Advances in genomic studies are revealing that gene flow between species is more frequent than previously understood, although the ways in which hybridization can bias gene flow across species boundaries or the extent to which introgression might be adaptive remain unexplored in most systems. We report on an annotated chromosome-level genome assembly for the Gilbert's skink, Plestiodon gilberti, one of 18 clades of reptiles and amphibians selected for reference genome sequencing in the California Conservation Genomics Project. This assembly was produced using Pacific Biosciences HiFi long reads and Omni-C proximity ligation data. Although members of the Scincidae comprise nearly one-quarter of all lizard species (1785 described species), this de novo assembly represents one of only 10 skink species globally and the first North American skink with a reference genome. The assembly has a total length of ~ 1.57 Gb, a scaffold N50 length of ~ 231.32 Mb, read coverage of ~56X, and BUSCO completeness score of 97.2% based on the Tetrapoda ortholog database. Plestiodon gilberti is a member of the Plestiodon skiltonianus species complex, a group with many of the characteristics of ecological speciation but where ancient hybridization and biased introgression present challenges to retracing the initial patterns of lineage divergence. Combined with dense sampling of resequenced genomes in the California Conservation Genomics Project, including other members of the P. skiltonianus complex, this reference genome will enable future analyses of the links between divergent selection and the genes underlying speciation, as well as the potential for introgression to enable adaptation to new or changing environments.

Bull kelp, Nereocystis luetkeana, is a northeastern Pacific kelp with a broad distribution from Alaska to central California. Its population declines have caused severe concerns in northern California, the Salish Sea in Washington, and recently in some populations in Oregon. Despite bull kelp's accumulated ecological and physiological studies, an assembled and annotated genomic reference was still unavailable. Here, we report the complete and annotated genome of N. luetkeana, produced by the California Conservation Genomics Project (CCGP), which aims to reveal genomic diversity patterns across California by sequencing the complete genomes of approximately 150 carefully selected species. The genome was assembled into 1,562 scaffolds with 449.82 Mb, 80× of coverage, and 22,952 gene models. BUSCO assembly showed a completeness score of 72% for the stramenopiles gene set. The mitochondria and chloroplast genome sequences have 37 Kb and 131 Mb, respectively. The orthology analysis between 10 Phaeophycean genomes showed 1,065 expanded and 286 unique orthogroups for this species. Pairwise comparisons showed 542 orthogroups present only in N. luetkeana and Macrocystis pyrifera, another large-body kelp. The enrichment analysis of these orthogroups showed important functions related to central metabolism and signaling due to ATPase enrichment in these two species. This genome assembly will provide an essential resource for the ecology, evolution, conservation, and breeding of bull kelp.

The flowering plant genus Aquilegia (columbine) is an important contributor to biodiversity and an example of both biotic and abiotic niche adaptation across much of the Northern Hemisphere, especially in California. Here we report a near-chromosome level draft genome assembly for A. eximia, a California endemic species. A. eximia is a serpentine-soil specialist and is very closely related to 2 columbine species also being studied for the California Conservation Genomics Project (CCGP), A. formosa (widespread) and A. pubescens (high alpine). Utilizing high throughput, long reads (PacBio) and chromatin capture (Omni-C), the A. eximia genome makes marked contiguity improvements compared to the existing reference genome for another North American columbine, A. coerulea "Goldsmith." The A. eximia genome will also be more useful for aligning whole genome resequencing data from California columbines than the genomes for more distantly related columbine species, the Asian A. oxysepala var. kansuensis and the European A. vulgaris. Notably, we found evidence that A. eximia, A. coerulea "Goldsmith," and A. vulgaris all share the same overall genome structure and differ from A. oxysepala var. kansuensis by the same reciprocal translocation. The A. eximia reference genome will be a valuable tool for identifying patterns of plant biodiversity across California for the CCGP, as well as for future population genomic and trait mapping studies.

