1
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Ward PS, Cash EI, Ferger K, Escalona M, Sahasrabudhe R, Miller C, Toffelmier E, Fairbairn C, Seligmann W, Shaffer HB, Tsutsui ND. Reference genome of the bicolored carpenter ant, Camponotus vicinus. J Hered 2024; 115:120-129. [PMID: 37751380 PMCID: PMC10838126 DOI: 10.1093/jhered/esad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023] Open
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, Camponotus 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 15.9 Mb, 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.
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Affiliation(s)
- Philip S Ward
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, United States
| | - Elizabeth I Cash
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Kailey Ferger
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Cores, Genome Center, University of California, Davis, Davis, CA 95616, United States
| | - Courtney Miller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Neil D Tsutsui
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, United States
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2
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Curti JN, Fraser D, Escalona M, Fairbairn CW, Sacco S, Sahasrabudhe R, Nguyen O, Seligmann W, Sudmant PH, Toffelmier E, Vazquez JM, Wayne R, Shaffer HB, Buchalski MR. A genome assembly of the Yuma myotis bat, Myotis yumanensis. J Hered 2024; 115:139-148. [PMID: 37712349 PMCID: PMC10838121 DOI: 10.1093/jhered/esad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/16/2023] Open
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 12 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 12 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. 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.
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Affiliation(s)
- Joseph N Curti
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, United States
| | - Devaughn Fraser
- Connecticut Department of Energy and Environmental Protection, Hartford, CT, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Colin W Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, United States
| | - Juan Manuel Vazquez
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Robert Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles (UCLA), Los Angeles, CA, United States
- Institute of the Environment and Sustainability, La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles (UCLA), Los Angeles, CA, United States
| | - Michael R Buchalski
- Wildlife Genetics Research Unit, Wildlife Health Laboratory, California Department of Fish and Wildlife, Sacramento, CA, United States
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3
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Westeen EP, Escalona M, Holding ML, Beraut E, Fairbairn C, Marimuthu MPA, Nguyen O, Perri R, Fisher RN, Toffelmier E, Shaffer HB, Wang IJ. A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex. J Hered 2023; 114:681-689. [PMID: 37493092 PMCID: PMC10650947 DOI: 10.1093/jhered/esad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023] Open
Abstract
Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake (Crotalus oreganus) is one of the widest ranging rattlesnake species, with a distribution from British Columbia, where it is listed as threatened, to Baja California and east across the Great Basin to western Wyoming, Colorado and New Mexico. Here, we report a new reference genome assembly for one of six currently recognized subspecies, C. oreganus helleri, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomic sequencing 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 a total of 698 scaffolds spanning 1,564,812,557 base pairs, has a contig N50 of 64.7 Mb, a scaffold N50 of 110.8 Mb, and BUSCO complete score of 90.5%. This reference genome will be valuable for studies on the genomic basis of venom evolution and variation within Crotalus, in resolving the taxonomy of C. oreganus and its relatives, and for the conservation and management of rattlesnakes in general.
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Affiliation(s)
- Erin P Westeen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Matthew L Holding
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Ralph Perri
- 1001 Foothill Drive, Fillmore, CA, 93015, United States
| | - Robert N Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, 92101, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, United States
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
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4
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Westeen EP, Escalona M, Beraut E, Marimuthu MPA, Nguyen O, Fisher RN, Toffelmier E, Shaffer HB, Wang IJ. A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus. J Hered 2023; 114:690-697. [PMID: 37688363 PMCID: PMC10650948 DOI: 10.1093/jhered/esad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/07/2023] [Indexed: 09/10/2023] Open
Abstract
Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus, has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed "ring species" around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis, as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.
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Affiliation(s)
- Erin P Westeen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, United States
| | - Robert N Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, 92101, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
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5
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Bishop AP, Westeen EP, Yuan ML, Escalona M, Beraut E, Fairbairn C, Marimuthu MPA, Nguyen O, Chumchim N, Toffelmier E, Fisher RN, Shaffer HB, Wang IJ. Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis. J Hered 2023; 114:521-528. [PMID: 37335574 PMCID: PMC10445515 DOI: 10.1093/jhered/esad037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023] Open
Abstract
Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics 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 a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.
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Affiliation(s)
- Anusha P Bishop
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
| | - Erin P Westeen
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
| | - Michael L Yuan
- Center for Population Biology, University of California, Davis, Davis, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Noravit Chumchim
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Robert N Fisher
- U.S. Geological Survey Western Ecological Research Center, San Diego, CA, United States
| | - H. Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
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6
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Richmond JQ, McGuire JA, Escalona M, Marimuthu MPA, Nguyen O, Sacco S, Beraut E, Toffelmier E, Fisher RN, Wang IJ, Shaffer HB. Reference genome of an iconic lizard in western North America, Blainville's horned lizard Phrynosoma blainvillii. J Hered 2023; 114:410-417. [PMID: 37195437 DOI: 10.1093/jhered/esad032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/19/2023] [Indexed: 05/18/2023] Open
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.
