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Caña-Bozada V, Morales-Serna FN, Fajer-Ávila EJ, Llera-Herrera R. De novo transcriptome assembly and identification of G-Protein-Coupled-Receptors (GPCRs) in two species of monogenean parasites of fish. Parasite 2022; 29:51. [PMID: 36350193 PMCID: PMC9645230 DOI: 10.1051/parasite/2022052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/13/2022] [Indexed: 11/11/2022] Open
Abstract
Genomic resources for Platyhelminthes of the class Monogenea are scarce, despite the diversity of these parasites, some species of which are highly pathogenic to their fish hosts. This work aimed to generate de novo-assembled transcriptomes of two monogenean species, Scutogyrus longicornis (Dactylogyridae) and Rhabdosynochus viridisi (Diplectanidae), providing a protocol for cDNA library preparation with low input samples used in single cell transcriptomics. This allowed us to work with sub-microgram amounts of total RNA with success. These transcriptomes consist of 25,696 and 47,187 putative proteins, respectively, which were further annotated according to the Swiss-Prot, Pfam, GO, KEGG, and COG databases. The completeness values of these transcriptomes evaluated with BUSCO against Metazoa databases were 54.1% and 73%, respectively, which is in the range of other monogenean species. Among the annotations, a large number of terms related to G-protein-coupled receptors (GPCRs) were found. We identified 109 GPCR-like sequences in R. viridisi, and 102 in S. longicornis, including family members specific for Platyhelminthes. Rhodopsin was the largest family according to GRAFS classification. Two putative melatonin receptors found in S. longicornis represent the first record of this group of proteins in parasitic Platyhelminthes. Forty GPCRs of R. viridisi and 32 of S. longicornis that were absent in Vertebrata might be potential drug targets. The present study provides the first publicly available transcriptomes for monogeneans of the subclass Monopisthocotylea, which can serve as useful genomic datasets for functional genomic research of this important group of parasites.
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Affiliation(s)
- Víctor Caña-Bozada
- Centro de Investigación en Alimentación y Desarrollo, A.C. Unidad Mazatlán en Acuicultura y Manejo Ambiental Mazatlán Sinaloa 82112 Mexico
| | - F. Neptalí Morales-Serna
- Instituto de Ciencias del Mar y Limnología, Unidad Académica Mazatlán, Universidad Nacional Autónoma de México Mazatlán Sinaloa 82040 Mexico
| | - Emma J. Fajer-Ávila
- Centro de Investigación en Alimentación y Desarrollo, A.C. Unidad Mazatlán en Acuicultura y Manejo Ambiental Mazatlán Sinaloa 82112 Mexico
| | - Raúl Llera-Herrera
- Instituto de Ciencias del Mar y Limnología, Unidad Académica Mazatlán, Universidad Nacional Autónoma de México Mazatlán Sinaloa 82040 Mexico
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Geraerts M, Huyse T, Barson M, Bassirou H, Bilong Bilong CF, Bitja Nyom AR, Chocha Manda A, Cruz-Laufer AJ, Kalombo Kabalika C, Kapepula Kasembele G, Muterezi Bukinga F, Njom S, Artois T, Vanhove MPM. Mosaic or melting pot: The use of monogeneans as a biological tag and magnifying glass to discriminate introduced populations of Nile tilapia in sub-Saharan Africa. Genomics 2022; 114:110328. [PMID: 35276332 DOI: 10.1016/j.ygeno.2022.110328] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 02/10/2022] [Accepted: 03/06/2022] [Indexed: 01/14/2023]
Abstract
The origin of introduced Nile tilapia stocks in sub-Saharan Africa is largely unknown. In this study, the potential of monogeneans as a biological tag and magnifying glass is tested to reveal their hosts' stocking history. The monogenean gill community of different Nile tilapia populations in sub-Saharan Africa was explored, and a phylogeographic analysis was performed based on the mitogenomes of four dactylogyrid species (Cichlidogyrus halli, C. sclerosus, C. thurstonae, and Scutogyrus longicornis). Our results encourage the use of dactylogyrids as biological tags. The magnifying glass hypothesis is only confirmed for C. thurstonae, highlighting the importance of the absence of other potential hosts as prerequisites for a parasite to act as a magnifying glass. With the data generated here, we are the first to extract mitogenomes from individual monogeneans and to perform an upscaled survey of the comparative phylogeography of several monogenean species with unprecedented diagnostic resolution.
