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Ilík V, Schwarz EM, Nosková E, Pafčo B. Hookworm genomics: dusk or dawn? Trends Parasitol 2024; 40:452-465. [PMID: 38677925 DOI: 10.1016/j.pt.2024.04.003] [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: 02/27/2024] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/29/2024]
Abstract
Hookworms are parasites, closely related to the model nematode Caenorhabditis elegans, that are a major economic and health burden worldwide. Primarily three hookworm species (Necator americanus, Ancylostoma duodenale, and Ancylostoma ceylanicum) infect humans. Another 100 hookworm species from 19 genera infect primates, ruminants, and carnivores. Genetic data exist for only seven of these species. Genome sequences are available from only four of these species in two genera, leaving 96 others (particularly those parasitizing wildlife) without any genomic data. The most recent hookworm genomes were published 5 years ago, leaving the field in a dusk. However, assembling genomes from single hookworms may bring a new dawn. Here we summarize advances, challenges, and opportunities for studying these neglected but important parasitic nematodes.
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Affiliation(s)
- Vladislav Ilík
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Eva Nosková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
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Aharonoff A, Kim J, Washington A, Ercan S. SMC-mediated dosage compensation in C. elegans evolved in the presence of an ancestral nematode mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595224. [PMID: 38826443 PMCID: PMC11142195 DOI: 10.1101/2024.05.21.595224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Mechanisms of X chromosome dosage compensation have been studied extensively in a few model species representing clades of shared sex chromosome ancestry. However, the diversity within each clade as a function of sex chromosome evolution is largely unknown. Here, we anchor ourselves to the nematode Caenorhabditis elegans, for which a well-studied mechanism of dosage compensation occurs through a specialized structural maintenance of chromosomes (SMC) complex, and explore the diversity of dosage compensation in the surrounding phylogeny of nematodes. Through phylogenetic analysis of the C. elegans dosage compensation complex and a survey of its epigenetic signatures, including X-specific topologically associating domains (TADs) and X-enrichment of H4K20me1, we found that the condensin-mediated mechanism evolved recently in the lineage leading to Caenorhabditis through an SMC-4 duplication. Intriguingly, an independent duplication of SMC-4 and the presence of X-specific TADs in Pristionchus pacificus suggest that condensin-mediated dosage compensation arose more than once. mRNA-seq analyses of gene expression in several nematode species indicate that dosage compensation itself is ancestral, as expected from the ancient XO sex determination system. Indicative of the ancestral mechanism, H4K20me1 is enriched on the X chromosomes in Oscheius tipulae, which does not contain X-specific TADs or SMC-4 paralogs. Together, our results indicate that the dosage compensation system in C. elegans is surprisingly new, and condensin may have been co-opted repeatedly in nematodes, suggesting that the process of evolving a chromosome-wide gene regulatory mechanism for dosage compensation is constrained. Significance statement X chromosome dosage compensation mechanisms evolved in response to Y chromosome degeneration during sex chromosome evolution. However, establishment of dosage compensation is not an endpoint. As sex chromosomes change, dosage compensation strategies may have also changed. In this study, we performed phylogenetic and epigenomic analyses surrounding Caenorhabditis elegans and found that the condensin-mediated dosage compensation mechanism in C. elegans is surprisingly new, and has evolved in the presence of an ancestral mechanism. Intriguingly, condensin-based dosage compensation may have evolved more than once in the nematode lineage, the other time in Pristionchus. Together, our work highlights a previously unappreciated diversity of dosage compensation mechanisms within a clade, and suggests constraints in evolving new mechanisms in the presence of an existing one.
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Affiliation(s)
- Avrami Aharonoff
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Jun Kim
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Aaliyah Washington
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003
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Kashyap D, Baliyan R, Panwar A, Kumar Y, Sharma B, Singh HS, Chaudhary A. Occurrence and First Molecular Characterization of Spinitectus notopteri Karve et Naik, 1951, Infected Bronze Featherback (Notopterus notopterus) in India. Acta Parasitol 2024; 69:1067-1072. [PMID: 38438771 DOI: 10.1007/s11686-024-00823-0] [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: 05/18/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024]
Abstract
PURPOSE The nematode genus Spinitectus Fourment, 1883, comprises species that are mainly parasitic on freshwater and marine fishes. However, our knowledge of the distribution and molecular identification of Spinitectus spp. in the Indian region is rather limited. This study aims to fill this gap in our knowledge using molecular data as evidence for Spinitectus species characterization. METHODS Bronze featherback were obtained opportunistically from the fish markets of district Muzaffarnagar (29.4727° N, 77.7085° E), Uttar Pradesh, India. Nematode species collected from the gastrointestinal tract were characterized morphologically and molecularly. Partial sequences of the ribosomal 18S rRNA gene were used for molecular characterization of the present specimens. RESULTS The current study represented molecular analysis that determined the presence of the species Spinitectus notopteri Karve et Naik, 1951. The sequences obtained were closely related to representatives of the family Rhabdochonidae. CONCLUSION This first molecular exploration of S. notopteri Karve et Naik, 1951, in the GenBank database and for any species of Spinitectus from India indicates a lack of genetic data for parasitic nematodes.