We assembled and annotated a chromosome-level genome for the Western Spadefoot, Spea hammondii (Anura, Scaphiopodidae) representing one of only three amphibians included in the California Conservation Genomics Project (CCGP). Spea hammondii is a vernal pool breeding anuran native to California and northwestern Baja California which has undergone both range contractions and local extirpations across its distribution, primarily due to habitat loss and degradation and drought. The species is recognized by the state of California as a Species of Special Concern and is proposed for listing under the United States Endangered Species Act. Using the established CCGP pipeline, this S. hammondii genome was produced using Pacific Biosciences HiFi long-reads and Omni-C proximity ligation, resulting in a de novo genome assembly 1.14 Gb in length, distributed across 479 scaffolds (scaffold N50 = 120.8 Mb; largest scaffold = 183.6 Mb) with a BUSCO completeness score of 90.9% using a conserved tetrapod ortholog set. Our assembly shows high base accuracy (quality value [QV] = 63.7) and low frameshift error in coding regions (QV 50.42). Annotation of this genome yielded 20,434 genes with a BUSCO completeness score of 94.7%. This genome assembly, in combination with range-wide resequencing data from CCGP, will facilitate statewide population genomic assessments to delineate conservation units, quantify inbreeding and genomic load, and test for adaptive variation associated with vernal pool hydrology and drought tolerance, all of which are important considerations in the proposed federal listing.

The ornate shrew (Sorex ornatus) is a small predatory mammal with a broad distribution in northern, central, and southern California as well as in Baja California, Mexico. The ornate shrew is a highly productive consumer in wetland environments and is known to hybridize with the closely related vagrant shrew, Sorex vagrans. Here we present a high-quality de novo genome assembly for S. ornatus generated as a part of the California Conservation Genomics Project. The S. ornatus genome was generated using PacBio HiFi long reads and Omni-C chromatin interaction sequencing. The primary assembly is highly contiguous, with a contig N50 of 15.9 Mb, a scaffold N50 of 115.2 Mb, and a BUSCO completeness score of 95.10%. The ornate shrew genome will serve as a valuable resource for future North American Sorex conservation genomics as well as for research into shrew biology more generally.

We present genome assemblies for two cyprinoid fishes, the tui chub (Siphateles bicolor) and the arroyo chub (Gila orcuttii). These fishes are ecologically important representatives of native fish assemblages in the western United States and are both species of conservation concern. The two species hybridize where introductions bring them into contact, with potentially important ecological and evolutionary implications that have not yet been thoroughly examined from a genomic perspective. We present de novo assemblies for both species, representing the first scaffold-level genomes within their respective genera, which were developed as part of the California Conservation Genomics Project using Pacific Biosciences HiFi and Omni-C data. Our tui chub assembly consists of 258 scaffolds spanning 1,148,084,093 base pairs, has a scaffold N50 of 45.9 mb, a contig N50 of 23.7 mb, and a BUSCO completeness score of 98.1%. Our arroyo chub assembly consists of 179 scaffolds spanning 1,263,410,250 base pairs, has a scaffold N50 of 50.5 mb, a contig N50 of 13.1 mb, and a BUSCO completeness score of 97.8%. A comparative analysis of the two species revealed relatively conserved genomes, with the exception of two inversions at chromosome 20. We annotated a total of 34,090 genes with a BUSCO completeness score of 98.1% for the tui chub, and 28,193 genes with a score of 97.4% for the arroyo chub. These assemblies will be valuable resources for characterizing the species' phylogeographic histories and delineating the role of hybridization in their evolution.

We generated the first chromosome-level genome assembly for California grunion, Leuresthes tenuis, using PacBio HiFi long reads and Omni-C chromatin-proximity sequencing, yielding a 0.917 Gb genome with a scaffold N50 of 35 Mb and a BUSCO completeness score of 99.37. This beach-spawning marine silverside is the target of a unique recreational hand-grab fishery during its nocturnal spawning runs. Regulation of this fishery, initiated in 1927, remained unchanged from 1949 to 2022, when recent data suggesting a stock decrease led California Department of Fish and Wildlife to reduce the fishing season length. California grunion are endemic to the coast of California and northern Baja California, but within the last two decades the northern limit of spawning has expanded roughly 470 km from Point Conception to north of San Francisco Bay. This genome will facilitate studies addressing the temporal and spatial genetic stock structure, and recent range expansion, of this unique charismatic native species and will also allow assessment of genetic responses to present and future environmental challenges such as changing temperature, and pollution as well as the impacts of harvest and effects of management.

