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  • 1
    Online Resource
    Online Resource
    Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project
    Oxford University Press (OUP) ; 2022
    In:  Journal of Heredity Vol. 113, No. 6 ( 2022-11-30), p. 577-588
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 113, No. 6 ( 2022-11-30), p. 577-588
    Abstract: 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 2 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.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esac020
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
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    detail.hit.zdb_id: 2518163-4
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    A genome assembly of the Yuma myotis bat, Myotis yumanensis
    Oxford University Press (OUP) ; 2023
    In:  Journal of Heredity ( 2023-09-15)
    Details
    In: Journal of Heredity, Oxford University Press (OUP), ( 2023-09-15)
    Abstract: The Yuma myotis bat (Myotis yumanensis) is a small vespertilionid bat and one of 52 species of new world Myotis bats in the subgenus Pizonyx. While M. yumanensis populations currently appear relatively stable, it is one of twelve bat species known or suspected to be susceptible to white-nose syndrome, the fungal disease causing declines in bat populations across North America. Only two of these twelve species have genome resources available, which limits the ability of resource managers to use genomic techniques to track the responses of bat populations to white-nose syndrome generally. Here we present the first de novo genome assembly for Yuma myotis, generated as a part of the California Conservation Genomics Project (CCGP). The M. yumanensis genome was generated using a combination of PacBio HiFi long reads and Omni-C chromatin-proximity sequencing technology. This high-quality genome is one of the most complete bat assemblies available, with a contig N50 of 28.03 Mb, scaffold N50 of 99.14 Mb and BUSCO completeness score of 93.7%. The Yuma myotis genome provides a high quality resource that will aid in comparative genomic and evolutionary studies, as well as inform conservation management related to white-nose syndrome.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esad053
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1466720-4
    detail.hit.zdb_id: 2518163-4
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Reference Genome of the Northwestern Pond Turtle, Actinemys marmorata
    Oxford University Press (OUP) ; 2022
    In:  Journal of Heredity Vol. 113, No. 6 ( 2022-11-30), p. 624-631
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 113, No. 6 ( 2022-11-30), p. 624-631
    Abstract: 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 chromatin-proximity 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.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esac021
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1466720-4
    detail.hit.zdb_id: 2518163-4
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Reference Genome of the California Sheephead, Semicossyphus pulcher (Labridae, Perciformes), A Keystone Fish Predator in Kelp Forest Ecosystems
    Oxford University Press (OUP) ; 2022
    In:  Journal of Heredity Vol. 113, No. 6 ( 2022-11-30), p. 649-656
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 113, No. 6 ( 2022-11-30), p. 649-656
    Abstract: Keystone species are known to play a critical role in kelp forest health, including the well-known killer whales, sea otter, sea urchin, kelp trophic cascade in the Aleutian Islands, Alaska, USA. In California, a major player in the regulation of sea urchin abundance, and in turn, the health of kelp forests ecosystems, is a large wrasse, the California Sheephead, Semicossyphus pulcher. We present a reference genome for this ecologically important species that will serve as a key resource for future conservation research of California’s inshore marine environment utilizing genomic tools to address changes in life-history traits, dispersal, range shifts, and ecological interactions among members of the kelp forest ecological assemblages. Our genome assembly of S. pulcher has a total length of 0.794 Gb, which is similar to many other marine fishes. The assembly is largely contiguous (N50 = 31.9 Mb) and nearly complete (BUSCO single-copy core gene content = 98.1%). Within the context of the California Conservation Genomics Project (CCGP), the genome of S. pulcher will be used as an important reference resource for ongoing whole genome resequencing efforts of the species.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esac032
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1466720-4
    detail.hit.zdb_id: 2518163-4
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Reference genome of the rubber boa, Charina bottae (Serpentes: Boidae)
    Oxford University Press (OUP) ; 2022
    In:  Journal of Heredity Vol. 113, No. 6 ( 2022-11-30), p. 641-648
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 113, No. 6 ( 2022-11-30), p. 641-648