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Affiliation(s)
- Mare Geraerts
- UHasselt - Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium.
| | - Tine Huyse
- Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Maxwell Barson
- Department of Biological Sciences, University of Zimbabwe, Harare, Zimbabwe; Department of Biological Sciences, University of Botswana, Gaborone, Botswana; Lake Kariba Research Station, University of Zimbabwe, Kariba, Zimbabwe
| | - Hassan Bassirou
- Department of Biological Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon
| | | | - Arnold R Bitja Nyom
- Department of Biological Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon; Department of Management of Fisheries and Aquatic Ecosystems, Institute of Fisheries, University of Douala, Douala, Cameroon
| | - Auguste Chocha Manda
- Unité de Recherche en Biodiversité et Exploitation durable des Zones Humides (BEZHU), Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Armando J Cruz-Laufer
- UHasselt - Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
| | - Clément Kalombo Kabalika
- Unité de Recherche en Biodiversité et Exploitation durable des Zones Humides (BEZHU), Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Gyrhaiss Kapepula Kasembele
- Unité de Recherche en Biodiversité et Exploitation durable des Zones Humides (BEZHU), Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Fidel Muterezi Bukinga
- Section de Parasitologie, Département de Biologie, Centre de Recherche en Hydrobiologie, Uvira, Democratic Republic of the Congo
| | - Samuel Njom
- Department of Biological Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon
| | - Tom Artois
- UHasselt - Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
| | - Maarten P M Vanhove
- UHasselt - Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium; Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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3
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Cruz-Laufer AJ, Pariselle A, Jorissen MWP, Muterezi Bukinga F, Al Assadi A, Van Steenberge M, Koblmüller S, Sturmbauer C, Smeets K, Huyse T, Artois T, Vanhove MPM. Somewhere I belong: phylogeny and morphological evolution in a species-rich lineage of ectoparasitic flatworms infecting cichlid fishes. Cladistics 2022; 38:465-512. [PMID: 35488795 DOI: 10.1111/cla.12506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
A substantial portion of biodiversity has evolved through adaptive radiation. However, the effects of explosive speciation on species interactions remain poorly understood. Metazoan parasites infecting radiating host lineages could improve our knowledge because of their intimate host relationships. Yet limited molecular, phenotypic and ecological data discourage multivariate analyses of evolutionary patterns and encourage the use of discrete characters. Here, we assemble new molecular, morphological and host range data widely inferred from a species-rich lineage of parasites (Cichlidogyrus, Platyhelminthes: Monogenea) infecting cichlid fishes to address data scarcity. We infer a multimarker (28S/18S rDNA, ITS1, COI mtDNA) phylogeny of 58 of 137 species and characterize major lineages through synapomorphies inferred from mapping morphological characters. We predict the phylogenetic position of species without DNA data through shared character states, a morphological phylogenetic analysis, and a classification analysis with support vector machines. Based on these predictions and a cluster analysis, we assess the systematic informativeness of continuous characters, search for continuous equivalents for discrete characters, and suggest new characters for morphological traits not analysed to date. We also model the attachment/reproductive organ and host range evolution using the data for 136 of 137 described species and multivariate phylogenetic comparative methods (PCMs). We show that discrete characters not only can mask phylogenetic signals, but also are key for characterizing species groups. Regarding the attachment organ morphology, a divergent evolutionary regime for at least one lineage was detected and a limited morphological variation indicates host and environmental parameters affecting its evolution. However, moderate success in predicting phylogenetic positions, and a low systematic informativeness and high multicollinearity of morphological characters call for a revaluation of characters included in species characterizations.
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Affiliation(s)
- Armando J Cruz-Laufer
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium
| | - Antoine Pariselle
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France.,Faculty of Sciences, Laboratory "Biodiversity, Ecology and Genome", Research Centre "Plant and Microbial Biotechnology, Biodiversity and Environment", Mohammed V University, Rabat, Morocco
| | - Michiel W P Jorissen
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium.,Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Fidel Muterezi Bukinga
- Section de Parasitologie, Département de Biologie, Centre de Recherche en Hydrobiologie, Uvira, Democratic Republic of the Congo
| | - Anwar Al Assadi
- Fraunhofer Institute for Manufacturing Engineering and Automation IPA, Nobelstraße 12, Stuttgart, 70569, Germany
| | - Maarten Van Steenberge
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium.,Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, Brussels, B-1000, Belgium
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Karen Smeets
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium
| | - Tine Huyse
- Section de Parasitologie, Département de Biologie, Centre de Recherche en Hydrobiologie, Uvira, Democratic Republic of the Congo.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| | - Tom Artois
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium
| | - Maarten P M Vanhove
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
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Rahmouni C, Vanhove MP, Koblmüller S, Šimková A. Molecular phylogeny and speciation patterns in host-specific monogeneans (Cichlidogyrus, Dactylogyridae) parasitizing cichlid fishes (Cichliformes, Cichlidae) in lake tanganyika. Int J Parasitol 2022; 52:359-375. [DOI: 10.1016/j.ijpara.2021.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 12/01/2022]
