1
|
Rothmann-Meyer W, Naidoo K, de Waal PJ. Spirocerca lupi draft genome, vaccine and anthelmintic targets. Mol Biochem Parasitol 2024; 259:111632. [PMID: 38834134 DOI: 10.1016/j.molbiopara.2024.111632] [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: 01/10/2024] [Revised: 05/13/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024]
Abstract
Spirocerca lupi is a parasitic nematode affecting predominantly domestic dogs. It causes spirocercosis, a disease that is often fatal. The assembled draft genome of S. lupi consists of 13,627 predicted protein-coding genes and is approximately 150 Mb in length. Several known anthelmintic gene targets such as for β-Tubulin, glutamate, and GABA receptors as well as known vaccine gene targets such as cysteine protease inhibitor and cytokines were identified in S. lupi by comparing orthologs of C. elegans anthelmintic gene targets as well as orthologs to known vaccine candidates. New anthelmintic targets were predicted through an inclusion-exclusion strategy and new vaccine targets were predicted through an immunoinformatics approach. New anthelminthic targets include DNA-directed RNA polymerases, chitin synthase, polymerases, and other enzymes. New vaccine targets include cuticle collagens. These gene targets provide a starting platform for new drug identification and vaccine design.
Collapse
Affiliation(s)
- Wiekolize Rothmann-Meyer
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Kershney Naidoo
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa; Thermo Fisher Scientific, Hybrid Field Application Scientist & Field Service Engineer, South Africa
| | - Pamela J de Waal
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| |
Collapse
|
2
|
Alkan C, Brésard G, Frézal L, Richaud A, Ruaud A, Zhang G, Félix MA. Natural variation in infection specificity of Caenorhabditis briggsae isolates by two RNA viruses. PLoS Pathog 2024; 20:e1012259. [PMID: 38861582 DOI: 10.1371/journal.ppat.1012259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
Antagonistic relationships such as host-virus interactions potentially lead to rapid evolution and specificity in interactions. The Orsay virus is so far the only horizontal virus naturally infecting the nematode C. elegans. In contrast, several related RNA viruses infect its congener C. briggsae, including Santeuil (SANTV) and Le Blanc (LEBV) viruses. Here we focus on the host's intraspecific variation in sensitivity to these two intestinal viruses. Many temperate-origin C. briggsae strains, including JU1264 and JU1498, are sensitive to both, while many tropical strains, such as AF16, are resistant to both. Interestingly, some C. briggsae strains exhibit a specific resistance, such as the HK104 strain, specifically resistant to LEBV. The viral sensitivity pattern matches the strains' geographic and genomic relationships. The heavily infected strains mount a seemingly normal small RNA response that is insufficient to suppress viral infection, while the resistant strains show no small RNA response, suggesting an early block in viral entry or replication. We use a genetic approach from the host side to map genomic regions participating in viral resistance polymorphisms. Using Advanced Intercrossed Recombinant Inbred Lines (RILs) between virus-resistant AF16 and SANTV-sensitive HK104, we detect Quantitative Trait Loci (QTLs) on chromosomes IV and III. Building RILs between virus-sensitive JU1498 and LEBV-resistant HK104 followed by bulk segregant analysis, we identify a chromosome II QTL. In both cases, further introgressions of the regions confirmed the QTLs. This diversity provides an avenue for studying virus entry, replication, and exit mechanisms, as well as host-virus specificity and the host response to a specific virus infection.