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Affiliation(s)
- Deepa Kashyap
- Department of Zoology, D.A.V. College, Muzaffarnagar, Uttar Pradesh, 251001, India
| | - Rakhi Baliyan
- Department of Zoology, Dhanauri P.G. College, Dhanauri, Uttarakhand, 247667, India
| | - Anju Panwar
- Department of Zoology, D.A.V. College, Muzaffarnagar, Uttar Pradesh, 251001, India
| | - Yougesh Kumar
- Department of Zoology, D.A.V. College, Muzaffarnagar, Uttar Pradesh, 251001, India
| | - Bindu Sharma
- Laboratory of Molecular Parasitology, Department of Zoology, Chaudhary Charan Singh University, University Road, Meerut, Uttar Pradesh, 250004, India
| | - Hridaya S Singh
- Molecular Taxonomy Laboratory, Department of Zoology, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, 250004, India
- Maa Shakumbhari University, Saharanpur, Uttar Pradesh, 247120, India
| | - Anshu Chaudhary
- Molecular Taxonomy Laboratory, Department of Zoology, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, 250004, India.
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Zeng JL, Chen HX, Ni XF, Kang JY, Li L. Molecular phylogeny of the family Rhabdiasidae (Nematoda: Rhabditida), with morphology, genetic characterization and mitochondrial genomes of Rhabdias kafunata and R. bufonis. Parasit Vectors 2024; 17:100. [PMID: 38429838 PMCID: PMC10908064 DOI: 10.1186/s13071-024-06201-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: 12/16/2023] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND The family Rhabdiasidae (Nematoda: Rhabditida) is a globally distributed group of nematode parasites, with over 110 species parasitic mainly in amphibians and reptiles. However, the systematic position of the family Rhabdiasidae in the order Rhabditida remains unsolved, and the evolutionary relationships among its genera are still unclear. Moreover, the present knowledge of the mitochondrial genomes of rhabdiasids remains limited. METHODS Two rhabdiasid species: Rhabdias kafunata Sata, Takeuchi & Nakano, 2020 and R. bufonis (Schrank, 1788) collected from the Asiatic toad Bufo gargarizans Cantor (Amphibia: Anura) in China, were identified based on morphology (light and scanning electron microscopy) and molecular characterization (sequencing of the nuclear 28S and ITS regions and mitochondrial cox1 and 12S genes). The complete mitochondrial genomes of R. kafunata and R. bufonis were also sequenced and annotated for the first time. Moreover, phylogenetic analyses based on the amino acid sequences of 12 protein-coding genes (PCGs) of the mitochondrial genomes were performed to clarify the systematic position of the family Rhabdiasidae in the order Rhabditida using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses based on the 28S + ITS sequences, were also inferred to assess the evolutionary relationships among the genera within Rhabdiasidae. RESULTS The detailed morphology of the cephalic structures, vulva and eggs in R. kafunata and R. bufonis was revealed using scanning electron microscopy (SEM) for the first time. The characterization of 28S and ITS regions of R. kafunata was reported for the first time. The mitogenomes of R. kafunata and R. bufonis are 15,437 bp and 15,128 bp long, respectively, and both contain 36 genes, including 12 PCGs (missing atp8). Comparative mitogenomics revealed that the gene arrangement of R. kafunata and R. bufonis is different from all of the currently available mitogenomes of nematodes. Phylogenetic analyses based on the ITS + 28S data showed Neoentomelas and Kurilonema as sister lineages, and supported the monophyly of Entomelas, Pneumonema, Serpentirhabdias and Rhabdias. Mitochondrial phylogenomic results supported Rhabdiasidae as a member of the superfamily Rhabditoidea in the suborder Rhabditina, and its occurrance as sister to the family Rhabditidae. CONCLUSIONS The complete mitochondrial genome of R. kafunata and R. bufonis were reported for the first time, and two new gene arrangements of mitogenomes in Nematoda were revealed. Mitogenomic phylogenetic results indicated that the family Rhabdiasidae is a member of Rhabditoidea in Rhabditina, and is closely related to Rhabditidae. Molecular phylogenies based on the ITS + 28S sequence data supported the validity of Kurilonema, and showed that Kurilonema is sister to Neoentomelas. The present phylogenetic results also indicated that the ancestors of rhabdiasids seem to have initially infected reptiles, then spreading to amphibians.