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Affiliation(s)
- Jonathan Q Richmond
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, United States
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Robert N Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego, CA, United States
| | - Ian J Wang
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
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7
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Hall LA, Wang IJ, Escalona M, Beraut E, Sacco S, Sahasrabudhe R, Nguyen O, Toffelmier E, Shaffer HB, Beissinger SR. Reference genome of the Virginia rail, Rallus limicola. J Hered 2023; 114:428-435. [PMID: 37105531 PMCID: PMC10287147 DOI: 10.1093/jhered/esad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/27/2023] [Indexed: 04/29/2023] Open
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.
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Affiliation(s)
- Laurie A Hall
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Ian J Wang
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Eric Beraut
- Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Samuel Sacco
- Department of Ecology & Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, United States
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment & Sustainability, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment & Sustainability, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Steven R Beissinger
- Department of Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, United States
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8
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Hall LA, Wang IJ, Escalona M, Beraut E, Sacco S, Sahasrabudhe R, Nguyen O, Toffelmier E, Shaffer HB, Beissinger SR. Reference genome of the black rail, Laterallus jamaicensis. J Hered 2023; 114:436-443. [PMID: 37119047 PMCID: PMC10287143 DOI: 10.1093/jhered/esad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/27/2023] [Indexed: 04/30/2023] Open
Abstract
The black rail, Laterallus jamaicensis, is one of the most secretive and poorly understood birds in the Americas. Two of its five subspecies breed in North America: the Eastern black rail (L. j. jamaicensis), found primarily in the southern and mid-Atlantic states, and the California black rail (L. j. coturniculus), inhabiting California and Arizona, are recognized across the highly disjunct distribution. Population declines, due primarily to wetland loss and degradation, have resulted in conservation status listings for both subspecies. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the black 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 0.182%. The assembly consists of 964 scaffolds spanning 1.39 Gb, with a contig N50 of 7.4 Mb, scaffold N50 of 21.4 Mb, largest contig of 44.8 Mb, and largest scaffold of 101.2 Mb. The assembly has a high BUSCO completeness score of 96.8% and represents the first genome assembly available for the genus Laterallus. This genome assembly can help resolve questions about the complex evolutionary history of rails, assess black rail vagility and population connectivity, estimate effective population sizes, and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change, habitat loss and fragmentation, and disease.
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Affiliation(s)
- Laurie A Hall
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
| | - Ian J Wang
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of Califin JHornia, Santa Cruz, CA 95064, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of Califin JHornia, Santa Cruz, CA 95064, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, United States
| | - Steven R Beissinger
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, United States
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9
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Grether GF, Beninde J, Beraut E, Chumchim N, Escalona M, MacDonald ZG, Miller C, Sahasrabudhe R, Shedlock AM, Toffelmier E, Shaffer HB. Reference genome for the American rubyspot damselfly, Hetaerina americana. J Hered 2023; 114:385-394. [PMID: 37195415 PMCID: PMC10287145 DOI: 10.1093/jhered/esad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 05/07/2023] [Indexed: 05/18/2023] Open
Abstract
Damselflies and dragonflies (Order: Odonata) play important roles in both aquatic and terrestrial food webs and can serve as sentinels of ecosystem health and predictors of population trends in other taxa. The habitat requirements and limited dispersal of lotic damselflies make them especially sensitive to habitat loss and fragmentation. As such, landscape genomic studies of these taxa can help focus conservation efforts on watersheds with high levels of genetic diversity, local adaptation, and even cryptic endemism. Here, as part of the California Conservation Genomics Project (CCGP), we report the first reference genome for the American rubyspot damselfly, Hetaerina americana, a species associated with springs, streams and rivers throughout California. Following the CCGP assembly pipeline, we produced two de novo genome assemblies. The primary assembly includes 1,630,044,487 base pairs, with a contig N50 of 5.4 Mb, a scaffold N50 of 86.2 Mb, and a BUSCO completeness score of 97.6%. This is the seventh Odonata genome to be made publicly available and the first for the subfamily Hetaerininae. This reference genome fills an important phylogenetic gap in our understanding of Odonata genome evolution, and provides a genomic resource for a host of interesting ecological, evolutionary, and conservation questions for which the rubyspot damselfly genus Hetaerina is an important model system.
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Affiliation(s)
- Gregory F Grether
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-1606, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095-7239, United States
| | - Joscha Beninde
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095-7239, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Noravit Chumchim
- DNA Technologies and Expression Analysis Core Laboratory, University of California Davis, Davis, CA 95616, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Zachary G MacDonald
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095-7239, United States
| | - Courtney Miller
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-1606, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095-7239, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, University of California Davis, Davis, CA 95616, United States
| | - Andrew M Shedlock
- Department of Biology, College of Charleston, Charleston, SC 29424, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-1606, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095-7239, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-1606, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA 90095-7239, United States
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10
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Adams SA, Graham NR, Holmquist AJ, Sheffer MM, Steigerwald EC, Sahasrabudhe R, Nguyen O, Beraut E, Fairbairn C, Sacco S, Seligmann W, Escalona M, Shaffer HB, Toffelmier E, Gillespie RG. Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae). J Hered 2023; 114:395-403. [PMID: 37042574 PMCID: PMC10287146 DOI: 10.1093/jhered/esad013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/27/2023] [Indexed: 04/13/2023] Open
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.
