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Kozak KM, Escalona M, Chumchim N, Fairbairn C, Marimuthu MPA, Nguyen O, Sahasrabudhe R, Seligmann W, Conroy C, Patton JL, Bowie RCK, Nachman MW. A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris. J Hered 2024; 115:130-138. [PMID: 37793045 PMCID: PMC10838119 DOI: 10.1093/jhered/esad060] [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: 06/29/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023] Open
Abstract
The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.
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Affiliation(s)
- Krzysztof M Kozak
- Museum of Vertebrate Zoology and Department of Integrative Biology, 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
| | - Noravit Chumchim
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, 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
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States
| | - William Seligmann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States
| | - Chris Conroy
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, United States
| | - James L Patton
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, United States
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, United States
| | - Michael W Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, United States
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Zeng Q, Zhou Z, He Q, Li L, Pu F, Yan M, Xu P. Chromosome-level haplotype-resolved genome assembly for Takifugu ocellatus using PacBio and Hi-C technologies. Sci Data 2023; 10:22. [PMID: 36631464 PMCID: PMC9834249 DOI: 10.1038/s41597-023-01937-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Takifugu species serve as a model system for evolutionary studies due to their compact genomes and diverse phenotypes. The ocellated puffer (Takifugu ocellatus), characterized by special colouration, is a scarce anadromous species in the genus Takifugu. As an ornamental and tasty fish species, T. ocellatus has moderate economic value. However, the available genomic resources for this pufferfish are still limited. Here, a chromosome-level reference genome, as well as two haploid genomes, was constructed by PacBio HiFi long sequencing and Hi-C technologies. The total length of the reference genome was 375.62 Mb with a contig N50 of 11.55 Mb. The assembled sequences were anchored to 22 chromosomes with an integration efficiency of 93.78%. Furthermore, 28,808 protein-coding genes were predicted. The haplotype-resolved reference genome of T. ocellatus provides a crucial resource for investigating the explosive speciation of the Takifugu genus, such as elucidating evolutionary histories, determining the genetic basis of trait evolution, and supporting future conservation efforts.
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Affiliation(s)
- Qingmin Zeng
- Fisheries Research Institute of Fujian, Xiamen, 361000, China
| | - Zhixiong Zhou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Qian He
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Leibin Li
- Fisheries Research Institute of Fujian, Xiamen, 361000, China
| | - Fei Pu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Mengzhen Yan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
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Wilder AP, Dudchenko O, Curry C, Korody M, Turbek SP, Daly M, Misuraca A, Gaojianyong WANG, Khan R, Weisz D, Fronczek J, Aiden EL, Houck ML, Shier DM, Ryder OA, Steiner CC. A chromosome-length reference genome for the endangered Pacific pocket mouse reveals recent inbreeding in a historically large population. Genome Biol Evol 2022; 14:6650481. [PMID: 35894178 PMCID: PMC9348616 DOI: 10.1093/gbe/evac122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
High-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity (ROH) >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load.
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Affiliation(s)
- Aryn P Wilder
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA.,Center for Theoretical Biological Physics and Department of Computer Science, Rice University, USA
| | - Caitlin Curry
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Marisa Korody
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Sheela P Turbek
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA.,Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | | | - Ann Misuraca
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - W A N G Gaojianyong
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
| | - Julie Fronczek
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA.,Center for Theoretical Biological Physics and Department of Computer Science, Rice University, USA.,UWA School of Agriculture and Environment, The University of Western Australia, Australia.,Broad Institute of MIT and Harvard, USA.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, China
| | - Marlys L Houck
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Debra M Shier
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA.,Department of Ecology & Evolutionary Biology, University of California Los Angeles, USA
| | - Oliver A Ryder
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Cynthia C Steiner
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
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