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Affiliation(s)
- Jia-Lu Zeng
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
- Hebei Research Center of the Basic Discipline Cell Biology; Ministry of Education Key Laboratory of Molecular and Cellular Biology, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Hui-Xia Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Xue-Feng Ni
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Jia-Yi Kang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China
| | - Liang Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology; Hebei Collaborative Innovation Center for Eco-Environment; College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, People's Republic of China.
- Hebei Research Center of the Basic Discipline Cell Biology; Ministry of Education Key Laboratory of Molecular and Cellular Biology, Shijiazhuang, 050024, Hebei, People's Republic of China.
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Fox BW, Helf MJ, Burkhardt RN, Artyukhin AB, Curtis BJ, Palomino DF, Schroeder AF, Chaturbedi A, Tauffenberger A, Wrobel CJJ, Zhang YK, Lee SS, Schroeder FC. Evolutionarily related host and microbial pathways regulate fat desaturation in C. elegans. Nat Commun 2024; 15:1520. [PMID: 38374083 PMCID: PMC10876521 DOI: 10.1038/s41467-024-45782-2] [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: 08/11/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression, but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPARα in C. elegans. Untargeted metabolomics of a β-oxidation mutant, acdh-11, in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a β-cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli. Screening for structurally related endogenous metabolites revealed a β-methyl fatty acid, bemeth#1, which mimics the activity of microbiota-dependent becyp#1 but is derived from a methyltransferase, fcmt-1, that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated β-oxidation pathway, while the endogenous bemeth#1 is metabolized via α-oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPARα to regulate fat desaturation.
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Affiliation(s)
- Bennett W Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Maximilian J Helf
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Russell N Burkhardt
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Alexander B Artyukhin
- Chemistry Department, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
| | - Brian J Curtis
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Diana Fajardo Palomino
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Allen F Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Amaresh Chaturbedi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Arnaud Tauffenberger
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Chester J J Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ying K Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
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Hass JK, Henriquez MC, Churcher J, Hamou H, Morales SR, Melin AD. Assessing morphological preservation of gastrointestinal parasites from fecal samples of wild capuchin monkeys (Cebus imitator) stored in ethanol versus formalin. Sci Rep 2024; 14:3623. [PMID: 38351262 PMCID: PMC10864282 DOI: 10.1038/s41598-024-53915-2] [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: 10/09/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
The copromicroscopic identification of gastrointestinal parasites is a common, cost-effective method vital to understanding host-parasite interactions. However, its efficacy depends on effective preservation of the samples. In this study, we compare the preservation of ethanol and formalin preserved gastrointestinal parasites collected from a wild population of Costa Rican capuchin monkeys (Cebus imitator). Fecal samples were collected, halved, and stored in either 10% formalin or 96% ethanol at ambient temperature, then microscopically screened for the presence of parasites. Parasites were morphologically identified and rated based on their preservation using a newly developed rubric. We identified more parasitic morphotypes in formalin-preserved samples but found no difference in the number of parasites per fecal gram (PFG) between mediums. There was no difference in the PFG of two most prevalent parasite morphotypes, Filariopsis barretoi larvae and Strongyle-type eggs, and while Filariopsis larvae were better preserved in formalin, strongyle eggs showed no preservation difference between mediums. Our results support the suitability of both ethanol and formalin for morphological parasite identification in samples stored over 1 year, describe the morphological changes and challenges associated with parasite degradation, and highlight the potential for future studies to use both morphological and molecular methods in non-invasively collected samples.
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Affiliation(s)
- Joelle K Hass
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada.
- Host Parasite Interactions Network, University of Calgary, Calgary, AB, Canada.
| | - Megan C Henriquez
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada.
- Host Parasite Interactions Network, University of Calgary, Calgary, AB, Canada.
- Department of Anthropology, The Graduate Center, City University of New York, New York, NY, USA.
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY, USA.
| | - Jessica Churcher
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
- Host Parasite Interactions Network, University of Calgary, Calgary, AB, Canada
| | - Hadjira Hamou
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
- Host Parasite Interactions Network, University of Calgary, Calgary, AB, Canada
| | | | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada.
- Host Parasite Interactions Network, University of Calgary, Calgary, AB, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada.
