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Bailey CA, Righton AL, Reeves A, Ray D, Krebs J, Louis EE. Facultative parthenogenesis discovered for the first time in Jamaican boa (Chilabothrus subflavus) using novel microsatellite markers. Zoo Biol 2024. [PMID: 39172112 DOI: 10.1002/zoo.21852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 08/23/2024]
Abstract
The mode of reproduction most often seen in snakes is sexual, but studies have noted facultative parthenogenesis in at least six families. Here, we provide evidence for the first observed case of facultative parthenogenesis in a captive Jamaican boa (Chilabothrus subflavus). A 7-year-old female Jamaican boa, isolated since birth, was found to have produced a litter of 15 offspring. To provide molecular DNA evidence of parthenogenesis, 13 new microsatellite loci were isolated in the species. All offspring were found to be homozygous at each locus and only possess alleles found in the dam, implicating that they were born from asexual reproduction. Several developmental abnormalities, including stillbirths and spinal deformities, were noted in the litter which may be explained by their increased level of homozygosity. To preserve genetic diversity in the captive population, research should be conducted to understand the prevalence of this mode of reproduction and to guide future management decisions of this IUCN listed Vulnerable species.
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Affiliation(s)
- Carolyn A Bailey
- Department of Genetics, Bill and Berniece Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA
| | | | - Andy Reeves
- Department of Reptiles, Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA
| | - Dylan Ray
- Department of Reptiles, Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA
| | - Jessi Krebs
- Department of Reptiles, Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA
| | - Edward E Louis
- Department of Genetics, Bill and Berniece Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA
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2
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Sperling AL, Fabian DK, Garrison E, Glover DM. Protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies. STAR Protoc 2024; 5:102974. [PMID: 38581676 PMCID: PMC11002874 DOI: 10.1016/j.xpro.2024.102974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/02/2023] [Accepted: 03/06/2024] [Indexed: 04/08/2024] Open
Abstract
De novo genome assemblies are common tools for examining novel biological phenomena in non-model organisms. Here, we present a protocol for preparing Drosophila genomic DNA to create chromosome-level de novo genome assemblies. We describe steps for high-molecular-weight DNA preparation with phenol or Genomic-tips, quality control, long-read nanopore sequencing, short-read DNA library preparation, and sequencing. We then detail procedures of genome assembly, annotation, and assessment that can be used for downstream comparison and functional analysis. For complete details on the use and execution of this protocol, please refer to Sperling et al.1.
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Affiliation(s)
- Alexis L Sperling
- University of Cambridge; Department of Genetics, Cambridge CB2 3EH, UK.
| | - Daniel K Fabian
- University of Cambridge; Department of Genetics, Cambridge CB2 3EH, UK
| | - Erik Garrison
- University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - David M Glover
- University of Cambridge; Department of Genetics, Cambridge CB2 3EH, UK; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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3
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Ho DV, Tormey D, Odell A, Newton AA, Schnittker RR, Baumann DP, Neaves WB, Schroeder MR, Sigauke RF, Barley AJ, Baumann P. Post-meiotic mechanism of facultative parthenogenesis in gonochoristic whiptail lizard species. eLife 2024; 13:e97035. [PMID: 38847388 PMCID: PMC11161175 DOI: 10.7554/elife.97035] [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: 02/18/2024] [Accepted: 05/17/2024] [Indexed: 06/09/2024] Open
Abstract
Facultative parthenogenesis (FP) has historically been regarded as rare in vertebrates, but in recent years incidences have been reported in a growing list of fish, reptile, and bird species. Despite the increasing interest in the phenomenon, the underlying mechanism and evolutionary implications have remained unclear. A common finding across many incidences of FP is either a high degree of homozygosity at microsatellite loci or low levels of heterozygosity detected in next-generation sequencing data. This has led to the proposal that second polar body fusion following the meiotic divisions restores diploidy and thereby mimics fertilization. Here, we show that FP occurring in the gonochoristic Aspidoscelis species A. marmoratus and A. arizonae results in genome-wide homozygosity, an observation inconsistent with polar body fusion as the underlying mechanism of restoration. Instead, a high-quality reference genome for A. marmoratus and analysis of whole-genome sequencing from multiple FP and control animals reveals that a post-meiotic mechanism gives rise to homozygous animals from haploid, unfertilized oocytes. Contrary to the widely held belief that females need to be isolated from males to undergo FP, females housed with conspecific and heterospecific males produced unfertilized eggs that underwent spontaneous development. In addition, offspring arising from both fertilized eggs and parthenogenetic development were observed to arise from a single clutch. Strikingly, our data support a mechanism for facultative parthenogenesis that removes all heterozygosity in a single generation. Complete homozygosity exposes the genetic load and explains the high rate of congenital malformations and embryonic mortality associated with FP in many species. Conversely, for animals that develop normally, FP could potentially exert strong purifying selection as all lethal recessive alleles are purged in a single generation.