Collapse
Affiliation(s)
- Cigdem Alkan
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Gautier Brésard
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Lise Frézal
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
- Institut Pasteur, Université Paris Cité, Unité des Bactéries pathogènes entériques Paris, Paris, France
| | - Aurélien Richaud
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Albane Ruaud
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Gaotian Zhang
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Marie-Anne Félix
- IBENS, Department of Biology, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| |
Collapse
|
3
|
Lyu H, Moya ND, Andersen EC, Chamberlin HM. Gene duplication and evolutionary plasticity of lin-12/Notch gene function in Caenorhabditis. Genetics 2024:iyae064. [PMID: 38809718 DOI: 10.1093/genetics/iyae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/16/2024] [Indexed: 05/31/2024] Open
Abstract
Gene duplication is an important substrate for the evolution of new gene functions, but the impacts of gene duplicates on their own activities and on the developmental networks in which they act are poorly understood. Here, we use a natural experiment of lin-12/Notch gene duplication within the nematode genus Caenorhabditis, combined with characterization of loss- and gain-of-function mutations, to uncover functional distinctions between the duplicate genes in 1 species (Caenorhabditis briggsae) and their single-copy ortholog in Caenorhabditis elegans. First, using improved genomic sequence and gene model characterization, we confirm that the C. briggsae genome includes 2 complete lin-12 genes, whereas most other genes encoding proteins that participate in the LIN-12 signaling pathway retain a one-to-one orthology with C. elegans. We use CRISPR-mediated genome editing to introduce alleles predicted to cause gain-of-function (gf) or loss-of-function (lf) into each C. briggsae gene and find that the gf mutations uncover functional distinctions not apparent from the lf alleles. Specifically, Cbr-lin-12.1(gf), but not Cbr-lin-12.2(gf), causes developmental defects similar to those observed in Cel-lin-12(gf). In contrast to Cel-lin-12(gf), however, the Cbr-lin-12.1(gf) alleles do not cause dominant phenotypes as compared to the wild type, and the mutant phenotype is observed only when 2 gf alleles are present. Our results demonstrate that gene duplicates can exhibit differential capacities to compensate for each other and to interfere with normal development, and uncover coincident gene duplication and evolution of developmental sensitivity to LIN-12/Notch activity.
Collapse
Affiliation(s)
- Haimeng Lyu
- Department of Molecular Genetics, Ohio State University, 484 W 12th Ave, Columbus, OH 43210, USA
| | - Nicolas D Moya
- Department of Biology, Johns Hopkins University, Bascom UTL 383, 3400 North Charles St., Baltimore, MD 21218, USA
| | - Erik C Andersen
- Department of Biology, Johns Hopkins University, Bascom UTL 383, 3400 North Charles St., Baltimore, MD 21218, USA
| | - Helen M Chamberlin
- Department of Molecular Genetics, Ohio State University, 484 W 12th Ave, Columbus, OH 43210, USA
| |
Collapse
|
4
|
Woodruff GC, Willis JH, Phillips PC. Patterns of Genomic Diversity in a Fig-Associated Close Relative of Caenorhabditis elegans. Genome Biol Evol 2024; 16:evae020. [PMID: 38302111 PMCID: PMC10883733 DOI: 10.1093/gbe/evae020] [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: 08/22/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
The evolution of reproductive mode is expected to have profound impacts on the genetic composition of populations. At the same time, ecological interactions can generate close associations among species, which can in turn generate a high degree of overlap in their spatial distributions. Caenorhabditis elegans is a hermaphroditic nematode that has enabled extensive advances in developmental genetics. Caenorhabditis inopinata, the sister species of C. elegans, is a gonochoristic nematode that thrives in figs and obligately disperses on fig wasps. Here, we describe patterns of genomic diversity in C. inopinata. We performed RAD-seq on individual worms isolated from the field across three Okinawan island populations. C. inopinata is about five times more diverse than C. elegans. Additionally, C. inopinata harbors greater differences in diversity among functional genomic regions (such as between genic and intergenic sequences) than C. elegans. Conversely, C. elegans harbors greater differences in diversity between high-recombining chromosome arms and low-recombining chromosome centers than C. inopinata. FST is low among island population pairs, and clear population structure could not be easily detected among islands, suggesting frequent migration of wasps between islands. These patterns of population differentiation appear comparable with those previously reported in its fig wasp vector. These results confirm many theoretical population genetic predictions regarding the evolution of reproductive mode and suggest C. inopinata population dynamics may be driven by wasp dispersal. This work sets the stage for future evolutionary genomic studies aimed at understanding the evolution of sex as well as the evolution of ecological interactions.