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Albrechtová M, Kašparová EŠ, Langrová I, Hart V, Neuhaus B, Jankovská I, Petrtýl M, Magdálek J, Špakulová M. A revision of the trichostrongylid nematode Cooperia Ransom, 1907, from deer game: recent integrative research confirms the existence of the ancient host-specific species Cooperia ventricosa (Rudolphi, 1809). Front Vet Sci 2024; 11:1346417. [PMID: 38389582 PMCID: PMC10881869 DOI: 10.3389/fvets.2024.1346417] [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: 11/29/2023] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
The trichostrongylid roundworms of the genus Cooperia, which are important in veterinary medicine, currently comprise 19 valid species that parasitize the small intestine of both free-living and domestic ruminants. Only four Cooperia spp. have been reported in Europe, namely C. oncophora, C. punctata, C. curticei and C. pectinata. In 2018-2022, 25 red deer (Cervus elaphus) and 30 sika deer (Cervus nippon) of both sexes and various ages from several remote locations in the Czech Republic were parasitologically examined. Intestinal nematodes of the genus Cooperia were found only in two northern regions. Using the globally recognized key book on trichostrongylid nematodes, they were preliminarily identified as C. pectinata. However, a molecular analysis of cox2 and ITS rDNA gene sequences revealed that Cooperia sp. parasitizing Czech deer is a separate taxon that is more closely related to C. oncophora than to C. pectinata. A subsequent morphological analysis and literature survey confirmed the independence of deer Cooperia sp., which is similar but not identical to bovid C. pectinata. Previous long-term correct identifications of bovid C. pectinata and misidentifications of deer Cooperia species were caused by a fundamental error in the key book mentioned above. Interestingly, the ancient trichostrongylid nematode Strongylus ventricosus from the type host red deer (Cervus elaphus) shot near Greifswald (Germany) was described by Rudolphi in 1809. Rudolphi's type material (one male and four females) was deposited in the Museum für Naturkunde (Berlin). Later, the ancient species S. ventricosus was taken as a synonym for various Cooperia spp. Our current re-examination of the type male indicated that there is a relatively good agreement with our new material from Czech deer regarding the most important characteristics of S. ventricosus (i.e., the shape and size of the male spicules); however, Rudolphi's type material is in rather poor condition. The suggested resurrection of the deer Cooperia sp. in this study as Cooperia ventricosa (Rudolphi, 1809) requires verification by collecting and analyzing new nematode material from the type locality near Greifswald.
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Affiliation(s)
- Martina Albrechtová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Prague, Czechia
| | - Eva Štefková Kašparová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Prague, Czechia
| | - Iva Langrová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Prague, Czechia
| | - Vlastimil Hart
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Science Prague, Prague, Czechia
| | - Birger Neuhaus
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity, Berlin, Germany
| | - Ivana Jankovská
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Prague, Czechia
| | - Miroslav Petrtýl
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Prague, Czechia
| | - Jan Magdálek
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Prague, Czechia
| | - Marta Špakulová
- Institute of Parasitology, Slovak Academy of Sciences, Košice, Slovakia
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Mota APZ, Koutsovoulos GD, Perfus-Barbeoch L, Despot-Slade E, Labadie K, Aury JM, Robbe-Sermesant K, Bailly-Bechet M, Belser C, Péré A, Rancurel C, Kozlowski DK, Hassanaly-Goulamhoussen R, Da Rocha M, Noel B, Meštrović N, Wincker P, Danchin EGJ. Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats. Nat Commun 2024; 15:773. [PMID: 38316773 PMCID: PMC10844300 DOI: 10.1038/s41467-024-44914-y] [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: 04/20/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Using long-read sequencing, we assembled and unzipped the polyploid genomes of Meloidogyne incognita, M. javanica and M. arenaria, three of the most devastating plant-parasitic nematodes. We found the canonical nematode telomeric repeat to be missing in these and other Meloidogyne genomes. In addition, we find no evidence for the enzyme telomerase or for orthologs of C. elegans telomere-associated proteins, suggesting alternative lengthening of telomeres. Instead, analyzing our assembled genomes, we identify species-specific composite repeats enriched mostly at one extremity of contigs. These repeats are G-rich, oriented, and transcribed, similarly to canonical telomeric repeats. We confirm them as telomeric using fluorescent in situ hybridization. These repeats are mostly found at one single end of chromosomes in these species. The discovery of unusual and specific complex telomeric repeats opens a plethora of perspectives and highlights the evolutionary diversity of telomeres despite their central roles in senescence, aging, and chromosome integrity.
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Affiliation(s)
- Ana Paula Zotta Mota
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France.
| | - Georgios D Koutsovoulos
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Laetitia Perfus-Barbeoch
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Evelin Despot-Slade
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Karine Robbe-Sermesant
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Marc Bailly-Bechet
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Arthur Péré
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Corinne Rancurel
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Djampa K Kozlowski
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
- Université Côte d'Azur, Center of Modeling, Simulation, and Interactions, 28 Avenue Valrose, 06000, Nice, France
| | - Rahim Hassanaly-Goulamhoussen
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Martine Da Rocha
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Nevenka Meštrović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 400 routes des Chappes, 06903, Sophia-Antipolis, France.