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Affiliation(s)
- David V Ho
- Department of Biology, Johannes Gutenberg UniversityMainzGermany
- Institute of Quantitative and Computational Biosciences, Johannes Gutenberg UniversityMainzGermany
| | - Duncan Tormey
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Aaron Odell
- Department of Biology, Johannes Gutenberg UniversityMainzGermany
| | | | | | - Diana P Baumann
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | | | | | - Anthony J Barley
- School of Mathematical and Natural Sciences, Arizona State University–West Valley CampusGlendaleUnited States
| | - Peter Baumann
- Department of Biology, Johannes Gutenberg UniversityMainzGermany
- Institute of Quantitative and Computational Biosciences, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular BiologyMainzGermany
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Chen Q, Wu B, Li C, Ding L, Huang S, Wang J, Zhao J. Deciphering male influence in gynogenetic Pengze crucian carp ( Carassius auratus var. pengsenensis): insights from Nanopore sequencing of structural variations. Front Genet 2024; 15:1392110. [PMID: 38784042 PMCID: PMC11111978 DOI: 10.3389/fgene.2024.1392110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/11/2024] [Indexed: 05/25/2024] Open
Abstract
In this study, we investigate gynogenetic reproduction in Pengze Crucian Carp (Carassius auratus var. pengsenensis) using third-generation Nanopore sequencing to uncover structural variations (SVs) in offspring. Our objective was to understand the role of male genetic material in gynogenesis by examining the genomes of both parents and their offspring. We discovered a notable number of male-specific structural variations (MSSVs): 1,195 to 1,709 MSSVs in homologous offspring, accounting for approximately 0.52%-0.60% of their detected SVs, and 236 to 350 MSSVs in heterologous offspring, making up about 0.10%-0.13%. These results highlight the significant influence of male genetic material on the genetic composition of offspring, particularly in homologous pairs, challenging the traditional view of asexual reproduction. The gene annotation of MSSVs revealed their presence in critical gene regions, indicating potential functional impacts. Specifically, we found 5 MSSVs in the exonic regions of protein-coding genes in homologous offspring, suggesting possible direct effects on protein structure and function. Validation of an MSSV in the exonic region of the polyunsaturated fatty acid 5-lipoxygenase gene confirmed male genetic material transmission in some offspring. This study underscores the importance of further research on the genetic diversity and gynogenesis mechanisms, providing valuable insights for reproductive biology, aquaculture, and fostering innovation in biological research and aquaculture practices.
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Affiliation(s)
- Qianhui Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Biyu Wu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Chao Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Liyun Ding
- Jiangxi Fisheries Research Institute, Nanchang, China
| | - Shiting Huang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jun Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
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Sperling AL, Glover DM. Aneuploidy during development in facultative parthenogenetic Drosophila. Heredity (Edinb) 2024; 132:89-97. [PMID: 38017115 PMCID: PMC10844303 DOI: 10.1038/s41437-023-00664-z] [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: 07/22/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
From concatenated chromosomes to polyploidization, large-scale genome changes are known to occur in parthenogenetic animals. Here, we report mosaic aneuploidy in larval brains of facultatively parthenogenetic Drosophila. We identified a background of aneuploidy in D. mercatorum strains and found increased levels of aneuploidy in the larval brain tissue of animals arising parthenogenetically versus those arising from sexual reproduction. There is also intra-individual variation in germline-derived aneuploidy within the same strain. To determine if this is a general feature of facultative parthenogenesis in drosophilids, we compared sexually reproduced and parthenogenetic offspring from an engineered facultative parthenogenetic strain of D. melanogaster. In addition to germline-derived aneuploidy, this revealed somatic aneuploidy that increased by up to fourfold in parthenogens compared to sexually reproduced offspring. Therefore, the genetic combination identified in D. mercatorum that causes facultative parthenogenesis in D. melanogaster results in aneuploidy, which indicates that the loss of mitotic control resulting in parthenogenesis causes subsequent genome variation within the parthenogenetic offspring. Our findings challenge the assumption that parthenogenetic offspring are near genetic replicas of their mothers.
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Affiliation(s)
- A L Sperling
- Department of Genetics, University of Cambridge, Cambridge, UK.
| | - D M Glover
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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Sperling AL, Glover DM. Protocol for screening facultative parthenogenesis in Drosophila. STAR Protoc 2023; 4:102585. [PMID: 37740913 PMCID: PMC10520562 DOI: 10.1016/j.xpro.2023.102585] [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: 07/12/2023] [Revised: 08/01/2023] [Accepted: 08/30/2023] [Indexed: 09/25/2023] Open
Abstract
Most species of sexually reproducing Drosophila are capable of some degree of facultative parthenogenesis, which involves the initiation of development in an unfertilized egg. Here, we present an optimized protocol to screen facultative parthenogenesis in Drosophila. We describe steps for the collection and maintenance of virgin flies. We then detail offspring screening for the analysis of parthenogenesis. This protocol can be applied to different Drosophila strains and can be adapted for the analysis of parthenogenesis in other animals. For complete details on the use and execution of this protocol, please refer to Sperling et al.1.
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Affiliation(s)
- Alexis L Sperling
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH Cambridgeshire, UK.
| | - David M Glover
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH Cambridgeshire, UK; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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Thomalla JM, Wolfner MF. Reproductive biology: A genetic recipe for parthenogenesis. Curr Biol 2023; 33:R904-R906. [PMID: 37699347 PMCID: PMC10753294 DOI: 10.1016/j.cub.2023.07.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
New work reveals differences in oogenic gene expression between parthenogenetic and sexually reproducing Drosophila mercatorum strains. Recapitulating those changes in D. melanogaster oocytes induced parthenogenesis in this normally sexually reproducing species, providing molecular insight into how these reproductive modes arise.
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Affiliation(s)
- Jonathon M Thomalla
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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Oza A. 'Virgin birth' genetically engineered into female animals for the first time. Nature 2023:10.1038/d41586-023-02404-z. [PMID: 37507507 DOI: 10.1038/d41586-023-02404-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
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