Reference Genome Assembly of the Big Berry Manzanita ( Arctostaphylos glauca )

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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 northwestern pond turtle following the CCGP assembly protocol Version 2.0, which is adapted from the initial CCGP assembly efforts (see Huang et al 2021 ). The main difference between versions is the use of Omni-C instead of Hi-C data, alongside PacBio HiFi Reads, for the generation of high-quality and highly contiguous nuclear genome assemblies.…”

Section: Methodsmentioning

confidence: 99%

“…Many of these taxa are threatened or endangered, and the combined reference genome sequences plus the landscape genomics approach of the CCGP will enable the identification of hotspots of diversity across California, providing a unique framework for informed conservation decisions and management plants ( Shaffer et al 2022 ). This is the first completed animal reference genome constructed for the CCGP and follows our first plant taxon ( Huang et al 2021 ). This genome assembly will provide a foundational resource for future studies on the unique ecology, biogeography, evolutionary history, and conservation of A. marmorata .…”

mentioning

confidence: 99%

Reference Genome of the Northwestern Pond Turtle,Actinemys marmorata

Todd

Jenkinson

Escalona

et al. 2022

The northwestern pond turtle, Actinemys marmorata, and its recently recognized sister species, the southwestern pond turtle, A. pallida, are the sole aquatic testudines occurring over most of western North America, and the only living representatives of the genus Actinemys. Although it historically ranged from Washington state through central California, USA, populations of the northwestern pond turtle have been in decline for decades and the species is afforded state-level protection across its range; it is currently being considered for protection under the US Endangered Species Act. Here, we report a new, chromosome-level assembly of A. marmorata 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 chromatinproximity sequencing technology to produce a de novo assembled genome. The assembly comprises 198 scaffolds spanning 2,319,339,408 base pairs, has a contig N50 of 75 Mb, a scaffold N50 of 146Mb, and BUSCO complete score of 96.7%, making it the most complete testudine assembly of the 24 species from 13 families that are currently available. In combination with the A. pallida reference genome that is currently under construction through the CCGP, the A. marmorata genome will be a powerful tool for documenting landscape genomic diversity, the basis of adaptations to salt tolerance and thermal capacity, and hybridization dynamics between these recently diverged species.

“…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.