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9
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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.
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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
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10
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Mishina T, Chiu MC, Hashiguchi Y, Oishi S, Sasaki A, Okada R, Uchiyama H, Sasaki T, Sakura M, Takeshima H, Sato T. Massive horizontal gene transfer and the evolution of nematomorph-driven behavioral manipulation of mantids. Curr Biol 2023; 33:4988-4994.e5. [PMID: 37863060 DOI: 10.1016/j.cub.2023.09.052] [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: 07/20/2023] [Revised: 08/21/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023]
Abstract
To complete their life cycle, a wide range of parasites must manipulate the behavior of their hosts.1 This manipulation is a well-known example of the "extended phenotype,2" where genes in one organism have phenotypic effects on another organism. Recent studies have explored the parasite genes responsible for such manipulation of host behavior, including the potential molecular mechanisms.3,4 However, little is known about how parasites have acquired the genes involved in manipulating phylogenetically distinct hosts.4 In a fascinating example of the extended phenotype, nematomorph parasites have evolved the ability to induce their terrestrial insect hosts to enter bodies of water, where the parasite then reproduces. Here, we comprehensively analyzed nematomorphs and their mantid hosts, focusing on the transcriptomic changes associated with host manipulations and sequence similarity between host and parasite genes to test molecular mimicry. The nematomorph's transcriptome changed during host manipulation, whereas no distinct changes were found in mantids. We then discovered numerous possible host-derived genes in nematomorphs, and these genes were frequently up-regulated during host manipulation. Our findings suggest a possible general role of horizontal gene transfer (HGT) in the molecular mechanisms of host manipulation, as well as in the genome evolution of manipulative parasites. The evidence of HGT between multicellular eukaryotes remains scarce but is increasing and, therefore, elucidating its mechanisms will advance our understanding of the enduring influence of HGT on the evolution of the web of life.
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Affiliation(s)
- Tappei Mishina
- Laboratory for Chromosome Segregation, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 6500047, Japan.
| | - Ming-Chung Chiu
- Department of Biology, Graduate School of Sciences, Kobe University, Kobe 6578501, Japan; Department of Entomology, National Taiwan University, Taipei 50007, Taiwan
| | - Yasuyuki Hashiguchi
- Department of Biology, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki 5690801, Japan.
| | - Sayumi Oishi
- Department of Biology, Graduate School of Sciences, Kobe University, Kobe 6578501, Japan
| | - Atsunari Sasaki
- Department of Biology, Graduate School of Sciences, Kobe University, Kobe 6578501, Japan
| | - Ryuichi Okada
- Department of Biology, Graduate School of Sciences, Kobe University, Kobe 6578501, Japan
| | - Hironobu Uchiyama
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 1568502, Japan
| | - Takeshi Sasaki
- Graduate School of Bioresource Development, Tokyo University of Agriculture, Atsugi 2430034, Japan
| | - Midori Sakura
- Department of Biology, Graduate School of Sciences, Kobe University, Kobe 6578501, Japan
| | - Hirohiko Takeshima
- Research Center of Marine Bioresources, Department of Marine Bioscience, Fukui Prefectural University, 49-8-2, Katsumi, Obama, Fukui Prefecture 9170116, Japan
| | - Takuya Sato
- Department of Biology, Graduate School of Sciences, Kobe University, Kobe 6578501, Japan; Center for Ecological Research, Kyoto University, Otsu 5202113, Japan.
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11
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Huo C, Bao F, Long H, Qin T, Zhang S. The complete mitochondrial genome of Wellcomia compar (Spirurina: Oxyuridae) and its genome characterization and phylogenetic analysis. Sci Rep 2023; 13:14426. [PMID: 37660220 PMCID: PMC10475117 DOI: 10.1038/s41598-023-41638-9] [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: 03/27/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023] Open
Abstract
Wellcomia compar (Spirurina: Oxyuridae) is a pinworm that infects wild and captive porcupines. Despite clear records of its morphological structure, its genetics, systematics, and biology are poorly understood. This study aimed to determine the complete mitochondrial (mt) genome of W. compar and reconstruct its phylogenetic relationship with other nematodes. We sequenced the complete mt genome of W. comparand conducted phylogenetic analyses using concatenated coding sequences of 12 protein-coding genes (PCGs) by maximum likelihood and Bayesian inference. The complete mt genome is 14,373 bp in size and comprises 36 genes, including 12 protein-coding, two rRNA and 22 tRNA genes. Apart from 28 intergenic regions, one non-coding region and one overlapping region also occur. A comparison of the gene arrangements of Oxyuridomorpha revealed relatively similar features in W. compar and Wellcomia siamensis. Phylogenetic analysis also showed that W. compar and W. siamensis formed a sister group. In Oxyuridomorpha the genetic distance between W. compar and W. siamensis was 0.0805. This study reports, for the first time, the complete W. compar mt genome sequence obtained from Chinese porcupines. It provides genetic markers for investigating the taxonomy, population genetics, and phylogenetics of pinworms from different hosts and has implications for the diagnosis, prevention, and control of parasitic diseases in porcupines and other animals.