We report on an annotated chromosome-level genome assembly for the long-nosed leopard lizard, Gambelia wislizenii, as part of the California Conservation Genomics Project (CCGP). All 17 species of reptiles, including two turtles, seven lizards, and seven snakes targeted for reference genome sequencing by the CCGP are now complete and posted on NCBI, and this article is the third of seven CCGP lizard release papers to be published. It is also the first species of the family Crotaphytidae to have a released reference genome. Following the CCGP pipeline, the G. wislizenii genome was produced using Pacific Biosciences HiFi long reads and Omni-C proximity ligation data. The de novo assembly includes 69 scaffolds and has a total length of ~ 2.47 Gb, a scaffold N50 length of 380.1 Mb, and a BUSCO completeness score of 97.4% based on the tetrapod gene set. We improved the annotation of the genome using transcriptome sequencing (seven tissue types), identifying 23,279 genes, with BUSCO completeness of 98.9%. This reference genome, when combined with CCGP's on-going state-wide resequencing efforts for the three species of Gambelia in California, including the federally endangered blunt-nosed leopard lizard (Gambelia sila), and Cope's leopard lizard (Gambelia copei), will be a powerful tool enabling researchers to characterize hybridization dynamics between Gambelia species, document the remaining diversity within G. sila, and explore the genetic underpinnings of key traits that vary between the three Gambelia species, such as territoriality, sexual size dimorphism, presence versus absence of male breeding coloration, and skull morphologies.

The northern elephant seal (Mirounga angustirostris) is the largest pinniped species in the northern hemisphere. The species is classified as being of least conservation concern by the IUCN-a triumph of conservation efforts despite hunting pressure that nearly led to its extinction more than a century ago. The historical range of the northern elephant seal extended from Baja California to Alaska, but overexploitation caused a severe demographic collapse and genetic bottleneck, with only an estimated 10 to 30 survivors left on Isla Guadalupe, Mexico. As part of the California Conservation Genomics Project, we generated a de novo reference genome and annotation for M. angustirostris, combining PacBio HiFi long-read sequencing data with Dovetail Omni-C chromatin conformation data. Our assembly has a primary haplotype genome length of 2,430,321,998 base pairs (2.4 Gb), with the longest contig of 144 Mb, contig N50 of 58 Mb, largest scaffold of 215 Mb, and scaffold N50 of 154 Mb. The secondary assembly haplotype consists of 422 scaffolds, spanning 2.45 Gb, with contig N50 of 61.24 Mb, scaffold N50 of 152.94 Mb, the largest contig of 204.14 Mb, and the largest scaffold of 216.16 Mb. We used the primary assembly and annotation for a preliminary investigation of repeat element content, historical demography, genome-wide heterozygosity, and loss-of-function variants. We found that M. angustirostris has one of the lowest estimates of genetic diversity of any marine mammal and a complex demographic history that may have reduced genetic diversity several times. This newly constructed genome will facilitate future in-depth explorations into the mechanisms behind resilience and recovery after a severe population bottleneck.

The wrentit (Chamaea fasciata) is a chaparral and scrub specialist bird found from coastal Oregon to northern Baja California. We generated a draft reference assembly for the species using PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project. Sequenced reads were assembled into 1342 scaffolds totaling 1.19 gigabase in length. A contig N50 of 4.5 Mb, scaffold N50 of 73.3 Mb, and Benchmarking Universal Single-Copy Orthologs completeness score of 96.8% indicate that the wrentit genome is a highly contiguous assembly in line with other high quality avian assemblies. An annotation of the assembly identified 16 821 protein-coding genes. We detected a translocation between chromosome 4A of the zebra finch to the Z chromosome of the wrentit. This translocation has previously been identified as a neo-sex chromosome shared across the superfamily Sylvioidea. Finally, we found a negative correlation between transposable element richness and gene density across the genome, but a positive relationship between guanine-cytosine content and gene density. This reference will serve as an essential resource for studies on the biogeography, local adaptation, and conservation genetics of this iconic species of California's chaparral.

