Simone M. Gable

The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species. Organized in four phases, it progressively targets all vertebrate orders, families, genera, and eventually all species. Here we present the completion of VGP Phase I, delivering reference genomes for ∼97% of vertebrate orders, along with additional lineages within those orders, totaling 815 species and 1.6 trillion base pairs of main haplotype sequence. These genomes were assembled and annotated over an 8-year period (2018-2026) of rapid advances in genome sequencing, assembly, and annotation methods, alongside the growth of associated consortium initiatives and international collaborations. They represent some of the highest-quality vertebrate genomes currently available, and most have become the primary reference for their respective species in public databases. Comparative analyses across a subset of 579 species when we reached a threshold of 85% of orders allowed us to reconstruct the genome of the last common ancestor of all vertebrates 500 million years ago, identify diverse modes of sex chromosome evolution, reveal clade-specific three-dimensional genome architecture, discover methylated epigenetic landscapes across vertebrates, and provide a framework for studying gene and pseudogene evolution, immune loci, cancer-associated genes, and other trait-associated loci. Approximately a quarter of this subset are listed as Vulnerable to Critically Endangered by the IUCN Red List of Threatened Species, and have enabled more advanced genomic investigations of extinction risk. VGP Phase I delivers the reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine.

In most animal species, the sex-determining pathway is typically initiated by the presence/absence of a primary genetic cue at a critical point during development. This primary genetic cue is often located on a single locus—referred to as sex chromosomes—and can be limited to females (in a ZZ/ZW system) or males (in an XX/XY system). One trademark of sex chromosomes is a restriction or cessation of recombination surrounding the sex-limited region (to prevent its inheritance in the homogametic sex). This may lead to—through a variety of mechanisms—higher amounts of genetic divergence within this region, ie between the X/Z and Y/W chromosomes, especially when compared with their autosomal counterparts. Recent advances in genome sequencing and computation have brought with them the ability to resolve haplotypes within a diploid individual, permitting assembly of previously challenging genomic regions like sex chromosomes. Leveraging these advances, we identified replicable diagnostic characteristics between typical autosomes and sex chromosomes (within a single genome assembly). Under this framework, we can use this information to identify putative sex chromosome linkage groups across divergent vertebrate taxa and simultaneously curate misassembled regions on autosomes. Here, we present this conceptual framework and associated tool for identifying candidate sex chromosome linkage groups from a single, diploid individual dubbed Sex Chromosome Identification by Negating Kmer Densities.

Phylogenomic-scale studies of the same clades using different markers and methods often support highly confident yet different species trees, obscuring many phylogenetic relationships and hampering comparative studies. Among reptiles, the >11,000 extant species of squamates (Order Squamata: lizards, snakes, and amphisbaenians) comprise a highly diverse and well-studied clade, yet many unresolved questions about squamate origins remain, including the root of the squamate phylogeny and the relationships of snakes to other toxicoferans. To understand biological, molecular, and methodological sources of phylogenomic heterogeneity in squamates, we analyzed four genome-scale marker datasets, including thousands of protein-coding genes, anchored hybrid enrichment loci, and ultra-conserved elements. We applied standardized alignment, filtering, and tree-building methods across marker sets, analyzed patterns in substitutional saturation and codon positions, and measured gene tree-species tree discordance across all data partitions. We found that many contentious relationships in squamate phylogenetics are driven by conflicts stemming from input data quality, incorrect model fit, and sampling bias, and that biological drivers of heterogeneity include both incomplete lineage sorting and introgression. We account for these sources of heterogeneity and strengthen resolution of the squamate phylogeny. Using a simulation approach, we find that current ultra-conserved element datasets for squamates deviate the most from phylogenetic expectations among marker types. Our work demonstrates that identifying sources of phylogenomic heterogeneity while accounting for input data limitations can resolve phylogenetic conflicts.

Phylogenomic-scale studies of the same clades using different markers and methods often support highly confident yet different species trees, obscuring many phylogenetic relationships and hampering comparative studies. Among reptiles, the >11,000 extant species of squamates (Order Squamata: lizards, snakes, and amphisbaenians) comprise a highly diverse and well-studied clade, yet many unresolved questions about squamate origins remain, including the root of the squamate phylogeny and the relationships of snakes to other toxicoferans. To understand biological, molecular, and methodological sources of phylogenomic heterogeneity in squamates, we analyzed four genome-scale marker datasets, including thousands of protein-coding genes, anchored hybrid enrichment loci, and ultra-conserved elements. We applied standardized alignment, filtering, and tree-building methods across marker sets, analyzed patterns in substitutional saturation and codon positions, and measured gene tree-species tree discordance across all data partitions. We found that many contentious relationships in squamate phylogenetics are driven by conflicts stemming from input data quality, incorrect model fit, and sampling bias, and that biological drivers of heterogeneity include both incomplete lineage sorting and introgression. We account for these sources of heterogeneity and strengthen resolution of the squamate phylogeny. Using a simulation approach, we find that current ultra-conserved element datasets for squamates deviate the most from phylogenetic expectations among marker types. Our work demonstrates that identifying sources of phylogenomic heterogeneity while accounting for input data limitations can resolve phylogenetic conflicts.

In most animal species, the sex determining pathway is typically initiated by the presence/absence of a primary genetic cue at a critical point during development. This primary genetic cue is often located on a single locus—referred to as sex chromosomes—and can be limited to females (in a ZZ/ZW system) or males (in an XX/XY system). One trademark of sex chromosomes is a restriction or cessation of recombination surrounding the sex-limited region (to prevent its inheritance in the homogametic sex). This may lead to—through a variety of mechanisms—higher amounts of genetic divergence within this region, i.e. between the X/Z and Y/W chromosomes, especially when compared to their autosomal counterparts. Recent advances in genome sequencing and computation have brought with them the ability to resolve haplotypes within a diploid individual, permitting assembly of previously challenging genomic regions like sex chromosomes. Leveraging these advances, we identified replicable diagnostic characteristics between typical autosomes and sex chromosomes (within a single genome assembly). Under this framework, we can use this information to identify putative sex chromosome linkage groups across divergent vertebrate taxa and simultaneously curate misassembled regions on autosomes. Here, we present this conceptual framework and associated tool for identifying candidate sex chromosome linkage groups from a single, diploid individual dubbed Sex Chromosome Identification by Negating Kmer Densities, or SCINKD.

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.