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Affiliation(s)
- Chunmao Huo
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China
| | - Fengyun Bao
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China
| | - Hong Long
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China
| | - Tingyang Qin
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China
| | - Shibin Zhang
- Laboratory Animal Center, Zunyi Medical University, Zunyi, 563006, China.
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12
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Fox BW, Helf MJ, Burkhardt RN, Artyukhin AB, Curtis BJ, Palomino DF, Chaturbedi A, Tauffenberger A, Wrobel CJJ, Zhang YK, Lee SS, Schroeder FC. Evolutionarily related host and microbial pathways regulate fat desaturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555782. [PMID: 37693574 PMCID: PMC10491262 DOI: 10.1101/2023.08.31.555782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Fatty acid desaturation is central to metazoan lipid metabolism and provides building blocks of membrane lipids and precursors of diverse signaling molecules. Nutritional conditions and associated microbiota regulate desaturase expression1-4, but the underlying mechanisms have remained unclear. Here, we show that endogenous and microbiota-dependent small molecule signals promote lipid desaturation via the nuclear receptor NHR-49/PPARα in C. elegans. Untargeted metabolomics of a β-oxidation mutant, acdh-11, in which expression of the stearoyl-CoA desaturase FAT-7/SCD1 is constitutively increased, revealed accumulation of a β-cyclopropyl fatty acid, becyp#1, that potently activates fat-7 expression via NHR-49. Biosynthesis of becyp#1 is strictly dependent on expression of cyclopropane synthase by associated bacteria, e.g., E. coli. Screening for structurally related endogenous metabolites revealed a β-methyl fatty acid, bemeth#1, whose activity mimics that of microbiota-dependent becyp#1, but is derived from a methyltransferase, fcmt-1, that is conserved across Nematoda and likely originates from bacterial cyclopropane synthase via ancient horizontal gene transfer. Activation of fat-7 expression by these structurally similar metabolites is controlled by distinct mechanisms, as microbiota-dependent becyp#1 is metabolized by a dedicated β-oxidation pathway, while the endogenous bemeth#1 is metabolized via α-oxidation. Collectively, we demonstrate that evolutionarily related biosynthetic pathways in metazoan host and associated microbiota converge on NHR-49/PPARα to regulate fat desaturation.
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Affiliation(s)
- Bennett W Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Maximilian J Helf
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Russell N Burkhardt
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Alexander B Artyukhin
- Chemistry Department, College of Environmental Science and Forestry, State University of New York, Syracuse, New York 13210, United States
| | - Brian J Curtis
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Diana Fajardo Palomino
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Amaresh Chaturbedi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
| | - Arnaud Tauffenberger
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Chester J J Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Ying K Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, United States
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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13
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Suring W, Hoogduin D, Le Ngoc G, Brouwer A, van Straalen NM, Roelofs D. Nonribosomal Peptide Synthetases in Animals. Genes (Basel) 2023; 14:1741. [PMID: 37761881 PMCID: PMC10531068 DOI: 10.3390/genes14091741] [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: 07/23/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are a class of cytosolic enzymes that synthesize a range of bio-active secondary metabolites including antibiotics and siderophores. They are widespread among both prokaryotes and eukaryotes but are considered rare among animals. Recently, several novel NRPS genes have been described in nematodes, schistosomes, and arthropods, which led us to investigate how prevalent NRPS genes are in the animal kingdom. We screened 1059 sequenced animal genomes and showed that NRPSs were present in 7 out of the 19 phyla analyzed. A phylogenetic analysis showed that the identified NRPSs form clades distinct from other adenylate-forming enzymes that contain similar domains such as fatty acid synthases. NRPSs show a remarkably scattered distribution over the animal kingdom. They are especially abundant in rotifers and nematodes. In rotifers, we found a large variety of domain architectures and predicted substrates. In the nematode Plectus sambesii, we identified the beta-lactam biosynthesis genes L-δ-(α-aminoadipoyl)-L-cysteinyl-D-valine synthetase, isopenicillin N synthase, and deacetoxycephalosporin C synthase that catalyze the formation of beta-lactam antibiotics in fungi and bacteria. These genes are also present in several species of Collembola, but not in other hexapods analyzed so far. In conclusion, our survey showed that NRPS genes are more abundant and widespread in animals than previously known.
