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Golinelli L, Geens E, Irvine A, McCoy CJ, Vandewyer E, Atkinson LE, Mousley A, Temmerman L, Beets I. Global analysis of neuropeptide receptor conservation across phylum Nematoda. BMC Biol 2024; 22:223. [PMID: 39379997 PMCID: PMC11462694 DOI: 10.1186/s12915-024-02017-6] [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: 03/15/2024] [Accepted: 09/19/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND The phylum Nematoda is incredibly diverse and includes many parasites of humans, livestock, and plants. Peptide-activated G protein-coupled receptors (GPCRs) are central to the regulation of physiology and numerous behaviors, and they represent appealing pharmacological targets for parasite control. Efforts are ongoing to characterize the functions and define the ligands of nematode GPCRs, with already most peptide GPCRs known or predicted in Caenorhabditis elegans. However, comparative analyses of peptide GPCR conservation between C. elegans and other nematode species are limited, and many nematode GPCRs remain orphan. A phylum-wide perspective on peptide GPCR profiles will benefit functional and applied studies of nematode peptide GPCRs. RESULTS We constructed a pan-phylum resource of C. elegans peptide GPCR orthologs in 125 nematode species using a semi-automated pipeline for analysis of predicted proteome datasets. The peptide GPCR profile varies between nematode species of different phylogenetic clades and multiple C. elegans peptide GPCRs have orthologs across the phylum Nematoda. We identified peptide ligands for two highly conserved orphan receptors, NPR-9 and NPR-16, that belong to the bilaterian galanin/allatostatin A (Gal/AstA) and somatostatin/allatostatin C (SST/AstC) receptor families. The AstA-like NLP-1 peptides activate NPR-9 in cultured cells and are cognate ligands of this receptor in vivo. In addition, we discovered an AstC-type peptide, NLP-99, that activates the AstC-type receptor NPR-16. In our pan-phylum resource, the phylum-wide representation of NPR-9 and NPR-16 resembles that of their cognate ligands more than those of allatostatin-like peptides that do not activate these receptors. CONCLUSIONS The repertoire of C. elegans peptide GPCR orthologs varies across phylogenetic clades and several peptide GPCRs show broad conservation in the phylum Nematoda. Our work functionally characterizes the conserved receptors NPR-9 and NPR-16 as the respective GPCRs for the AstA-like NLP-1 peptides and the AstC-related peptide NLP-99. NLP-1 and NLP-99 are widely conserved in nematodes and their representation matches that of their receptor in most species. These findings demonstrate the conservation of a functional Gal/AstA and SST/AstC signaling system in nematodes. Our dataset of C. elegans peptide GPCR orthologs also lays a foundation for further functional studies of peptide GPCRs in the widely diverse nematode phylum.
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Affiliation(s)
- Luca Golinelli
- Animal Physiology and Neurobiology, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000, Leuven, Belgium
| | - Ellen Geens
- Animal Physiology and Neurobiology, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000, Leuven, Belgium
| | - Allister Irvine
- Microbes & Pathogen Biology, School of Biological Sciences, The Institute for Global Food Security, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Ciaran J McCoy
- Microbes & Pathogen Biology, School of Biological Sciences, The Institute for Global Food Security, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Elke Vandewyer
- Animal Physiology and Neurobiology, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000, Leuven, Belgium
| | - Louise E Atkinson
- Microbes & Pathogen Biology, School of Biological Sciences, The Institute for Global Food Security, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Angela Mousley
- Microbes & Pathogen Biology, School of Biological Sciences, The Institute for Global Food Security, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000, Leuven, Belgium.
| | - Isabel Beets
- Animal Physiology and Neurobiology, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59, 3000, Leuven, Belgium.