Phyllospadix spp. (surfgrass) are flowering plants and keystone species in the rocky intertidal and subtidal environments of the North Pacific Ocean. Here we report a chromosome level assembly for P. torreyi, which occurs along the coast of California, sometimes in sympatry with P. scouleri. Both of these species and their putative hybrids are being studied as part of the California Conservation Genomics Project. Phyllospadix are dioecious, and males are exceptionally rare compared to females. Using high throughput, long reads (PacBio) and chromatin capture (Omni-C), we assembled a chromosome level genome for a male individual and a contig level assembly for a female individual. Comparison between the male and female assembly confirmed that the male is the heterogametic sex and has a massive Y chromosome at 124.8 megabases, which encompasses over 27% of the male genome. We also compared the male P. torreyi assembly to a genome from its sister genus, the monoecious Zostera marina, and found relatively high levels of synteny, that syntenic gene blocks on the P. torreyi sex chromosomes align to a single chromosome of Z. marina, and an estimated divergence time of ca. 25 million years ago. The Phyllospadix genome will be a powerful tool for studying marine dispersal, sex ratios, genetic diversity, sex chromosome evolution, and other dynamics in a keystone marine species.

Acmispon is a legume genus that has diversified within the California Floristic Province. Acmispon species live in a variety of habitats, including coastal sage scrub, deserts, grasslands, and woodlands, and form symbiotic associations with nitrogen-fixing bacteria. Here, we report the first chromosome-level assembly of Acmispon strigosus (strigose bird's-foot trefoil or strigose lotus) as part of the California Conservation Genomics Project. Consistent with the reference genome pipelines of the California Conservation Genomics Project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly is 519 Mb in length, with a contig N50 of 22.97 Mb, scaffolded into seven pseudochromosomes. Using the NCBI EGAPx pipeline, we annotated a total of 21,347 genes resulting in a protein Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 91.5%. This is the first genome assembled for Acmispon and among the first genomic resources available for a native California legume. The assembly BUSCO completeness score of 94.8% makes it one of the most complete genomes for the tribe Loteae (Fabaceae). Generating whole-genome sequences will contribute to our general understanding of nitrogen-fixing legume's adaptations to diverse soil and environmental conditions, interactions with nitrogen fixing Bradyrhizobium and Mesorhizobium symbionts, and the degrading effects of pollution-induced nitrogen deposition on the legume-rhizobium symbiosis in California. These data will also help to reconstruct phylogenetic relationships among Acmispon spp., which remain unresolved.

The transition from small genetic to genome-scale datasets for studying biodiversity has revealed that genetic exchange through introgressive hybridization is a widespread phenomenon in nature. Despite this, a lack of high-quality reference genomes for most non-model species limits our understanding of the impact of this process for many taxonomic groups. This restricts the range of insights that genomic tools can provide for conservation biologists, who often hope to employ genomic datasets to accurately identify historically isolated lineages to protect and to predict their evolutionary fate in the face of environmental change. Tiger whiptail lizards (Aspidoscelis tigris complex) are an abundant and important ecological component of ecosystems across the southwestern United States. In this study, we assembled and annotated a chromosome-level reference genome for A. t. stejnegeri from coastal California. We then used this reference genome to reconstruct patterns of speciation and admixture within the larger species complex, finding evidence that gene flow is widespread both geographically and across the genome.

The Pacific banana slug, Ariolimax columbianus, is endemic to the forests of the Pacific Northern West. Found throughout the coastal foothills and mountains of California, the hermaphroditic molluscs Ariolimax spp. are niche-constrained, hyper-localized, and phenotypically diverse. The evolutionary history, recent population history and environmental conditions leading to their phenotypic and genetic variation are not understood. To facilitate such research, we present the first high-quality de novo genome assembly of A. columbianus as part of the California Conservation Genomics Project. Pacific Biosciences HiFi long reads and Omni-C chromatin-proximity sequencing technologies were used to produce a de novo genome assembly, consistent with the standard California Conservation Genomics Project genome assembly protocol. This assembly comprises 401 scaffolds spanning 2.29 Gb, represented by a scaffold N50 of 94.9 Mb, a contig N50 of 3.7 Mb, and a benchmarking universal single-copy ortholog completeness score of 93.9%. Future work will use the A. columbianus genome to study the population structure of Ariolimax spp. across California to understand patterns of population structure, genetic diversity, and the broader ecological connections with their habitat. This data will contribute to the California Conservation Genomics Project, expanding the knowledge about the partitioning of genomic variation across the different ecoregions of California.