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Affiliation(s)
- Seira A Adams
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
- Center for Population Biology, University of California, Davis, CA, United States
- Department of Evolution and Ecology, University of California, Davis, CA, United States
| | - Natalie R Graham
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
| | - Anna J Holmquist
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
| | - Monica M Sheffer
- Department of Biology, University of Washington, Seattle, WA, United States
- eScience Institute, University of Washington, Seattle, WA, United States
| | - Emma C Steigerwald
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, United States
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute for Environment and Sustainability, University of California, Los Angeles, CA, United States
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute for Environment and Sustainability, University of California, Los Angeles, CA, United States
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
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11
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van Riemsdijk I, Arntzen JW, Bucciarelli GM, McCartney-Melstad E, Rafajlović M, Scott PA, Toffelmier E, Shaffer HB, Wielstra B. Two transects reveal remarkable variation in gene flow on opposite ends of a European toad hybrid zone. Heredity (Edinb) 2023:10.1038/s41437-023-00617-6. [PMID: 37106116 DOI: 10.1038/s41437-023-00617-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Speciation entails a reduction in gene flow between lineages. The rates at which genomic regions become isolated varies across space and time. Barrier markers are linked to putative genes involved in (processes of) reproductive isolation, and, when observed over two transects, indicate species-wide processes. In contrast, transect-specific putative barrier markers suggest local processes. We studied two widely separated transects along the 900 km hybrid zone between Bufo bufo and B. spinosus, in northern and southern France, for ~1200 RADseq markers. We used genomic and geographic cline analyses to identify barrier markers based on their restricted introgression, and found that some markers are transect-specific, while others are shared between transects. Twenty-six barrier markers were shared across both transects, of which some are clustered in the same chromosomal region, suggesting that their associated genes are involved in reduced gene flow across the entire hybrid zone. Transect-specific barrier markers were twice as numerous in the southern than in the northern transect, suggesting that the overall barrier effect is weaker in northern France. We hypothesize that this is consistent with a longer period of secondary contact in southern France. The smaller number of introgressed genes in the northern transect shows considerably more gene flow towards the southern (B. spinosus) than the northern species (B. bufo). We hypothesize that hybrid zone movement in northern France and hybrid zone stability in southern France explain this pattern. The Bufo hybrid zone provides an excellent opportunity to separate a general barrier effect from localized gene flow-reducing conditions.
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Affiliation(s)
- I van Riemsdijk
- Naturalis Biodiversity Center, Leiden, the Netherlands.
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands.
- Institute for Evolution and Ecology, Plant Evolutionary Ecology, Tübingen University, Tübingen, Germany.
| | - J W Arntzen
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - G M Bucciarelli
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
- Institute of the Environment, UC Davis, Davis, CA, USA
- Department of Wildlife, Fish, and Conservation Biology, UC Davis, Davis, CA, USA
| | - E McCartney-Melstad
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - M Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - P A Scott
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Natural Sciences Collegium, Eckerd College, 4200 54 Ave S, St Petersburg, FL, 33711, USA
| | - E Toffelmier
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - H B Shaffer
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - B Wielstra
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
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12
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Wright DB, Escalona M, Marimuthu MPA, Sahasrabudhe R, Nguyen O, Sacco S, Beraut E, Toffelmier E, Miller C, Shaffer HB, Bernardi G. Reference genome of the Woolly Sculpin, Clinocottus analis. J Hered 2023; 114:60-67. [PMID: 36107748 PMCID: PMC10019020 DOI: 10.1093/jhered/esac055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Sculpins (Family Cottidae) are generally cold-temperate intertidal reef fishes most commonly found in the North Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Woolly Sculpin, Clinocottus analis, to establish a genomic model for understanding phylogeographic structure of inshore marine taxa along the California coast. These patterns, in turn, should further inform the design of marine protected areas using dispersal models based on genomic data. The small genome of C. analis is typical of marine fishes at less than 1 Gb (genome size = 538 Mb), and our assembly is near-chromosome level (contig N50 = 9.1 Mb, scaffold N50 = 21 Mb, BUSCO completeness = 97.9%). Within the context of the CCGP, the Woolly Sculpin genome will be used as a reference for future whole-genome resequencing projects aimed at enhancing our knowledge of the population structure of the species, and efficacy of marine protected areas across the state.
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Affiliation(s)
- Daniel B Wright
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Courtney Miller
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
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13
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Wright DB, Escalona M, Marimuthu MPA, Sahasrabudhe R, Nguyen O, Sacco S, Beraut E, Toffelmier E, Miller C, Shaffer HB, Bernardi G, German DP. Reference genome of the Monkeyface Prickleback, Cebidichthys violaceus. J Hered 2023; 114:52-59. [PMID: 36321765 PMCID: PMC10019021 DOI: 10.1093/jhered/esac054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/13/2022] [Indexed: 11/06/2022] Open
Abstract
Pricklebacks (Family Stichaeidae) are generally cold-temperate fishes most commonly found in the north Pacific. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Monkeyface Prickleback, Cebidichthys violaceus, to establish a genomic model for understanding phylogeographic patterns of marine organisms in California. These patterns, in turn, may inform the design of marine protected areas using dispersal models based on forthcoming population genomic data. The genome of C. violaceus is typical of many marine fishes at less than 1 Gb (genome size = 575.6 Mb), and our assembly is near-chromosome level (contig N50 = 1 Mb, scaffold N50 = 16.4 Mb, BUSCO completeness = 93.2%). Within the context of the CCGP, the genome will be used as a reference for future whole genome resequencing projects, enhancing our knowledge of the population structure of the species and more generally, the efficacy of marine protected areas as a primary conservation tool across California's marine ecosystems.
