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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] [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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Marino A, Reboud EL, Chevalier E, Tilak MK, Contreras-Garduño J, Nabholz B, Condamine FL. Genomics of the relict species Baronia brevicornis sheds light on its demographic history and genome size evolution across swallowtail butterflies. G3 (BETHESDA, MD.) 2023; 13:jkad239. [PMID: 37847748 PMCID: PMC10700114 DOI: 10.1093/g3journal/jkad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 05/22/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023]
Abstract
Relict species, like coelacanth, gingko, tuatara, are the remnants of formerly more ecologically and taxonomically diverse lineages. It raises the questions of why they are currently species-poor, have restrained ecology, and are often vulnerable to extinction. Estimating heterozygosity level and demographic history can guide our understanding of the evolutionary history and conservation status of relict species. However, few studies have focused on relict invertebrates compared to vertebrates. We sequenced the genome of Baronia brevicornis (Lepidoptera: Papilionidae), which is an endangered species, the sister species of all swallowtail butterflies, and is the oldest lineage of all extant butterflies. From a dried specimen, we were able to generate both long-read and short-read data and assembled a genome of 406 Mb for Baronia. We found a fairly high level of heterozygosity (0.58%) compared to other swallowtail butterflies, which contrasts with its endangered and relict status. Taking into account the high ratio of recombination over mutation, demographic analyses indicated a sharp decline of the effective population size initiated in the last million years. Moreover, the Baronia genome was used to study genome size variation in Papilionidae. Genome sizes are mostly explained by transposable elements activities, suggesting that large genomes appear to be a derived feature in swallowtail butterflies as transposable elements activity is recent and involves different transposable elements classes among species. This first Baronia genome provides a resource for assisting conservation in a flagship and relict insect species as well as for understanding swallowtail genome evolution.
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Affiliation(s)
- Alba Marino
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Eliette L Reboud
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Emmanuelle Chevalier
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Marie-Ka Tilak
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Jorge Contreras-Garduño
- Universidad Nacional Autónoma de México, Escuela Nacional de Estudios Superiores, campus Morelia, Antigua Carretera a Pátzcuaro #8701, Col. Ex-Hacienda San José de la Huerta, 58190 Morelia, Michoacán, Mexico
| | - Benoit Nabholz
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Place Eugène Bataillon, 34095 Montpellier, France
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