, Grayia smithii, Imantodes cenchoa, Mimophis mahfalensis, Oxyrhabdium leporinum, Pareas carinatus, Psammodynastes pulverulentus, Pseudoxenodon macrops, Pseudoxyrhopus heterurus, Sibynophis collaris, Stegonotus admiraltiensis, Toxicocalamus goodenoughensis, Trimeresurus albolabris, and Tropidonophis doriae. From these new genome assemblies, we extracted thousands of loci commonly used in systematic and phylogenomic studies on snakes, including target-capture datasets composed of ultraconserved elements (UCEs) and anchored hybrid enriched loci (AHEs), as well as traditional Sanger loci. Phylogenies inferred from the two target-capture loci datasets were identical with each other and strongly congruent with previously published snake phylogenies. To show the additional utility of these non-model genomes for investigative evolutionary research, we mined the genome assemblies of two New Guinea island endemics in our dataset (S. admiraltiensis and T. doriae) for the ATP1a3 gene, a thoroughly researched indicator of resistance to toad toxin ingestion by squamates. We find that both these snakes possess the genotype for toad toxin resistance despite their endemism to New Guinea, a region absent of any toads until the human-mediated introduction of Cane Toads in the 1930s. These species possess identical substitutions that suggest the same bufotoxin resistance as their Australian congenerics (Stegonotus australis and Tropidonophis mairii) which forage on invasive Cane Toads. Herein, we show the utility of short-read high-coverage genomes, as well as improving the deficit of available squamate genomes with associated voucher specimens.

Differential Conservation and Loss of Chicken Repeat 1 (CR1) Retrotransposons in Squamates Reveal Lineage-Specific Genome Dynamics Across Reptiles

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniote vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; including ∼11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific genome dynamics have evolved over the course of squamate evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the chicken repeat 1 (CR1) retrotransposon, a TE family found in most tetrapod genomes which is the dominant TE in most reptiles. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.

Karyotype Diversification and Chromosome Rearrangements in Squamate Reptiles

Karyotype diversification represents an important, yet poorly understood, driver of evolution. Squamate reptiles are characterized by a high taxonomic diversity which is reflected at the karyotype level in terms of general structure, chromosome number and morphology, and insurgence of differentiated simple or multiple-sex-chromosome systems with either male or female heterogamety. The potential of squamate reptiles as unique model organisms in evolutionary cytogenetics has been recognised in recent years in several studies, which have provided novel insights into the chromosome evolutionary dynamics of different taxonomic groups. Here, we review and summarize the resulting complex, but promising, general picture from a systematic perspective, mapping some of the main squamate karyological characteristics onto their phylogenetic relationships. We highlight how all the major categories of balanced chromosome rearrangements contributed to the karyotype evolution in different taxonomic groups. We show that distinct karyotype evolutionary trends may occur, and coexist, with different frequencies in different clades. Finally, in light of the known squamate chromosome diversity and recent research advances, we discuss traditional and novel hypotheses on karyotype evolution and propose a scenario of circular karyotype evolution.

Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniotic vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; ~11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific dynamics have evolved over the course of squamate evolution to constrain genome size across the order. Thus, squamates may represent a prime model for investigations into TE diversity and evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the CR1 retrotransposon, a TE family found in most tetrapod genomes. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds, and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.