    Abstract: The rubber boa, Charina bottae is a semi-fossorial, cold-temperature adapted snake that ranges across the wetter and cooler ecoregions of the California Floristic Province. The rubber boa is 1 of 2 species in the family Boidae native to California and currently has 2 recognized subspecies, the Northern rubber boa C. bottae bottae and the Southern rubber boa C. bottae umbratica. Recent genomic work on C. bottae indicates that these 2 subspecies are collectively composed of 4 divergent lineages that separated during the late Miocene. Analysis of habitat suitability indicates that C. bottae umbratica montane sky-island populations from southern California will lose the majority of their habit over the next 70 yr, and is listed as Threatened under the California Endangered Species Act. Here, we report a new, chromosome-level assembly of C. bottae bottae 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 289 scaffolds covering 1,804,944,895 bp, has a contig N50 of 37.3 Mb, a scaffold N50 of 97 Mb, and BUSCO completeness score of 96.3%, and represents the first reference genome for the Boidae snake family. This genome will enable studies of genetic differentiation and connectivity among C. bottae bottae and C. bottae umbratica populations across California and help manage locally endemic lineages as they confront challenges from human-induced climate warming, droughts, and wildfires across California.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esac048
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1466720-4
    detail.hit.zdb_id: 2518163-4
    SSG: 12
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  • 6
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    Online Resource
    Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae)
    Oxford University Press (OUP) ; 2023
    In:  Journal of Heredity Vol. 114, No. 4 ( 2023-06-22), p. 395-403
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 114, No. 4 ( 2023-06-22), p. 395-403
    Abstract: Climate-driven changes in hydrological regimes are of global importance and are particularly significant in riparian ecosystems. Riparian ecosystems in California provide refuge to many native and vulnerable species within a xeric landscape. California Tetragnatha spiders play a key role in riparian ecosystems, serving as a link between terrestrial and aquatic elements. Their tight reliance on water paired with the widespread distributions of many species make them ideal candidates to better understand the relative role of waterways versus geographic distance in shaping the population structure of riparian species. To assist in better understanding population structure, we constructed a reference genome assembly for Tetragnatha versicolor using long-read sequencing, scaffolded with proximity ligation Omni-C data. The near-chromosome-level assembly is comprised of 174 scaffolds spanning 1.06 Gb pairs, with a scaffold N50 of 64.1 Mb pairs and BUSCO completeness of 97.6%. This reference genome will facilitate future study of T. versicolor population structure associated with the rapidly changing environment of California.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esad013
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1466720-4
    detail.hit.zdb_id: 2518163-4
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    Reference genome of the Virginia rail, Rallus limicola
    Oxford University Press (OUP) ; 2023
    In:  Journal of Heredity Vol. 114, No. 4 ( 2023-06-22), p. 428-435
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 114, No. 4 ( 2023-06-22), p. 428-435
    Abstract: The Virginia rail, Rallus limicola, is a member of the family Rallidae, which also includes many other species of secretive and poorly studied wetland birds. It is recognized as a single species throughout its broad distribution in North America where it is exploited as a game bird, often with generous harvest limits, despite a lack of systematic population surveys and evidence of declines in many areas due to wetland loss and degradation. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the Virginia rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.191%. The assembly consists of 1,102 scaffolds spanning 1.39 Gb, with a contig N50 of 11.0 Mb, scaffold N50 of 25.3 Mb, largest contig of 45 Mb, and largest scaffold of 128.4 Mb. It has a high BUSCO completeness score of 96.9% and represents the first genome assembly available for the genus Rallus. This genome assembly will help resolve questions about the complex evolutionary history of rails and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change and habitat loss and fragmentation. It will also provide a valuable resource for rail conservation efforts by quantifying Virginia rail vagility, population connectivity, and effective population sizes.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esad026
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1466720-4
    detail.hit.zdb_id: 2518163-4
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Reference genome of an iconic lizard in western North America, Blainville’s horned lizard Phrynosoma blainvillii