Collapse
Affiliation(s)
- Gavin C Woodruff
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
- Present address: Department of Biology, University of Oklahoma, Norman, OK 73019, USA
| | - John H Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| |
Collapse
|
5
|
Crombie TA, McKeown R, Moya ND, Evans K, Widmayer S, LaGrassa V, Roman N, Tursunova O, Zhang G, Gibson S, Buchanan C, Roberto N, Vieira R, Tanny R, Andersen E. CaeNDR, the Caenorhabditis Natural Diversity Resource. Nucleic Acids Res 2024; 52:D850-D858. [PMID: 37855690 PMCID: PMC10767927 DOI: 10.1093/nar/gkad887] [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] [Received: 08/23/2023] [Revised: 09/30/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Studies of model organisms have provided important insights into how natural genetic differences shape trait variation. These discoveries are driven by the growing availability of genomes and the expansive experimental toolkits afforded to researchers using these species. For example, Caenorhabditis elegans is increasingly being used to identify and measure the effects of natural genetic variants on traits using quantitative genetics. Since 2016, the C. elegans Natural Diversity Resource (CeNDR) has facilitated many of these studies by providing an archive of wild strains, genome-wide sequence and variant data for each strain, and a genome-wide association (GWA) mapping portal for the C. elegans community. Here, we present an updated platform, the Caenorhabditis Natural Diversity Resource (CaeNDR), that enables quantitative genetics and genomics studies across the three Caenorhabditis species: C. elegans, C. briggsae and C. tropicalis. The CaeNDR platform hosts several databases that are continually updated by the addition of new strains, whole-genome sequence data and annotated variants. Additionally, CaeNDR provides new interactive tools to explore natural variation and enable GWA mappings. All CaeNDR data and tools are accessible through a freely available web portal located at caendr.org.
Collapse
Affiliation(s)
- Timothy A Crombie
- Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Ryan McKeown
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Nicolas D Moya
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Cell, Molecular, Developmental biology, and Biophysics Graduate Program, ohns Hopkins University, Baltimore, MD, USA
| | - Kathryn S Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Samuel J Widmayer
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Vincent LaGrassa
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Natalie Roman
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Orzu Tursunova
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Sophia B Gibson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Claire M Buchanan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Nicole M Roberto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Rodolfo Vieira
- Northwestern University Information Technology, Media and Technology Innovation, Northwestern University, Evanston, IL USA
| | - Robyn E Tanny
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Erik C Andersen
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| |
Collapse
|
6
|
Rödelsperger C. Comparative Genomics of Sex, Chromosomes, and Sex Chromosomes in Caenorhabditis elegans and Other Nematodes. Methods Mol Biol 2024; 2802:455-472. [PMID: 38819568 DOI: 10.1007/978-1-0716-3838-5_15] [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] [Indexed: 06/01/2024]
Abstract
The nematode phylum has evolved a remarkable diversity of reproductive modes, including the repeated emergence of asexuality and hermaphroditism across divergent clades. The species-richness and small genome size of nematodes make them ideal systems for investigating the genome-wide causes and consequences of such major transitions. The availability of functional annotations for most Caenorhabditis elegans genes further allows the linking of patterns of gene content evolution with biological processes. Such gene-centric studies were recently complemented by investigations of chromosome evolution that made use of the first chromosome-scale genome assemblies outside the Caenorhabditis genus. This review highlights recent comparative genomic studies of reproductive mode evolution addressing the hybrid origin of asexuality and the parallel gene loss following the emergence of hermaphroditism. It further summarizes ongoing efforts to characterize ancient linkage blocks called Nigon elements, which form central units of chromosome evolution. Fusions between Nigon elements have been demonstrated to impact recombination and speciation. Finally, multiple recent fusions between autosomal and the sex-linked Nigon element reveal insights into the dynamic evolution of sex chromosomes across various timescales.
Collapse
Affiliation(s)
- Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany.
| |
Collapse
|
7
|
Jeong DE, Sundrani S, Hall RN, Krupovic M, Koonin EV, Fire AZ. DNA Polymerase Diversity Reveals Multiple Incursions of Polintons During Nematode Evolution. Mol Biol Evol 2023; 40:msad274. [PMID: 38069639 DOI: 10.1093/molbev/msad274] [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: 08/24/2023] [Revised: 11/01/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023] Open
Abstract
Polintons are double-stranded DNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family but encode a distinct protein-primed DNA polymerase B (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda. Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting interphylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of an HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.
