Reference Genome of the Northwestern Pond Turtle, Actinemys marmorata

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The California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at a regional scale. We describe the CCGP, including all aspects of project administration, data collection, current progress, and future challenges. The CCGP will generate, analyze, and curate a single high-quality reference genome and 100-150 resequenced genomes for each of 153 species projects (representing 235 individual species) that span the ecological and phylogenetic breadth of California’s marine, freshwater, and terrestrial ecosystems. The resulting portfolio of roughly 20,000 resequenced genomes will be analyzed with identical informatic and landscape genomic pipelines, providing a comprehensive overview of hotspots of within-species genomic diversity, potential and realized corridors connecting these hotspots, regions of reduced diversity requiring genetic rescue, and the distribution of variation critical for rapid climate adaptation. After two years of concerted effort, full funding ($12M USD) has been secured, species identified, and funds distributed to 68 laboratories and 114 investigators drawn from all 10 University of California campuses. The remaining phases of the CCGP include completion of data collection and analyses, and delivery of the resulting genomic data and inferences to state and federal regulatory agencies to help stabilize species declines. The aspirational goals of the CCGP are to identify geographic regions that are critical to long term preservation of California biodiversity, prioritize those regions based on defensible genomic criteria, and provide foundational knowledge that informs management strategies at both the individual species and ecosystem levels.

Section: Looking Forwardsupporting

confidence: 54%

Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project

Shaffer

Toffelmier

Corbett‐Detig

et al. 2022

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“…We assembled the genome of the black abalone following the California Conservation Genomics Project (CCGP) assembly protocol Version 2.0 ( Shaffer et al 2022 ; Todd et al 2022 ), which uses PacBio HiFi reads and Omni-C data for the generation of high-quality and highly contiguous nuclear genome assemblies.…”

Section: Methodsmentioning

confidence: 99%

A Draft Reference Genome Assembly of the Critically Endangered Black Abalone,Haliotis cracherodii

Orland

Escalona

Sahasrabudhe

et al. 2022

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The once abundant black abalone, Haliotis cracherodii, is a large, long-lived grazing marine mollusk that inhabits the rocky intertidal along the coast of California. The species has experienced dramatic declines since the mid-1980s largely due to the fatal bacterial disease called withering syndrome, leading to the collapse of an economically important fishery and to its inclusion into the IUCN listing as a critically endangered species. In some places impacted by the disease, populations of black abalone have declined by more than 90%, prompting population crashes associated with very little recruitment of new individuals and changes to intertidal communities. Habitats that were dominated by crustose coralline algae and bare rock have become dominated instead by fleshy algae and sessile invertebrates. Here, we present the first high-quality black abalone reference genome, assembled with PacBio HiFi long-reads and assembled with Dovetail Omni-C data to generate a scaffold-level assembly. The black abalone reference genome will be an essential resource in understanding the evolutionary history of this species as well as for exploring its current levels of genetic diversity and establishing future management and restoration plans.

“…Using the newly generated reference genomes and resequenced individuals from across the state, the CCGP are developing tools to identify important hotspots of genetic diversity for multiple species and providing a framework for informed conservation decisions and management plans. The CCGP have successfully assembled the genomes for a few species, including the black abalone, northwestern pond turtle, and Big Berry Manzanita ( Huang et al 2022 ; Orland et al 2022 ; Todd et al 2022 ). With support from CCGP, we generated a scaffold-level assembly using a hybrid de novo approach that combines Hi-C chromatin-proximity and PacBio HiFi long-read sequencing data.…”

Section: Introductionmentioning

confidence: 99%

A draft reference genome of the red abalone, Haliotis rufescens, for conservation genomics

Griffiths

Sahasrabudhe

Marimuthu

et al. 2022

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Red abalone, Haliotis rufencens, are herbivorous marine gastropods that primarily feed on kelp. They are the largest and longest-lived of abalone species with a range distribution in North America from central Oregon, USA, to Baja California, MEX. Recently, red abalone have been in decline as a consequence of over-harvesting, disease, and climate change, resulting in the closure of the commercial fishery in the 1990s and the recreational fishery in 2018. Protecting this ecologically and economically important species requires an understanding of their current population dynamics and connectivity. Here, we present a new red abalone reference genome as part of the California Conservation Genomics project (CCGP). Following the CCGP genome strategy, we used Pacific Biosciences HiFi long-reads and Dovetail Omni-C data to generate a scaffold-level assembly. The assembly comprises 616 scaffolds for a total size of 1.3 Gb, a scaffold N50 of 45.7 Mb, and a BUSCO complete score of 97.3 %. This genome represents a significant improvement over a previous assembly and will serve as a powerful tool for investigating seascape genomic diversity, local adaptation to temperature and ocean acidification, and informing management strategies.