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Affiliation(s)
- Wouter Suring
- A-LIFE Ecology and Evolution, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
- Department of Academy Technology & Innovation, NHL Stenden University of Applied Sciences, Rengerslaan 8-10, 8917 DD Leeuwarden, The Netherlands
| | - Dylan Hoogduin
- A-LIFE Ecology and Evolution, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Giang Le Ngoc
- A-LIFE Ecology and Evolution, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
- Biomedical Primate Research Centre, Lange Kleiweg 161, 2282 GJ Rijswijk, The Netherlands
| | - Abraham Brouwer
- BioDetection Systems, Science Park 406, 1098 XH Amsterdam, The Netherlands
| | - Nico M. van Straalen
- A-LIFE Ecology and Evolution, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Dick Roelofs
- A-LIFE Ecology and Evolution, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
- Keygene N.V., Agro Business Park 90, 6708 PW Wageningen, The Netherlands
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14
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Lee YC, Ke HM, Liu YC, Lee HH, Wang MC, Tseng YC, Kikuchi T, Tsai IJ. Single-worm long-read sequencing reveals genome diversity in free-living nematodes. Nucleic Acids Res 2023; 51:8035-8047. [PMID: 37526286 PMCID: PMC10450198 DOI: 10.1093/nar/gkad647] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively, from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from early-branching species in Chromadoria, Dorylaimia and Enoplia. The basal Chromadoria and Enoplia species had larger genome sizes, ranging from 136.6 to 738.8 Mb, compared with those in the other clades. Nine mitogenomes were fully assembled, and displayed a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.
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Affiliation(s)
- Yi-Chien Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, 116 Wenshan, Taipei, Taiwan
| | - Huei-Mien Ke
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Min-Chen Wang
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, 262 I-Lan County, Taiwan
| | - Yung-Che Tseng
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, 262 I-Lan County, Taiwan
| | - Taisei Kikuchi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Isheng Jason Tsai
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
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15
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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.
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16
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Ceron-Noriega A, Almeida MV, Levin M, Butter F. Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis. Genome Res 2023; 33:112-128. [PMID: 36653121 PMCID: PMC9977148 DOI: 10.1101/gr.277070.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/18/2022] [Indexed: 01/19/2023]
Abstract
Nematodes encompass more than 24,000 described species, which were discovered in almost every ecological habitat, and make up >80% of metazoan taxonomic diversity in soils. The last common ancestor of nematodes is believed to date back to ∼650-750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry-based proteomics and machine-learning quality control in an approach called proteotranscriptomics, we improve gene annotations for nine genome-sequenced nematode species and provide new gene annotations for three additional species without genome assemblies. Emphasizing the sensitivity of our methodology, we provide evidence for two hitherto undescribed genes in the model organism Caenorhabditis elegans Extensive phylogenetic systems analysis using this comprehensive proteome annotation provides new insights into evolutionary processes of this metazoan group.
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Affiliation(s)
| | | | - Michal Levin
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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17
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Wang B, Pandey T, Long Y, Delgado-Rodriguez SE, Daugherty MD, Ma DK. Co-opted genes of algal origin protect C. elegans against cyanogenic toxins. Curr Biol 2022; 32:4941-4948.e3. [PMID: 36223775 PMCID: PMC9691542 DOI: 10.1016/j.cub.2022.09.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/31/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
Abstract
Amygdalin is a cyanogenic glycoside enriched in the tissues of many edible plants, including seeds of stone fruits such as cherry (Prunus avium), peach (Prunus persica), and apple (Malus domestica). These plants biosynthesize amygdalin in defense against herbivore animals, as amygdalin generates poisonous cyanide upon plant tissue destruction.1,2,3,4 Poisonous to many animals, amygdalin-derived cyanide is detoxified by potent enzymes commonly found in bacteria and plants but not most animals.5 Here we show that the nematode C. elegans can detoxify amygdalin by a genetic pathway comprising cysl-1, egl-9, hif-1, and cysl-2. A screen of a natural product library for hypoxia-independent regulators of HIF-1 identifies amygdalin as a potent activator of cysl-2, a HIF-1 transcriptional target that encodes a cyanide detoxification enzyme in C. elegans. As a cysl-2 paralog similarly essential for amygdalin resistance, cysl-1 encodes a protein homologous to cysteine biosynthetic enzymes in bacteria and plants but functionally co-opted in C. elegans. We identify exclusively HIF-activating egl-9 mutations in a cysl-1 suppressor screen and show that cysl-1 confers amygdalin resistance by regulating HIF-1-dependent cysl-2 transcription to protect against amygdalin toxicity. Phylogenetic analysis indicates that cysl-1 and cysl-2 were likely acquired from green algae through horizontal gene transfer (HGT) and functionally co-opted in protection against amygdalin. Since acquisition, these two genes evolved division of labor in a cellular circuit to detect and detoxify cyanide. Thus, algae-to-nematode HGT and subsequent gene function co-option events may facilitate host survival and adaptation to adverse environmental stresses and biogenic toxins.