Collapse
Affiliation(s)
- Dae-Eun Jeong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sameer Sundrani
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Present address: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
| | - Eugene V Koonin
- National National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
8
|
Stevens L, Martínez-Ugalde I, King E, Wagah M, Absolon D, Bancroft R, Gonzalez de la Rosa P, Hall JL, Kieninger M, Kloch A, Pelan S, Robertson E, Pedersen AB, Abreu-Goodger C, Buck AH, Blaxter M. Ancient diversity in host-parasite interaction genes in a model parasitic nematode. Nat Commun 2023; 14:7776. [PMID: 38012132 PMCID: PMC10682056 DOI: 10.1038/s41467-023-43556-w] [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: 05/26/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
Host-parasite interactions exert strong selection pressures on the genomes of both host and parasite. These interactions can lead to negative frequency-dependent selection, a form of balancing selection that is hypothesised to explain the high levels of polymorphism seen in many host immune and parasite antigen loci. Here, we sequence the genomes of several individuals of Heligmosomoides bakeri, a model parasite of house mice, and Heligmosomoides polygyrus, a closely related parasite of wood mice. Although H. bakeri is commonly referred to as H. polygyrus in the literature, their genomes show levels of divergence that are consistent with at least a million years of independent evolution. The genomes of both species contain hyper-divergent haplotypes that are enriched for proteins that interact with the host immune response. Many of these haplotypes originated prior to the divergence between H. bakeri and H. polygyrus, suggesting that they have been maintained by long-term balancing selection. Together, our results suggest that the selection pressures exerted by the host immune response have played a key role in shaping patterns of genetic diversity in the genomes of parasitic nematodes.
Collapse
Affiliation(s)
- Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK.
| | - Isaac Martínez-Ugalde
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Erna King
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Martin Wagah
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | | | - Rowan Bancroft
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Jessica L Hall
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | | | - Sarah Pelan
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Elaine Robertson
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Amy B Pedersen
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Cei Abreu-Goodger
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Amy H Buck
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK.
| |
Collapse
|
9
|
Moya ND, Stevens L, Miller IR, Sokol CE, Galindo JL, Bardas AD, Koh ESH, Rozenich J, Yeo C, Xu M, Andersen EC. Novel and improved Caenorhabditis briggsae gene models generated by community curation. BMC Genomics 2023; 24:486. [PMID: 37626289 PMCID: PMC10463891 DOI: 10.1186/s12864-023-09582-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The nematode Caenorhabditis briggsae has been used as a model in comparative genomics studies with Caenorhabditis elegans because of their striking morphological and behavioral similarities. However, the potential of C. briggsae for comparative studies is limited by the quality of its genome resources. The genome resources for the C. briggsae laboratory strain AF16 have not been developed to the same extent as C. elegans. The recent publication of a new chromosome-level reference genome for QX1410, a C. briggsae wild strain closely related to AF16, has provided the first step to bridge the gap between C. elegans and C. briggsae genome resources. Currently, the QX1410 gene models consist of software-derived gene predictions that contain numerous errors in their structure and coding sequences. In this study, a team of researchers manually inspected over 21,000 gene models and underlying transcriptomic data to repair software-derived errors. RESULTS We designed a detailed workflow to train a team of nine students to manually curate gene models using RNA read alignments. We manually inspected the gene models, proposed corrections to the coding sequences of over 8,000 genes, and modeled thousands of putative isoforms and untranslated regions. We exploited the conservation of protein sequence length between C. briggsae and C. elegans to quantify the improvement in protein-coding gene model quality and showed that manual curation led to substantial improvements in the protein sequence length accuracy of QX1410 genes. Additionally, collinear alignment analysis between the QX1410 and AF16 genomes revealed over 1,800 genes affected by spurious duplications and inversions in the AF16 genome that are now resolved in the QX1410 genome. CONCLUSIONS Community-based, manual curation using transcriptome data is an effective approach to improve the quality of software-derived protein-coding genes. The detailed protocols provided in this work can be useful for future large-scale manual curation projects in other species. Our manual curation efforts have brought the QX1410 gene models to a comparable level of quality as the extensively curated AF16 gene models. The improved genome resources for C. briggsae provide reliable tools for the study of Caenorhabditis biology and other related nematodes.