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Kim S, Kim J. Units containing telomeric repeats are prevalent in subtelomeric regions of a Mesorhabditis isolate collected from the Republic of Korea. Genes Genomics 2024:10.1007/s13258-024-01576-w. [PMID: 39367283 DOI: 10.1007/s13258-024-01576-w] [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: 03/18/2024] [Accepted: 09/11/2024] [Indexed: 10/06/2024]
Abstract
BACKGROUND Mesorhabditis is known for its somatic genome being only a small portion of the germline genome due to programmed DNA elimination. This phenotype may be associated with the maintenance of telomeres at the ends of fragmented somatic chromosomes. OBJECTIVE To comprehensively investigate the telomeric regions of Mesorhabditis nematodes at the sequence level, we endeavored to collect a Mesorhabditis nematode in the Republic of Korea and acquire its highly contiguous genome sequences. METHODS We isolated a Mesorhabditis nematode and assembled its 108-Mb draft genome using both 6.3 Gb (53 ×) of short-read and 3.0 Gb (25 × , N50 = 5.7 kb) of nanopore-based long-read sequencing data. Our genome assembly exhibits comparable quality to the public genome of Mesorhabditis belari in terms of contiguity and evolutionary conserved genes. RESULTS Unexpectedly, our Mesorhabditis genome has many more interstitial telomeric sequences (ITSs), specifically subtelomeric ones, compared to the genomes of Caenorhabditis elegans and M. belari. Moreover, several subtelomeric sequences containing ITSs had 4-26 homologous sequences, implying they are highly repetitive. Based on this highly repetitive nature, we hypothesize that subtelomeric ITSs might have accumulated through the action of transposable elements containing ITSs. CONCLUSIONS It still remains elusive whether these ITS-containing units are associated with programmed DNA elimination, but they may facilitate new telomere formation after DNA elimination. Our genomic resources for Mesorhabditis can aid in understanding how its distinct phenotypes have evolved.
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Affiliation(s)
- Seoyeon Kim
- Department of Convergent Bioscience and Informatics, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jun Kim
- Department of Convergent Bioscience and Informatics, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Darras H, Pan Q. Clonal ants reveal a potentially hidden meiotic feature. Trends Genet 2024:S0168-9525(24)00208-7. [PMID: 39271396 DOI: 10.1016/j.tig.2024.08.011] [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: 08/26/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024]
Abstract
Meiosis is essential for eukaryotic reproduction and provides the basis for Mendel's segregation laws. A recent study by Lacy et al. identified a significant deviation from these laws in a clonal ant, hinting at a potentially overlooked meiotic feature. This discovery may have broader implications for recombination in nonclonal eukaryotes.
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Affiliation(s)
- Hugo Darras
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany.
| | - Qiaowei Pan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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Blanc C, Delattre M. A new type of non-Mendelian segregation. Nat Ecol Evol 2024; 8:1387-1388. [PMID: 39014143 DOI: 10.1038/s41559-024-02482-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Affiliation(s)
- Caroline Blanc
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Marie Delattre
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Inserm, UCBL, Lyon, France.
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Lacy KD, Hart T, Kronauer DJC. Co-inheritance of recombined chromatids maintains heterozygosity in a parthenogenetic ant. Nat Ecol Evol 2024; 8:1522-1533. [PMID: 39014144 PMCID: PMC11310076 DOI: 10.1038/s41559-024-02455-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: 02/08/2024] [Accepted: 05/30/2024] [Indexed: 07/18/2024]
Abstract
According to Mendel's second law, chromosomes segregate randomly in meiosis. Non-random segregation is primarily known for cases of selfish meiotic drive in females, in which particular alleles bias their own transmission into the oocyte. Here we report a rare example of unselfish meiotic drive for crossover inheritance in the clonal raider ant, Ooceraea biroi, in which both alleles are co-inherited at all loci across the entire genome. This species produces diploid offspring parthenogenetically via fusion of two haploid nuclei from the same meiosis. This process should cause rapid genotypic degeneration due to loss of heterozygosity, which results if crossover recombination is followed by random (Mendelian) segregation of chromosomes. However, by comparing whole genomes of mothers and daughters, we show that loss of heterozygosity is exceedingly rare, raising the possibility that crossovers are infrequent or absent in O. biroi meiosis. Using a combination of cytology and whole-genome sequencing, we show that crossover recombination is, in fact, common but that loss of heterozygosity is avoided because crossover products are faithfully co-inherited. This results from a programmed violation of Mendel's law of segregation, such that crossover products segregate together rather than randomly. This discovery highlights an extreme example of cellular 'memory' of crossovers, which could be a common yet cryptic feature of chromosomal segregation.