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Affiliation(s)
- Daniel B Wright
- Address correspondence to D.B. Wright at the address above, or e-mail:
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA, United States
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Courtney Miller
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Donovan P German
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
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14
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Grismer JL, Escalona M, Miller C, Beraut E, Fairbairn CW, Marimuthu MPA, Nguyen O, Toffelmier E, Wang IJ, Shaffer HB. Reference genome of the rubber boa, Charina bottae (Serpentes: Boidae). J Hered 2022; 113:641-648. [PMID: 36056886 PMCID: PMC9709994 DOI: 10.1093/jhered/esac048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Jesse L Grismer
- Department of Biology, La Sierra University, Riverside, CA, United States
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Courtney Miller
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Colin W Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA, United States
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, United States
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15
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Shaffer HB, Toffelmier E, Corbett-Detig RB, Escalona M, Erickson B, Fiedler P, Gold M, Harrigan RJ, Hodges S, Luckau TK, Miller C, Oliveira DR, Shaffer KE, Shapiro B, Sork VL, Wang IJ. Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project. J Hered 2022; 113:577-588. [PMID: 35395669 DOI: 10.1093/jhered/esac020] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/04/2022] [Indexed: 12/16/2022] Open
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.
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Affiliation(s)
- H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,California Department of Fish and Wildlife, Fisheries Branch, West Sacramento, CA 95605, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Russ B Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bjorn Erickson
- U.S. Fish and Wildlife Service, Sacramento, CA 95825, USA
| | - Peggy Fiedler
- Natural Reserve System, Office of the President, University of California, Oakland, CA 94607, USA
| | - Mark Gold
- California Natural Resources Agency, 1416 Ninth Street, Suite 1311, Sacramento, CA 95814, USA
| | - Ryan J Harrigan
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Center for Tropical Research, Institute for Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Scott Hodges
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Tara K Luckau
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Courtney Miller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Daniel R Oliveira
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Kevin E Shaffer
- California Department of Fish and Wildlife, Fisheries Branch, West Sacramento, CA 95605, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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16
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Bernardi G, Toy JA, Escalona M, Marimuthu MPA, Sahasrabudhe R, Nguyen O, Sacco S, Beraut E, Toffelmier E, Miller C, Shaffer HB. Reference Genome of the Black Surfperch, Embiotoca jacksoni (Embiotocidae, Perciformes), a California Kelp Forest Fish That Lacks a Pelagic Larval Stage. J Hered 2022; 113:657-664. [PMID: 35809222 PMCID: PMC9709976 DOI: 10.1093/jhered/esac034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Surfperches (Family Embiotocidae) are viviparous temperate reef fishes that brood their young. This life history trait translates into limited dispersal, strong population structure, and an unusually strong potential for local adaptation in a marine fish. As part of the California Conservation Genomics Project (CCGP), we sequenced the genome of the Black Surfperch, Embiotoca jacksoni, to establish a genomic model for understanding phylogeographic patterns of marine organisms in California. These patterns, in turn, may inform the design of marine protected areas using dispersal models based on genomic data. The genome of E. jacksoni is typical of marine fishes at less than 1Gb (genome size = 635 Mb), and our assembly is near-chromosome level (contig N50 = 6.5Mb, scaffold N50 = 15.5 Mb, BUSCO = 98.1%). Within the context of the CCGP, the genome will be used as a reference for future whole genome resequencing projects aimed at enhancing our knowledge of the population structure of the species, and efficacy of Marine Protected Areas across the state.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Jason A Toy
- Department of Ecology and Evolutionary Biology, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California–Davis, Davis, CA, USA
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California–Davis, Davis, CA, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California–Davis, Davis, CA, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California–Santa Cruz, Santa Cruz, CA, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, USA
| | - Courtney Miller
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California–Los Angeles, Los Angeles, CA, USA
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17
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Bernardi G, DeBiasse M, Escalona M, Marimuthu MPA, Nguyen O, Sacco S, Beraut E, Miller C, Toffelmier E, Shaffer HB. Reference Genome of the California Sheephead, Semicossyphus pulcher (Labridae, Perciformes), A Keystone Fish Predator in Kelp Forest Ecosystems. J Hered 2022; 113:649-656. [PMID: 35778264 PMCID: PMC9709978 DOI: 10.1093/jhered/esac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, CA 95060, USA
| | - Melissa DeBiasse
- School of Natural Sciences, University of California Merced, CA 95343, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, CA 95616, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, CA 95616, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, CA 95060, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, CA 95060, USA
| | - Courtney Miller
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA
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18
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Fiedler PL, Erickson B, Esgro M, Gold M, Hull JM, Norris J, Shapiro B, Westphal M, Toffelmier E, Shaffer HB. Seizing the Moment: The opportunity and relevance of the California Conservation Genomics Project to state and federal conservation policy. J Hered 2022; 113:589-596. [PMID: 36136001 PMCID: PMC9709969 DOI: 10.1093/jhered/esac046] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/05/2022] [Indexed: 11/14/2022] Open
Abstract
Conservation science and environmental regulation are sibling constructs of the latter half of the 20th century, part of a more general awakening to humanity's effect on the natural world in the wake of two world wars. Efforts to understand the evolution of biodiversity using the models of population genetics and the data derived from DNA sequencing, paired with legal and political mandates to protect biodiversity through novel laws, regulations, and conventions arose concurrently. The extremely rapid rate of development of new molecular tools to document and compare genetic identities, and the global goal of prioritizing species and habitats for protection are separate enterprises that have benefited from each other, ultimately leading to improved outcomes for each. In this article, we explore how the California Conservation Genomics Project has, and should, contribute to ongoing and future conservation implementation, and how it serves as a model for other geopolitical regions and taxon-oriented conservation efforts. One of our primary conclusions is that conservation genomics can now be applied, at scale, to inform decision-makers and identify regions and their contained species that are most resilient, and most in need of conservation interventions.