Collapse
Affiliation(s)
- Nicolas D Moya
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, 60208, USA
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Isabella R Miller
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Chloe E Sokol
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Joseph L Galindo
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Alexandra D Bardas
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Edward S H Koh
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Justine Rozenich
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Cassia Yeo
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Maryanne Xu
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, 4619 Silverman Hall 2205 Tech Drive, Evanston, IL, 60208, USA.
| |
Collapse
|
10
|
Jeong DE, Sundrani S, Hall RN, Krupovic M, Koonin EV, Fire AZ. DNA polymerase diversity reveals multiple incursions of Polintons during nematode evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554363. [PMID: 37662302 PMCID: PMC10473752 DOI: 10.1101/2023.08.22.554363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Polintons are dsDNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family, but encode a distinct protein-primed B family DNA polymerase (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda . Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting inter-phylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of a HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.
Collapse
|
11
|
Broitman-Maduro G, Maduro MF. Evolutionary Change in Gut Specification in Caenorhabditis Centers on the GATA Factor ELT-3 in an Example of Developmental System Drift. J Dev Biol 2023; 11:32. [PMID: 37489333 PMCID: PMC10366740 DOI: 10.3390/jdb11030032] [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: 06/02/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023] Open
Abstract
Cells in a developing animal embryo become specified by the activation of cell-type-specific gene regulatory networks. The network that specifies the gut in the nematode Caenorhabditis elegans has been the subject of study for more than two decades. In this network, the maternal factors SKN-1/Nrf and POP-1/TCF activate a zygotic GATA factor cascade consisting of the regulators MED-1,2 → END-1,3 → ELT-2,7, leading to the specification of the gut in early embryos. Paradoxically, the MED, END, and ELT-7 regulators are present only in species closely related to C. elegans, raising the question of how the gut can be specified without them. Recent work found that ELT-3, a GATA factor without an endodermal role in C. elegans, acts in a simpler ELT-3 → ELT-2 network to specify gut in more distant species. The simpler ELT-3 → ELT-2 network may thus represent an ancestral pathway. In this review, we describe the elucidation of the gut specification network in C. elegans and related species and propose a model by which the more complex network might have formed. Because the evolution of this network occurred without a change in phenotype, it is an example of the phenomenon of Developmental System Drift.
Collapse
Affiliation(s)
- Gina Broitman-Maduro
- Department of Molecular, Cell, and Systems Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - Morris F Maduro
- Department of Molecular, Cell, and Systems Biology, University of California-Riverside, Riverside, CA 92521, USA
| |
Collapse
|
12
|
Widen SA, Bes IC, Koreshova A, Pliota P, Krogull D, Burga A. Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities. Science 2023; 380:eade0705. [PMID: 37384706 DOI: 10.1126/science.ade0705] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 05/17/2023] [Indexed: 07/01/2023]
Abstract
Horizontal gene transfer, the movement of genetic material between species, has been reported across all major eukaryotic lineages. However, the underlying mechanisms of transfer and their impact on genome evolution are still poorly understood. While studying the evolutionary origin of a selfish element in the nematode Caenorhabditis briggsae, we discovered that Mavericks, ancient virus-like transposons related to giant viruses and virophages, are one of the long-sought vectors of horizontal gene transfer. We found that Mavericks gained a novel herpesvirus-like fusogen in nematodes, leading to the widespread exchange of cargo genes between extremely divergent species, bypassing sexual and genetic barriers spanning hundreds of millions of years. Our results show how the union between viruses and transposons causes horizontal gene transfer and ultimately genetic incompatibilities in natural populations.