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Affiliation(s)
- Kip D Lacy
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA.
| | - Taylor Hart
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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Perrier A, Guiglielmoni N, Naquin D, Gorrichon K, Thermes C, Lameiras S, Dammermann A, Schiffer PH, Brunstein M, Canman JC, Dumont J. Maternal inheritance of functional centrioles in two parthenogenetic nematodes. Nat Commun 2024; 15:6042. [PMID: 39025889 PMCID: PMC11258339 DOI: 10.1038/s41467-024-50427-5] [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: 08/14/2023] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
Centrioles are the core constituent of centrosomes, microtubule-organizing centers involved in directing mitotic spindle assembly and chromosome segregation in animal cells. In sexually reproducing species, centrioles degenerate during oogenesis and female meiosis is usually acentrosomal. Centrioles are retained during male meiosis and, in most species, are reintroduced with the sperm during fertilization, restoring centriole numbers in embryos. In contrast, the presence, origin, and function of centrioles in parthenogenetic species is unknown. We found that centrioles are maternally inherited in two species of asexual parthenogenetic nematodes and identified two different strategies for maternal inheritance evolved in the two species. In Rhabditophanes diutinus, centrioles organize the poles of the meiotic spindle and are inherited by both the polar body and embryo. In Disploscapter pachys, the two pairs of centrioles remain close together and are inherited by the embryo only. Our results suggest that maternally-inherited centrioles organize the embryonic spindle poles and act as a symmetry-breaking cue to induce embryo polarization. Thus, in these parthenogenetic nematodes, centrioles are maternally-inherited and functionally replace their sperm-inherited counterparts in sexually reproducing species.
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Affiliation(s)
- Aurélien Perrier
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Nadège Guiglielmoni
- Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Kevin Gorrichon
- Centre de Référence, d'Innovation, d'eXpertise et de transfert (CRefIX), US 039 CEA/INRIA/INSERM, Evry, France
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Claude Thermes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sonia Lameiras
- Institut Curie, PSL University, ICGex Next-Generation Sequencing Platform, 75005, Paris, France
| | - Alexander Dammermann
- Max Perutz Labs, Vienna Biocenter Campus (VBC), 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, 1030, Vienna, Austria
| | - Philipp H Schiffer
- Worm∼lab, Institute for Zoology, University of Cologne, Cologne, NRW, Germany
| | - Maia Brunstein
- Institut Pasteur, Université Paris Cité, INSERM, Institut de l'Audition, F-75012, Paris, France
| | - Julie C Canman
- Columbia University Irving Medical Center; Department of Pathology and Cell Biology, New York, NY, 10032, USA
| | - Julien Dumont
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France.
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Lacy KD, Hart T, Kronauer DJ. Unselfish meiotic drive maintains heterozygosity in a parthenogenetic ant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579553. [PMID: 38405725 PMCID: PMC10888755 DOI: 10.1101/2024.02.09.579553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
According to Mendel's second law, chromosomes segregate randomly in meiosis. Nonrandom segregation is primarily known for cases of selfish meiotic drive in females, in which particular alleles bias their own transmission into the oocyte1,2. Here, we report a rare example of unselfish meiotic drive for crossover inheritance in the clonal raider ant, Ooceraea biroi. This species produces diploid offspring parthenogenetically via fusion of two haploid nuclei from the same meiosis3. This process should cause rapid genotypic degeneration due to loss of heterozygosity, which results if crossover recombination is followed by random (Mendelian) segregation of chromosomes4,5. However, by comparing whole genomes of mothers and daughters, we show that loss of heterozygosity is exceedingly rare, raising the possibility that crossovers are infrequent or absent in O. biroi meiosis. Using a combination of cytology and whole genome sequencing, we show that crossover recombination is, in fact, common, but that loss of heterozygosity is avoided because crossover products are faithfully co-inherited. This results from a programmed violation of Mendel's law of segregation, such that crossover products segregate together rather than randomly. This discovery highlights an extreme example of cellular "memory" of crossovers, which could be a common yet cryptic feature of chromosomal segregation.
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Affiliation(s)
- Kip D. Lacy
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| | - Taylor Hart
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| | - Daniel J.C. Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
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