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Affiliation(s)
| | - Bjorn Erickson
- U.S. Fish and Wildlife Service, Sacramento, CA 95825 USA
| | - Michael Esgro
- Ocean Protection Council, California Resources Agency, Sacramento, California 95814 USA
| | - Mark Gold
- California Resources Agency, Sacramento, California 95814 USA
| | - Joshua M Hull
- U.S. Fish and Wildlife Service, Sacramento, CA 95825 USA
| | - Jennifer Norris
- California Resources Agency, Sacramento, California 95814 USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064 USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064 USA
| | - Michael Westphal
- U.S. Bureau of Land Management, 940 2nd Ave., Central Coast Field Office, Marina CA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA90095 USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095 USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA90095 USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095 USA
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19
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Anghel I, Jacobs SJ, Escalona M, Marimuthu MPA, Fairbairn CW, Beraut E, Nguyen O, Toffelmier E, Shaffer HB, Zapata F. Reference genome of the color polymorphic desert annual plant Linanthus parryae. J Hered 2022; 113:712-721. [DOI: 10.1093/jhered/esac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/12/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Linanthus parryae is a widespread annual plant species found in washes and sandy open habitats across the Mojave Desert and Eastern Sierra Nevada of California. Studies in this species have played a central role in evolutionary biology, serving as the first test cases of the shifting balance theory of evolution, models of isolation by distance, and metrics to describe the genetic structure of natural populations. Despite the importance of L. parryae in the development of landscape genetics and phylogeography, there are no genomic resources available for the species. Through the California Conservation Genomics Project, we assembled the first genome in the genus Linanthus. Using PacBio HiFi long reads and Hi-C chromatin conformation capture, we assembled 123 scaffolds spanning 1.51 Gb of the 1.96 Gb estimated genome, with a contig N50 of 18.7 Mb and a scaffold N50 of 124.8 Mb. This assembly, with a BUSCO completeness score of 88.7%, will allow us to revisit foundational ideas central to our understanding of how evolutionary forces operate in a geographic landscape. In addition, it will be a new resource to uncover adaptations to arid environments in the fragile desert habitat threatened by urban and solar farm development, climate change, and off-road vehicles.
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Affiliation(s)
- Ioana Anghel
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles , CA 90095, USA
| | - Sarah J Jacobs
- Department of Botany, California Academy of Sciences, San Francisco , CA, 94118, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz , CA 95064, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis , CA 95616, USA
| | - Colin W Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz , Santa Cruz, CA 95064, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz , Santa Cruz, CA 95064, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis , CA 95616, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles , CA 90095, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California , Los Angeles, Los Angeles, CA 90095-7239 USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles , CA 90095, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California , Los Angeles, Los Angeles, CA 90095-7239 USA
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles , CA 90095, USA
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20
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Cornwell BH, Beraut E, Fairbairn C, Nguyen O, Marimuthu MPA, Escalona M, Toffelmier E. "Reference genome assembly of the sunburst anemone, Anthopleura sola". J Hered 2022; 113:699-705. [PMID: 36074002 DOI: 10.1093/jhered/esac050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2022] [Indexed: 11/12/2022] Open
Abstract
The sunburst anemone Anthopleura sola is an abundant species inhabiting the intertidal zone of coastal California. Historically, this species has extended from Baja California, Mexico to as far north as Monterey Bay, CA. However, recently the geographic range of this species has expanded to Bodega Bay, CA, possibly as far north as Salt Point, CA. This species also forms symbiotic partnerships with the dinoflagellate Breviolum muscatinei, a member of the family Symbiodiniaceae. These partnerships are analogous to those formed between tropical corals and dinoflagellate symbionts, making A. sola an excellent model system to explore how hosts will (co)evolve with novel symbiont populations they encounter as they expand northward. This assembly will serve as the foundation for identifying the population genomic patterns associated with range expansions, and will facilitate future work investigating how hosts and their symbiont partners will evolve to interact with one another as geographic ranges shift due to climate change.