Collapse
Affiliation(s)
- Sonya A Widen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Israel Campo Bes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Alevtina Koreshova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Pinelopi Pliota
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Daniel Krogull
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Alejandro Burga
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| |
Collapse
|
13
|
Moya ND, Stevens L, Miller IR, Sokol CE, Galindo JL, Bardas AD, Koh ESH, Rozenich J, Yeo C, Xu M, Andersen EC. Novel and improved Caenorhabditis briggsae gene models generated by community curation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541014. [PMID: 37292880 PMCID: PMC10245686 DOI: 10.1101/2023.05.16.541014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background The nematode Caenorhabditis briggsae has been used as a model for genomics studies compared to Caenorhabditis elegans because of its striking morphological and behavioral similarities. These studies yielded numerous findings that have expanded our understanding of nematode development and evolution. However, the potential of C. briggsae to study nematode biology is limited by the quality of its genome resources. The reference genome and gene models for the C. briggsae laboratory strain AF16 have not been developed to the same extent as C. elegans . The recent publication of a new chromosome-level reference genome for QX1410, a C. briggsae wild strain closely related to AF16, has provided the first step to bridge the gap between C. elegans and C. briggsae genome resources. Currently, the QX1410 gene models consist of protein-coding gene predictions generated from short- and long-read transcriptomic data. Because of the limitations of gene prediction software, the existing gene models for QX1410 contain numerous errors in their structure and coding sequences. In this study, a team of researchers manually inspected over 21,000 software-derived gene models and underlying transcriptomic data to improve the protein-coding gene models of the C. briggsae QX1410 genome. Results We designed a detailed workflow to train a team of nine students to manually curate genes using RNA read alignments and predicted gene models. We manually inspected the gene models using the genome annotation editor, Apollo, and proposed corrections to the coding sequences of over 8,000 genes. Additionally, we modeled thousands of putative isoforms and untranslated regions. We exploited the conservation of protein sequence length between C. briggsae and C. elegans to quantify the improvement in protein-coding gene model quality before and after curation. Manual curation led to a substantial improvement in the protein sequence length accuracy of QX1410 genes. We also compared the curated QX1410 gene models against the existing AF16 gene models. The manual curation efforts yielded QX1410 gene models that are similar in quality to the extensively curated AF16 gene models in terms of protein-length accuracy and biological completeness scores. Collinear alignment analysis between the QX1410 and AF16 genomes revealed over 1,800 genes affected by spurious duplications and inversions in the AF16 genome that are now resolved in the QX1410 genome. Conclusions Community-based, manual curation using transcriptome data is an effective approach to improve the quality of software-derived protein-coding genes. Comparative genomic analysis using a related species with high-quality reference genome(s) and gene models can be used to quantify improvements in gene model quality in a newly sequenced genome. The detailed protocols provided in this work can be useful for future large-scale manual curation projects in other species. The chromosome-level reference genome for the C. briggsae strain QX1410 far surpasses the quality of the genome of the laboratory strain AF16, and our manual curation efforts have brought the QX1410 gene models to a comparable level of quality to the previous reference, AF16. The improved genome resources for C. briggsae provide reliable tools for the study of Caenorhabditis biology and other related nematodes.
Collapse
Affiliation(s)
- Nicolas D. Moya
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Isabella R. Miller
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Chloe E. Sokol
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Joseph L. Galindo
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Alexandra D. Bardas
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Edward S. H. Koh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Justine Rozenich
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Cassia Yeo
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Maryanne Xu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| |
Collapse
|
14
|
Yoshida K, Rödelsperger C, Röseler W, Riebesell M, Sun S, Kikuchi T, Sommer RJ. Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. Nat Ecol Evol 2023; 7:424-439. [PMID: 36717742 PMCID: PMC9998273 DOI: 10.1038/s41559-022-01980-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 12/29/2022] [Indexed: 02/01/2023]
Abstract
Large-scale genome-structural evolution is common in various organisms. Recent developments in speciation genomics revealed the importance of inversions, whereas the role of other genome-structural rearrangements, including chromosome fusions, have not been well characterized. We study genomic divergence and reproductive isolation of closely related nematodes: the androdioecious (hermaphroditic) model Pristionchus pacificus and its dioecious sister species Pristionchus exspectatus. A chromosome-level genome assembly of P. exspectatus using single-molecule and Hi-C sequencing revealed a chromosome-wide rearrangement relative to P. pacificus. Strikingly, genomic characterization and cytogenetic studies including outgroup species Pristionchus occultus indicated two independent fusions involving the same chromosome, ChrIR, between these related species. Genetic linkage analysis indicated that these fusions altered the chromosome-wide pattern of recombination, resulting in large low-recombination regions that probably facilitated the coevolution between some of the ~14.8% of genes across the entire genomes. Quantitative trait locus analyses for hybrid sterility in all three sexes revealed that major quantitative trait loci mapped to the fused chromosome ChrIR. While abnormal chromosome segregations of the fused chromosome partially explain hybrid female sterility, hybrid-specific recombination that breaks linkage of genes in the low-recombination region was associated with hybrid male sterility. Thus, recent chromosome fusions repatterned recombination rate and drove reproductive isolation during Pristionchus speciation.