    Oxford University Press (OUP) ; 2023
    In:  Journal of Heredity Vol. 114, No. 4 ( 2023-06-22), p. 410-417
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 114, No. 4 ( 2023-06-22), p. 410-417
    Abstract: Genome assemblies are increasingly being used to identify adaptive genetic variation that can help prioritize the population management of protected species. This approach may be particularly relevant to species like Blainville’s horned lizard, Phrynosoma blainvillii, due to its specialized diet on noxious harvester ants, numerous adaptative traits for avoiding predation (e.g. cranial horns, dorsoventrally compressed body, cryptic coloration, and blood squirting from the orbital sinuses), and status as Species of Special Concern in California. Rangewide decline since the early 20th century, the basis of its conservation status, has been driven mainly by habitat conversion, over-collecting, and invasion of a non-native ant that displaces its native ant prey base. Here, we report on a scaffold-level genome assembly for P. blainvillii as part of the California Conservation Genomics Project (CCGP), produced using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology. The de novo assembly has 78 scaffolds, a total length of ~2.21 Gb, a scaffold N50 length of ~352 Mb, and BUSCO score of 97.4%. This is the second species of Phrynosoma for which a reference genome has been assembled and represents a considerable improvement in terms of contiguity and completeness. Combined with the landscape genomics data being compiled by the CCGP, this assembly will help strategize efforts to maintain and/or restore local genetic diversity, where interventions like genetic rescue, translocation, and strategic land preservation may be the only means by which P. blainvillii and other low-vagility species can survive in the fragmented habitats of California.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esad032
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1466720-4
    detail.hit.zdb_id: 2518163-4
    SSG: 12
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  • 9
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    Online Resource
    Reference Genome Assembly of the Big Berry Manzanita ( Arctostaphylos glauca )
    Oxford University Press (OUP) ; 2022
    In:  Journal of Heredity Vol. 113, No. 2 ( 2022-05-16), p. 188-196
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 113, No. 2 ( 2022-05-16), p. 188-196
    Abstract: Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essential ecological roles in native ecosystems. Despite their importance in conservation management, and the many ecological and evolutionary studies that have focused on manzanitas, virtually no research has been conducted on the genomics of any manzanita species. Here, we report the first genome assembly of a manzanita species, the widespread Arctostaphylos glauca. Consistent with the genomics strategy 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 comprises a total of 271 scaffolds spanning 547Mb, close to the genome size estimated by flow cytometry. This assembly, with a scaffold N50 of 31Mb and BUSCO complete score of 98.2%, will be used as a reference genome for understanding the genetic diversity and the basis of adaptations of both common and rare and endangered manzanita species.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esab071
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1466720-4
    detail.hit.zdb_id: 2518163-4
    SSG: 12
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  • 10
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    Online Resource
    Reference genome of the bicolored carpenter ant, Camponotus vicinus
    Oxford University Press (OUP) ; 2023
    In:  Journal of Heredity ( 2023-09-26)
    Details
    In: Journal of Heredity, Oxford University Press (OUP), ( 2023-09-26)
    Abstract: Carpenter ants in the genus Camponotus are large, conspicuous ants that are abundant and ecologically influential in many terrestrial ecosystems. The bicolored carpenter ant, C. vicinus Mayr, is distributed across a wide range of elevations and latitudes in western North America, where it is a prominent scavenger and predator. Here, we present a high-quality genome assembly of C. vicinus from a sample collected in Sonoma County, California, near the type locality of the species. This genome assembly consists of 38 scaffolds spanning 302.74 Mb, with contig N50 of 15.9Mb, scaffold N50 of 19.9 Mb, and BUSCO completeness of 99.2%. This genome sequence will be a valuable resource for exploring the evolutionary ecology of C. vicinus and carpenter ants generally. It also provides an important tool for clarifying cryptic diversity within the C. vicinus species complex, a genetically diverse set of populations, some of which are quite localized and of conservation interest.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esad055
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1466720-4
    detail.hit.zdb_id: 2518163-4
    SSG: 12
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