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Affiliation(s)
- Brendan H Cornwell
- Hopkins Marine Station of Stanford University, Pacific Grove, CA 93950, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
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21
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Beninde J, Toffelmier E, Shaffer HB. A brief history of population genetic research in California and an evaluation of its utility for conservation decision-making. J Hered 2022; 113:604-614. [PMID: 36056714 PMCID: PMC9709982 DOI: 10.1093/jhered/esac049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/01/2022] [Indexed: 11/14/2022] Open
Abstract
A recently published macrogenetic dataset of California's flora and fauna, CaliPopGen, comprehensively summarizes population genetic research published between 1985-2020. Integrating these genetic data into the requisite "best available science" upon which conservation professionals rely should facilitate the prioritization of populations based on genetic health. We evaluate the extent to which the CaliPopGen Dataset provides genetic diversity estimates that are 1) unbiased, 2) sufficient in quantity, 3) cover entire species' ranges, and 4) include potentially adaptive loci. We identified genetic diversity estimates for 4,462 spatially-referenced populations of 432 species, confirming California's rich published history of population genetics research. Most recent studies used microsatellites markers, which have uniquely high levels of variation, and estimates of all genetic metrics varied significantly across marker types. Most studies used less than 10 loci for inferences, rendering parameter estimates potentially unreliable, and covered small spatial extents that include only a fraction of the studied species' California distribution (median 16.3%). In contrast, the ongoing California Conservation Genomics Project (CCGP) aims to cover the full geographical and environmental breadth of each species' occupied habitats, and uses a consistent approach based on whole-genome data. However, the CCGP will sequence only 12% of the number of individuals, and covers only about half the evolutionary diversity, of the CaliPopGen Database. There is clearly a place in the evaluation of the genetic health of California for both approaches going forward, especially if differences among studies can be minimized, and overlap emphasized. A complementary use of both datasets is warranted to inform optimal conservation decision-making.
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Affiliation(s)
- Joscha Beninde
- UCLA La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Member, IUCN WCPA Connectivity Conservation Specialist Group
| | - Erin Toffelmier
- UCLA La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - H Bradley Shaffer
- UCLA La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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22
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Toffelmier E, Beninde J, Shaffer HB. The phylogeny of California, and how it informs setting multi-species conservation priorities. J Hered 2022; 113:597-603. [PMID: 36048626 PMCID: PMC9709974 DOI: 10.1093/jhered/esac045] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Incorporating measures of taxonomic diversity into research and management plans has long been a tenet of conservation science. Increasingly, active conservation programs are turning towards multi-species landscape and regional conservation actions, and away from single species approaches. This is both a reflection of changing trends in conservation science and advances in foundational technologies, including genomics and geospatial science. Multi-species approaches may provide more fundamental insights into evolutionary processes and equip managers with a more holistic understanding of the landscapes under their jurisdiction. Central to this approach are data generation and analyses which embrace and reflect a broad range of taxonomic diversity. Here we examine the family-level phylogenetic breadth of the California Conservation Genomics Project (CCGP) based on family-level phylogenetic diversity, family-level phylogenetic distinctness, and family richness. We place this in the context of the diversity present in California and compare it to the 35-plus years of genetic research compiled in the CaliPopGen Database. We found that the family-level phylogenetic diversity in the CCGP reflected that of California very well, slightly over-representing chordates and under-representing arthropods, and that 42% of CCGP phylogenetic diversity represented new contributions to genetic data for the state. In one focused effort, the CCGP was able to achieve roughly half the family-level phylogenetic diversity studied over the last several decades. To maximize studied phylogenetic diversity, future work should focus on arthropods, a conclusion that likely reflects the overall lack of attention to this hyper diverse clade.
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Affiliation(s)
- Erin Toffelmier
- UCLA La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Joscha Beninde
- UCLA La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Member, IUCN WCPA Connectivity Conservation Specialist Group
| | - H Bradley Shaffer
- UCLA La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
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23
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Wood DA, Richmond JQ, Escalona M, Marimuthu MPA, Nguyen O, Sacco S, Beraut E, Westphal M, Fisher RN, Vandergast AG, Toffelmier E, Wang IJ, Shaffer HB. Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern. J Hered 2022; 113:632-640. [PMID: 35939354 PMCID: PMC9923794 DOI: 10.1093/jhered/esac040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California's coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis 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 technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.
