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Villegas LI, Ferretti L, Wiehe T, Waldvogel A, Schiffer PH. Parthenogenomics: Insights on mutation rates and nucleotide diversity in parthenogenetic Panagrolaimus nematodes. Ecol Evol 2024; 14:e10831. [PMID: 38192904 PMCID: PMC10771965 DOI: 10.1002/ece3.10831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024] Open
Abstract
Asexual reproduction is assumed to lead to the accumulation of deleterious mutations, and reduced heterozygosity due to the absence of recombination. Panagrolaimid nematode species display different modes of reproduction. Sexual reproduction with distinct males and females, asexual reproduction through parthenogenesis in the genus Panagrolaimus, and hermaphroditism in Propanagrolaimus. Here, we compared genomic features of free-living nematodes in populations and species isolated from geographically distant regions to study diversity, and genome-wide differentiation under different modes of reproduction. We firstly estimated genome-wide spontaneous mutation rates in a triploid parthenogenetic Panagrolaimus, and a diploid hermaphroditic Propanagrolaimus via long-term mutation accumulation lines. Secondly, we calculated population genetic parameters including nucleotide diversity, and fixation index (F ST) between populations of asexually and sexually reproducing nematodes. Thirdly, we used phylogenetic network methods on sexually and asexually reproducing Panagrolaimus populations to understand evolutionary relationships between them. The estimated mutation rate was slightly lower for the asexual population, as expected for taxa with this reproductive mode. Natural polyploid asexual populations revealed higher nucleotide diversity. Despite their common ancestor, a gene network revealed a high level of genetic differentiation among asexual populations. The elevated heterozygosity found in the triploid parthenogens could be explained by the third genome copy. Given their tendentially lower mutation rates it can be hypothesized that this is part of the mechanism to evade Muller's ratchet. Our findings in parthenogenetic triploid nematode populations seem to challenge common expectations of evolution under asexuality.
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Affiliation(s)
| | | | - Thomas Wiehe
- Institute for GeneticsUniversity of CologneKölnGermany
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Tran Van P, Anselmetti Y, Bast J, Dumas Z, Galtier N, Jaron KS, Martens K, Parker DJ, Robinson-Rechavi M, Schwander T, Simion P, Schön I. First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes. G3 (BETHESDA, MD.) 2021; 11:jkab043. [PMID: 33591306 PMCID: PMC8049415 DOI: 10.1093/g3journal/jkab043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 11/14/2022]
Abstract
Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of nonmarine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382 Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from nonmarine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.
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Affiliation(s)
- Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Yoann Anselmetti
- ISEM—Institut des Sciences de l’Evolution, Montpellier 34090, France
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Galtier
- ISEM—Institut des Sciences de l’Evolution, Montpellier 34090, France
| | - Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Koen Martens
- Royal Belgian Institute of Natural Sciences, OD Nature, Freshwater Biology, Brussels 1000, Belgium
- Department of Biology, University of Ghent, Ghent 9000, Belgium
| | - Darren J Parker
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Paul Simion
- ISEM—Institut des Sciences de l’Evolution, Montpellier 34090, France
- Université de Namur, LEGE, URBE, Namur 5000, Belgium
| | - Isa Schön
- Royal Belgian Institute of Natural Sciences, OD Nature, Freshwater Biology, Brussels 1000, Belgium
- University of Hasselt, Research Group Zoology, Diepenbeek 3590, Belgium
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de Oliveira EA, Bertollo LAC, Rab P, Ezaz T, Yano CF, Hatanaka T, Jegede OI, Tanomtong A, Liehr T, Sember A, Maruyama SR, Feldberg E, Viana PF, Cioffi MDB. Cytogenetics, genomics and biodiversity of the South American and African Arapaimidae fish family (Teleostei, Osteoglossiformes). PLoS One 2019; 14:e0214225. [PMID: 30908514 PMCID: PMC6433368 DOI: 10.1371/journal.pone.0214225] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/09/2019] [Indexed: 11/19/2022] Open
Abstract
Osteoglossiformes represents one of the most ancestral teleost lineages, currently widespread over almost all continents, except for Antarctica. However, data involving advanced molecular cytogenetics or comparative genomics are yet largely limited for this fish group. Therefore, the present investigations focus on the osteoglossiform family Arapaimidae, studying a unique fish model group with advanced molecular cytogenetic genomic tools. The aim is to better explore and clarify certain events and factors that had impact on evolutionary history of this fish group. For that, both South American and African representatives of Arapaimidae, namely Arapaima gigas and Heterotis niloticus, were examined. Both species differed markedly by diploid chromosome numbers, with 2n = 56 found in A. gigas and 2n = 40 exhibited by H. niloticus. Conventional cytogenetics along with fluorescence in situ hybridization revealed some general trends shared by most osteoglossiform species analyzed thus far, such as the presence of only one chromosome pair bearing 18S and 5S rDNA sites and karyotypes dominated by acrocentric chromosomes, resembling thus the patterns of hypothetical ancestral teleost karyotype. Furthermore, the genomes of A. gigas and H. niloticus display remarkable divergence in terms of repetitive DNA content and distribution, as revealed by comparative genomic hybridization (CGH). On the other hand, genomic diversity of single copy sequences studied through principal component analyses (PCA) based on SNP alleles genotyped by the DArT seq procedure demonstrated a very low genetic distance between the South American and African Arapaimidae species; this pattern contrasts sharply with the scenario found in other osteoglossiform species. Underlying evolutionary mechanisms potentially explaining the obtained data have been suggested and discussed.
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Affiliation(s)
- Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
- Secretaria de Estado de Educação de Mato Grosso–SEDUC-MT, Cuiabá, MT, Brazil
| | - Luiz Antonio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
| | - Petr Rab
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Czech Republic
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
| | | | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, KhonKaen University, Muang, KhonKaen, Thailand
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Czech Republic
| | - Sandra Regina Maruyama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Laboratório de Genética Animal, Petrópolis, CEP: Manaus, AM, Brazil
| | - Patrik Ferreira Viana
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Laboratório de Genética Animal, Petrópolis, CEP: Manaus, AM, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
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