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Kmentová N, Cruz-Laufer AJ, Pariselle A, Smeets K, Artois T, Vanhove MPM. Dactylogyridae 2022: a meta-analysis of phylogenetic studies and generic diagnoses of parasitic flatworms using published genetic and morphological data. Int J Parasitol 2022; 52:427-457. [PMID: 35245493 DOI: 10.1016/j.ijpara.2022.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/16/2022]
Abstract
Dactylogyridae is one of the most studied families of parasitic flatworms with more than 1000 species and 166 genera described to date including ecto- and endoparasites. Dactylogyrid monogeneans were suggested as model organisms for host-parasite macroevolutionary and biogeographical studies due to the scientific and economic importance of some of their host lineages. Consequently, an array of phylogenetic research into different dactylogyrid lineages has been produced over the past years but the last family-wide study was published 16 years ago. Here, we provide a meta-analysis of the phylogenetic relationships of Dactylogyridae including representatives of all genera with available molecular data (n=67). First, we investigate the systematic informativeness of morphological characters widely used to diagnose dactylogyrid genera through a parsimony analysis of the characters, character mapping, and phylogenetic comparative methods. Second, we provide an overview of the current state of the systematics of the family and its subfamilies, and summarise potentially poly- and paraphyletic genera. Third, we elaborate on the implications of taxonomic, citation, and confirmation bias in past studies. Fourth, we discuss host range, biogeographical, and freshwater-marine patterns. We found two well-supported macroclades which we assigned to the subfamilies Dactylogyrinae and Ancyrocephalinae. These subfamilies further include 16 well-supported clades with only a few synapomorphies that could be deduced from generic diagnoses in the literature. Furthermore, few morphological characters considered systematically informative at the genus level display a strong phylogenetic signal. However, the parsimony analysis suggests that these characters provide little information on the relationships between genera. We conclude that a strong taxonomic bias and low coverage of DNA sequences and regions limit knowledge on morphological and biogeographical evolutionary patterns that can be inferred from these results. We propose addressing potential citation and confirmation biases through a 'level playing field' multiple sequence alignment as provided by this study.
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Affiliation(s)
- Nikol Kmentová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic; Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Faculty of Sciences, UHasselt - Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium.
| | - Armando J Cruz-Laufer
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Faculty of Sciences, UHasselt - Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
| | - Antoine Pariselle
- ISEM, CNRS, Université de Montpellier, IRD, Montpellier, France; Laboratory "Biodiversity, Ecology and Genome", Mohammed V University in Rabat, Faculty of Sciences, 4 avenue Ibn Batouta, BP 1014, Rabat, Morocco
| | - Karen Smeets
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Faculty of Sciences, UHasselt - Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
| | - Tom Artois
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Faculty of Sciences, UHasselt - Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
| | - Maarten P M Vanhove
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic; Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Faculty of Sciences, UHasselt - Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
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Contrasting Host-Parasite Population Structure: Morphology and Mitogenomics of a Parasitic Flatworm on Pelagic Deepwater Cichlid Fishes from Lake Tanganyika. BIOLOGY 2021; 10:biology10080797. [PMID: 34440029 PMCID: PMC8389663 DOI: 10.3390/biology10080797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/11/2022]
Abstract
Little phylogeographic structure is presumed for highly mobile species in pelagic zones. Lake Tanganyika is a unique ecosystem with a speciose and largely endemic fauna famous for its remarkable evolutionary history. In bathybatine cichlid fishes, the pattern of lake-wide population differentiation differs among species. We assessed the congruence between the phylogeographic structure of bathybatine cichlids and their parasitic flatworm Cichlidogyrus casuarinus to test the magnifying glass hypothesis. Additionally, we evaluated the use of a PoolSeq approach to study intraspecific variation in dactylogyrid monogeneans. The lake-wide population structure of C. casuarinus ex Hemibates stenosoma was assessed based on a portion of the cox1 gene combined with morphological characterisation. Additionally, intraspecific mitogenomic variation among 80 parasite samples from one spatially constrained metapopulation was assessed using shotgun NGS. While no clear geographic genetic structure was detected in parasites, both geographic and host-related phenotypic variation was apparent. The incongruence with the genetic north-south gradient observed in H. stenosoma may be explained by the broad host range of this flatworm including eupelagic bathybatine host species that form panmictic populations across the lake. In addition, we present the first parasite mitogenome from Lake Tanganyika and propose a methodological framework for studying the intraspecific mitogenomic variation of dactylogyrid monogeneans.
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Mitochondrial genome of Rhabdosynochus viridisi (Monogenea: Diplectanidae), a parasite of Pacific white snook Centropomus viridis. J Helminthol 2021; 95:e21. [PMID: 33875027 DOI: 10.1017/s0022149x21000146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report the nearly complete mitochondrial genome of Rhabdosynochus viridisi - the first for this genus - achieved by combining shotgun sequencing of genomic and cDNA libraries prepared using low-input protocols. This integration of genomic information leads us to correct the annotation of the gene features. The mitochondrial genome consists of 13,863 bp. Annotation resulted in the identification of 12 protein-encoding genes, 22 tRNA genes and two rRNA genes. Three non-coding regions, delimited by three tRNAs, were found between the genes nad5 and cox3. A phylogenetic analysis grouped R. viridisi with three other species of diplectanid monogeneans for which mitochondrial genomes are available.
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