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Affiliation(s)
- Dustin A Wood
- Address correspondence to D.A. Wood at the address above, or e-mail:
| | - Jonathan Q Richmond
- Western Ecological Research Center, U.S. Geological Survey, 4165 Spruance Rd. Suite 200, San Diego CA 92101, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Michael Westphal
- U.S. Bureau of Land Management—Central Coast Field Office, Marina, CA 93933, USA
| | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, 4165 Spruance Rd. Suite 200, San Diego CA 92101, USA
| | - Amy G Vandergast
- Western Ecological Research Center, U.S. Geological Survey, 4165 Spruance Rd. Suite 200, San Diego CA 92101, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA,Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA
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24
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Grismer J, Scott P, Toffelmier E, Hinds B, Klabacka R, Stewart G, White V, Oaks J, Bradley Shaffer H. Genomic data reveal local endemism in Southern California Rubber Boas (Serpentes: Boidae, Charina) and the critical need for enhanced conservation actions. Mol Phylogenet Evol 2022; 174:107542. [PMID: 35690376 DOI: 10.1016/j.ympev.2022.107542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 10/18/2022]
Abstract
The mountains of southern California represent unique, isolated ecosystems that support distinct high-elevation habitats found nowhere else in the area. Analyses of several moisture-dependent species across these sky-islands indicate they exist as locally endemic lineages that occur across these fragmented mountains ranges. The Rubber Boa is a semi-fossorial snake species that is widely distributed in the cooler and more moist ecoregions regions of western North America, including isolated populations across southern California mountain ranges. We developed a genomic and ecological dataset to examine genetic diversity within Rubber Boas and to determine if the endemic Southern Rubber Boa represents a distinct lineage. We quantified current and future habitat suitability under a range of climate change scenarios, and discuss the possible environmental threats facing these unique montane isolates. Our results support four major lineages within Rubber Boas, with genetic breaks that are consistent with biogeographic boundaries observed in other co-distributed, cool-temperature, moisture adapted species. Our data support previous studies that the Southern Rubber Boa is an independent evolutionary unit and now includes multiple locally endemic sky-island populations, restricted to isolated mountain tops and ranges across southern California. Analyses of future habitat suitability indicate that many of these sky-island populations will lose most of their suitable habitat over the next 70 years given predicted increases in drought, rising temperatures, and wildfires. Collectively these data emphasize the critical conservation needs of these montane ecosystems in southern California under current and projected climate change conditions.
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Affiliation(s)
- Jesse Grismer
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA; Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA; Department of Biology, La Sierra University, Riverside, CA 92515, USA.
| | - Peter Scott
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA; Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, TX 79016, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Brian Hinds
- Department of Biology, La Sierra University, Riverside, CA 92515, USA
| | - Randy Klabacka
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - Glenn Stewart
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA 91768, USA
| | - Virginia White
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - Jamie Oaks
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
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25
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Todd BD, Jenkinson TS, Escalona M, Beraut E, Nguyen O, Sahasrabudhe R, Scott PA, Toffelmier E, Wang IJ, Shaffer HB. Reference genome of the northwestern pond turtle, Actinemys marmorata. J Hered 2022; 113:624-631. [PMID: 35665811 DOI: 10.1093/jhered/esac021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/10/2022] [Indexed: 11/12/2022] Open
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 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.
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Affiliation(s)
- Brian D Todd
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA, USA
| | - Thomas S Jenkinson
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, USA
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA, USA
| | - Peter A Scott
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, TX, USA
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - H B Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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Huang Y, Escalona M, Morrison G, Marimuthu MPA, Nguyen O, Toffelmier E, Shaffer HB, Litt A. Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca). J Hered 2022; 113:188-196. [PMID: 35575079 PMCID: PMC9113465 DOI: 10.1093/jhered/esab071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/18/2021] [Indexed: 01/30/2023] Open
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.
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Affiliation(s)
- Yi Huang
- Department of Botany and Plant Science, University of California, Riverside, Riverside, CA 92521, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Glen Morrison
- Department of Botany and Plant Science, University of California, Riverside, Riverside, CA 92521, USA
| | - Mohan P A Marimuthu
- UC Davis Genome Center, DNA Technologies and Expression Analysis Cores, University of California, Davis, CA 95691, USA
| | - Oanh Nguyen
- UC Davis Genome Center, DNA Technologies and Expression Analysis Cores, University of California, Davis, CA 95691, USA
| | - Erin Toffelmier
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA
- the La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA
| | - H Bradley Shaffer
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA
- the La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-7239, USA
| | - Amy Litt
- Department of Botany and Plant Science, University of California, Riverside, Riverside, CA 92521, USA
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Curd E, Pollinger J, Toffelmier E, Smith T. Rapid influenza A detection and quantitation in birds using a one-step real-time reverse transcriptase PCR and High Resolution Melting. J Virol Methods 2011; 176:125-30. [DOI: 10.1016/j.jviromet.2011.05.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 05/16/2011] [Accepted: 05/25/2011] [Indexed: 10/18/2022]
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Njabo KY, Cornel AJ, Bonneaud C, Toffelmier E, Sehgal RNM, Valkiūnas G, Russell AF, Smith TB. Nonspecific patterns of vector, host and avian malaria parasite associations in a central African rainforest. Mol Ecol 2010; 20:1049-61. [PMID: 21134011 DOI: 10.1111/j.1365-294x.2010.04904.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Malaria parasites use vertebrate hosts for asexual multiplication and Culicidae mosquitoes for sexual and asexual development, yet the literature on avian malaria remains biased towards examining the asexual stages of the life cycle in birds. To fully understand parasite evolution and mechanism of malaria transmission, knowledge of all three components of the vector-host-parasite system is essential. Little is known about avian parasite-vector associations in African rainforests where numerous species of birds are infected with avian haemosporidians of the genera Plasmodium and Haemoproteus. Here we applied high resolution melt qPCR-based techniques and nested PCR to examine the occurrence and diversity of mitochondrial cytochrome b gene sequences of haemosporidian parasites in wild-caught mosquitoes sampled across 12 sites in Cameroon. In all, 3134 mosquitoes representing 27 species were screened. Mosquitoes belonging to four genera (Aedes, Coquillettidia, Culex and Mansonia) were infected with twenty-two parasite lineages (18 Plasmodium spp. and 4 Haemoproteus spp.). Presence of Plasmodium sporozoites in salivary glands of Coquillettidia aurites further established these mosquitoes as likely vectors. Occurrence of parasite lineages differed significantly among genera, as well as their probability of being infected with malaria across species and sites. Approximately one-third of these lineages were previously detected in other avian host species from the region, indicating that vertebrate host sharing is a common feature and that avian Plasmodium spp. vector breadth does not always accompany vertebrate-host breadth. This study suggests extensive invertebrate host shifts in mosquito-parasite interactions and that avian Plasmodium species are most likely not tightly coevolved with vector species.