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Affiliation(s)
- Bingying Wang
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Taruna Pandey
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Yong Long
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | | | - Matthew D Daugherty
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA.
| | - Dengke K Ma
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
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18
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Tchesunov AV, Nikolaeva OV, Rusin LY, Sanamyan NP, Panina EG, Miljutin DM, Gorelysheva DI, Pegova AN, Khromova MR, Mardashova MV, Mikhailov KV, Yushin VV, Petrov NB, Lyubetsky VA, Nikitin MA, Aleoshin VV. Paraphyly of Marimermithida refines primary routes of transition to parasitism in roundworms. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Parasitic life-strategies in the phylum Nematoda (roundworms) are remarkably diverse and intricate in terms of evolution and taxonomy. By analysing novel rDNA data obtained on rare host-associated groups with unusual biology, we reveal paraphyly of the last major taxon with uncertain higher-rank classification that united solely parasitic nematodes (Marimermithida) to show that primarily marine parasitism only emerged independently and repeatedly in a few free-living lineages. We report secondary seaward ingression of land-based parasites (Mermithida) via invading hosts in the subtidal zone to illustrate the host-borne scenario of oceanic fish and mammal colonization by primarily terrestrial parasites (Spiruria). We also present the first molecular data on marine nematodes from unicellular hosts (foraminiferan protozoans) to demonstrate the independent origins of exploitative nematode associations at a microscopic scale. We argue that, in contrast with primarily intestinal associations arising from saprotrophy and commensalism, non-intestinal host capture (colonization of host body cavity or internal organs) is likely to be a primary route of transition to truly exploitative parasitism in roundworms. Predispositions to host capture in nematode morphology, ecology and life cycles imply its evolution as part of innate pre-adaptations to crossing environmental boundaries to enable multiple successful transitions to parasitism in the phylum history.
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Affiliation(s)
- Alexei V Tchesunov
- Faculty of Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | - Olga V Nikolaeva
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
| | - Leonid Yu Rusin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
| | - Nadezda P Sanamyan
- Kamchatka Branch of Pacific Geographical Institute, Far Eastern Branch of the Russian Academy of Sciences , Petropavlovsk-Kamchatsky , Russia
| | - Elena G Panina
- Kamchatka Branch of Pacific Geographical Institute, Far Eastern Branch of the Russian Academy of Sciences , Petropavlovsk-Kamchatsky , Russia
| | | | - Daria I Gorelysheva
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences , Moscow , Russia
| | - Anna N Pegova
- Faculty of Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | - Maria R Khromova
- Faculty of Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | - Maria V Mardashova
- Marine Research Center, Lomonosov Moscow State University , Moscow , Russia
| | - Kirill V Mikhailov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
| | - Vladimir V Yushin
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences , Vladivostok , Russia
| | - Nikolai B Petrov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
| | - Vassily A Lyubetsky
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
| | - Mikhail A Nikitin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
| | - Vladimir V Aleoshin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
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Complete Mitogenome of Cruznema Tripartitum Confirms Highly Conserved Gene Arrangement within Family Rhabditidae. J Nematol 2022; 54:20220029. [PMID: 36338422 PMCID: PMC9583413 DOI: 10.2478/jofnem-2022-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial genomes have widely been used as molecular markers in understanding the patterns and processes of nematode evolution. The species in genus Cruznema are free-living bacterivores as well as parasites of crickets and mollusks. The complete mitochondrial genome of C. tripartitum was determined through high-throughput sequencing as the first sequenced representative of the genus Cruznema. The genome is comprised of 14,067 bp nucleotides, and includes 12 protein-coding, two rRNA, and 22 tRNA genes. Phylogenetic analyses based on amino acid data support C. tripartitum as a sister to the clade containing Caenorhabditis elegans and Oscheius chongmingensis. The analysis of gene arrangement suggested that C. tripartitum shares the same gene order with O. chongmingensis, Litoditis marina, Diplocapter coronatus, genus Caenorhabditis, and Pristionchus pacificus. Thus, the mitochondrial gene arrangement is highly conserved in the family Rhabditidae as well as some species in Diplogasteridae.
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