Merriam's kangaroo rat (Dipodomys merriami) is a member of a unique family of primarily desert-adapted North American rodents (Heteromyidae). Of the 20 species in the genus, D. merriami is one of the most wide-ranging and ecologically flexible, inhabiting desert scrub, grassland, sagebrush steppe, and juniper-piñon woodland in the southwestern deserts of the United States and Mexico. We present a de novo reference genome for D. merriami generated from PacBio HiFi long-read and Omni-C chromatin proximity sequencing as a part of the California Conservation Genomics Project. The primary pseudo-haplotype assembly comprises 3,110 scaffolds, with a contig N50 of 8.6 Mb, scaffold N50 of 49.1 Mb, and a total length of 3.57 Gb. Further, a BUSCO completeness score of 97.8% suggests that the assembly is highly complete. This reference genome will serve as a resource for future studies of Dipodomys conservation genomics, desert adaptation, and phylogeography.

The Gophersnake, Pituophis catenifer, is a habitat generalist that ranges throughout the western half of the United States and southward into México. Five of the six subspecies, P. catenifer affinis (Sonoran Gophersnake), P. catenifer annectens (San Diego Gophersnake), P. catenifer catenifer (Pacific Gophersnake), P. catenifer deserticola (Great Basin Gophersanke), and P. catenifer pumilus (Santa Cruz Island Gophersnake), occur in California and span virtually all the state's diverse terrestrial habitats. These subspecies are ecologically and morphologically distinct from one another, although existing genetic data indicate there is genetic admixture across some of their contact zones. Given that these subspecies occur in such different environments they will not all respond to climate change and anthropogenic stressors equally. Here, we report a new, chromosome-level assembly of P. catenifer as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 426 scaffolds covering 1,804,944,895 bp, has a contig N50 of 37.5 Mb, a scaffold N50 of 161 Mb, and BUSCO completeness score of 95.3%. This genome will be a foundational resource for future studies on the conservation, adaptation, biogeography, and systematics of P. catenifer.

Few genomic resources currently exist for the American endemic family Cactaceae, a group of around 1850 species, which are world renowned for their amazing growth forms and succulent habits. These icons of arid landscapes across the Americas are threatened in many parts of their range, including in parts of California, and developing more comprehensive genomic data will aid efforts to better understand and preserve these plants. We sequenced and assembled the genome of the beavertail cactus, Opuntia basilaris, which is represented by three varieties in California, one of which is threatened, and another endangered. The genome assembly has a BUSCO complete score of 98.1%, and a total scaffold length of 980 Mb, with a scaffold N50 length of 83 Mb. The genome size of diploid O. basilaris is markedly smaller than other diploid members of Cactaceae that have been assembled to date. This is the first nuclear genome sequenced in subfamily Opuntioideae and the most complete nuclear genome for Cactaceae to date and will lay the foundation for future genomic work across the biologically and taxonomically complicated prickly pear cacti.

The American black bear, Ursus americanus, is a widespread and ecologically important species in North America. In California, the black bear plays an important role in a variety of ecosystems and serves as an important species for recreational hunting. While research suggests that the populations in California are currently healthy, continued monitoring is critical, with genomic analyses providing an important surveillance tool. Here we report a high-quality, near chromosome-level genome assembly from a U. americanus sample from California. The primary assembly has a total length of 2.5 Gb contained in 316 scaffolds, a contig N50 of 58.9 Mb, a scaffold N50 of 67.6 Mb, and a BUSCO completeness score of 96%. This U. americanus genome assembly will provide an important resource for the targeted management of black bear populations in California, with the goal of achieving an appropriate balance between the recreational value of black bears and the maintenance of viable populations. The high quality of this genome assembly will also make it a valuable resource for comparative genomic analyses among black bear populations and among bear species.

The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.

Island oak (Quercus tomentella) is a rare relictual island tree species that exists only on six islands off the coast of California and Mexico, but was once widespread throughout mainland California. Currently, this species is endangered by threats such as non-native plants, grazing animals, and human removal. Efforts for conservation and restoration of island oak currently underway could benefit from information about its range-wide genetic structure and evolutionary history. Here we present a high-quality genome assembly for Q. tomentella, assembled using PacBio HiFi and Omni-C sequencing, developed as part of the California Conservation Genomics Project (CCGP). The resulting assembly has a length of 781 Mb, with a contig N50 of 22.0 Mb and a scaffold N50 of 63.4 Mb. This genome assembly will provide a resource for genomics-informed conservation of this rare oak species. Additionally, this reference genome will be the first one available for a species in Quercus section Protobalanus, a unique oak clade present only in western North America.