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

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.

Section: Methodsmentioning

confidence: 99%

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

Orland

Sahasrabudhe

et al. 2022

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“…Here, we report the first chromosome-level genome assembly for the species, produced as part of the California Conservation Genomics Project (CCGP). The overarching goal of the CCGP is to discover patterns of genomic diversity across the state of California by sequencing the complete genomes of approximately 150 carefully selected species ( Shaffer et al 2022 ). 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 ).…”

mentioning

confidence: 99%

“…The overarching goal of the CCGP is to discover patterns of genomic diversity across the state of California by sequencing the complete genomes of approximately 150 carefully selected species ( Shaffer et al 2022 ). 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 ).…”

mentioning

confidence: 99%

Reference Genome of the Northwestern Pond Turtle,Actinemys marmorata

Todd

Jenkinson

et al. 2022

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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.

“…The California Conservation Genomics Project (CCGP) is generating a genomics variation database for hundreds of species with broad statewide distributions to help guide conservation of species and ecosystems under anthropogenic changes ( Shaffer et al 2022 ). As one of the study species focused on by the CCGP, here we present a high-quality de novo genome assembly of the bobcat, with high contiguity, base accuracy, and minimal gaps.…”

mentioning

confidence: 99%

A Reference Genome Assembly of the Bobcat, Lynx rufus

Lin

Sahasrabudhe

et al. 2022

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The bobcat (Lynx rufus) is a medium-sized carnivore well adapted to various environments and an indicator species for landscape connectivity. It is one of the four species within the extant Lynx genus in the family Felidae. Because of its broad geographic distribution and central role in food webs, the bobcat is important for conservation. Here we present a high quality de novo genome assembly of a male bobcat located in Mendocino County (California, USA) as part of the California Conservation Genomics Project (CCGP). The assembly was generated using the standard CCGP pipeline from a combination of Omni-C and HiFi technologies. The primary assembly comprises 76 scaffolds spanning 2.4 Gb, represented by a scaffold N50 of 142 Mb, a contig N50 of 66.2 Mb and a BUSCO completeness score of 95.90%. The bobcat genome will be an important resource for the effective management and conservation of this species and comparative genomics exploration.