Collapse
Affiliation(s)
- Kohta Yoshida
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany.
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Waltraud Röseler
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Metta Riebesell
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Simo Sun
- Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Taisei Kikuchi
- Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany.
| |
Collapse
|
15
|
Sun S, Kanzaki N, Dayi M, Maeda Y, Yoshida A, Tanaka R, Kikuchi T. The compact genome of Caenorhabditis niphades n. sp., isolated from a wood-boring weevil, Niphades variegatus. BMC Genomics 2022; 23:765. [PMID: 36418933 PMCID: PMC9682657 DOI: 10.1186/s12864-022-09011-8] [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: 09/10/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The first metazoan genome sequenced, that of Caenorhabditis elegans, has motivated animal genome evolution studies. To date > 50 species from the genus Caenorhabditis have been sequenced, allowing research on genome variation. RESULTS In the present study, we describe a new gonochoristic species, Caenorhabditis niphades n. sp., previously referred as C. sp. 36, isolated from adult weevils (Niphades variegatus), with whom they appear to be tightly associated during its life cycle. Along with a species description, we sequenced the genome of C. niphades n. sp. and produced a chromosome-level assembly. A genome comparison highlighted that C. niphades n. sp. has the smallest genome (59 Mbp) so far sequenced in the Elegans supergroup, despite being closely related to a species with an exceptionally large genome, C. japonica. CONCLUSIONS The compact genome of C. niphades n. sp. can serve as a key resource for comparative evolutionary studies of genome and gene number expansions in Caenorhabditis species.
Collapse
Affiliation(s)
- Simo Sun
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| | - Natsumi Kanzaki
- grid.417935.d0000 0000 9150 188XKansai Research Center, Forestry and Forest Products Research Institute, 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto, 612-0855 Japan
| | - Mehmet Dayi
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.412121.50000 0001 1710 3792Forestry Vocational School, Duzce University, 81620 Duzce, Türkiye
| | - Yasunobu Maeda
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| | - Akemi Yoshida
- grid.410849.00000 0001 0657 3887Genomics and Bioenvironmental Science, Frontier Science Research Center, University of Miyazaki, Miyazaki, 889-1692 Japan
| | - Ryusei Tanaka
- grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| | - Taisei Kikuchi
- grid.26999.3d0000 0001 2151 536XDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562 Japan ,grid.410849.00000 0001 0657 3887Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Miyazaki, 889-1692 Japan
| |
Collapse
|
16
|
Velazco-Cruz L, Ross JA. Genetic architecture and temporal analysis of Caenorhabditis briggsae hybrid developmental delay. PLoS One 2022; 17:e0272843. [PMID: 35951524 PMCID: PMC9371335 DOI: 10.1371/journal.pone.0272843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/27/2022] [Indexed: 11/18/2022] Open
Abstract
Identifying the alleles that reduce hybrid fitness is a major goal in the study of speciation genetics. It is rare to identify systems in which hybrid incompatibilities with minor phenotypic effects are segregating in genetically diverse populations of the same biological species. Such traits do not themselves cause reproductive isolation but might initiate the process. In the nematode Caenorhabditis briggsae, a small percent of F2 generation hybrids between two natural populations suffer from developmental delay, in which adulthood is reached after approximately 33% more time than their wild-type siblings. Prior efforts to identify the genetic basis for this hybrid incompatibility assessed linkage using one or two genetic markers on chromosome III and suggested that delay is caused by a toxin-antidote element. Here, we have genotyped F2 hybrids using multiple chromosome III markers to refine the developmental delay locus. Also, to better define the developmental delay phenotype, we measured the development rate of 66 F2 hybrids and found that delay is not restricted to a particular larval developmental stage. Deviation of the developmental delay frequency from hypothetical expectations for a toxin-antidote element adds support to the assertion that the epistatic interaction is not fully penetrant. Our mapping and refinement of the delay phenotype motivates future efforts to study the genetic architecture of hybrid dysfunction between genetically distinct populations of one species by identifying the underlying loci.
Collapse
Affiliation(s)
- Leonardo Velazco-Cruz
- Department of Biology, California State University, Fresno, California, United States of America
| | - Joseph A. Ross
- Department of Biology, California State University, Fresno, California, United States of America
- * E-mail:
| |
Collapse
|