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Affiliation(s)
- K Y Njabo
- Center for Tropical Research, UCLA Institute of the Environment, Los Angeles, CA 90095, USA.
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Fuller TL, Saatchi SS, Curd EE, Toffelmier E, Thomassen HA, Buermann W, DeSante DF, Nott MP, Saracco JF, Ralph CJ, Alexander JD, Pollinger JP, Smith TB. Mapping the risk of avian influenza in wild birds in the US. BMC Infect Dis 2010; 10:187. [PMID: 20573228 PMCID: PMC2912310 DOI: 10.1186/1471-2334-10-187] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2010] [Accepted: 06/23/2010] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Avian influenza virus (AIV) is an important public health issue because pandemic influenza viruses in people have contained genes from viruses that infect birds. The H5 and H7 AIV subtypes have periodically mutated from low pathogenicity to high pathogenicity form. Analysis of the geographic distribution of AIV can identify areas where reassortment events might occur and how high pathogenicity influenza might travel if it enters wild bird populations in the US. Modelling the number of AIV cases is important because the rate of co-infection with multiple AIV subtypes increases with the number of cases and co-infection is the source of reassortment events that give rise to new strains of influenza, which occurred before the 1968 pandemic. Aquatic birds in the orders Anseriformes and Charadriiformes have been recognized as reservoirs of AIV since the 1970s. However, little is known about influenza prevalence in terrestrial birds in the order Passeriformes. Since passerines share the same habitat as poultry, they may be more effective transmitters of the disease to humans than aquatic birds. We analyze 152 passerine species including the American Robin (Turdus migratorius) and Swainson's Thrush (Catharus ustulatus). METHODS We formulate a regression model to predict AIV cases throughout the US at the county scale as a function of 12 environmental variables, sampling effort, and proximity to other counties with influenza outbreaks. Our analysis did not distinguish between types of influenza, including low or highly pathogenic forms. RESULTS Analysis of 13,046 cloacal samples collected from 225 bird species in 41 US states between 2005 and 2008 indicates that the average prevalence of influenza in passerines is greater than the prevalence in eight other avian orders. Our regression model identifies the Great Plains and the Pacific Northwest as high-risk areas for AIV. Highly significant predictors of AIV include the amount of harvested cropland and the first day of the year when a county is snow free. CONCLUSIONS Although the prevalence of influenza in waterfowl has long been appreciated, we show that 22 species of song birds and perching birds (order Passeriformes) are influenza reservoirs in the contiguous US.
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Affiliation(s)
- Trevon L Fuller
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, La Kretz Hall, Suite 300, Box 951496, Los Angeles, CA 90095-1496, USA
| | - Sassan S Saatchi
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, La Kretz Hall, Suite 300, Box 951496, Los Angeles, CA 90095-1496, USA
- Radar Science Technical Group, Radar Science & Engineering Section, Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109-8099, USA
| | - Emily E Curd
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, La Kretz Hall, Suite 300, Box 951496, Los Angeles, CA 90095-1496, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Erin Toffelmier
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, La Kretz Hall, Suite 300, Box 951496, Los Angeles, CA 90095-1496, USA
| | - Henri A Thomassen
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, La Kretz Hall, Suite 300, Box 951496, Los Angeles, CA 90095-1496, USA
| | - Wolfgang Buermann
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, La Kretz Hall, Suite 300, Box 951496, Los Angeles, CA 90095-1496, USA
- Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles, Los Angeles, CA 90095-1565, USA
| | - David F DeSante
- The Institute for Bird Populations, P.O. Box 1346, Point Reyes Station, CA 94956-1346, USA
| | - Mark P Nott
- The Institute for Bird Populations, P.O. Box 1346, Point Reyes Station, CA 94956-1346, USA
| | - James F Saracco
- The Institute for Bird Populations, P.O. Box 1346, Point Reyes Station, CA 94956-1346, USA
| | - CJ Ralph
- U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station, Redwood Sciences Laboratory, 1700 Bayview Drive, Arcata, CA 95521, USA
| | | | - John P Pollinger
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, La Kretz Hall, Suite 300, Box 951496, Los Angeles, CA 90095-1496, USA
| | - Thomas B Smith
- Center for Tropical Research, Institute of the Environment, University of California, Los Angeles, La Kretz Hall, Suite 300, Box 951496, Los Angeles, CA 90095-1496, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA
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