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Vorel J, Kmentová N, Hahn C, Bureš P, Kašný M. An insight into the functional genomics and species classification of Eudiplozoon nipponicum (Monogenea, Diplozoidae), a haematophagous parasite of the common carp Cyprinus carpio. BMC Genomics 2023; 24:363. [PMID: 37380941 DOI: 10.1186/s12864-023-09461-8] [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: 03/10/2023] [Accepted: 06/16/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND Monogenea (Platyhelminthes, Neodermata) are the most species-rich class within the Neodermata superclass of primarily fish parasites. Despite their economic and ecological importance, monogenean research tends to focus on their morphological, phylogenetic, and population characteristics, while comprehensive omics analyses aimed at describing functionally important molecules are few and far between. We present a molecular characterisation of monogenean representative Eudiplozoon nipponicum, an obligate haematophagous parasite infecting the gills of the common carp. We report its nuclear and mitochondrial genomes, present a functional annotation of protein molecules relevant to the molecular and biochemical aspect of physiological processes involved in interactions with the fish hosts, and re-examinate the taxonomic position of Eudiplozoon species within the Diplozoidae family. RESULTS We have generated 50.81 Gbp of raw sequencing data (Illumina and Oxford Nanopore reads), bioinformatically processed, and de novo assembled them into a genome draft 0.94 Gbp long, consisting of 21,044 contigs (N50 = 87 kbp). The final assembly represents 57% of the estimated total genome size (~ 1.64 Gbp), whereby repetitive and low-complexity regions account for ~ 64% of the assembled length. In total, 36,626 predicted genes encode 33,031 proteins and homology-based annotation of protein-coding genes (PCGs) and proteins characterises 14,785 (44.76%) molecules. We have detected significant representation of functional proteins and known molecular functions. The numbers of peptidases and inhibitors (579 proteins), characterised GO terms (16,016 unique assigned GO terms), and identified KEGG Orthology (4,315 proteins) acting in 378 KEGG pathways demonstrate the variety of mechanisms by which the parasite interacts with hosts on a macromolecular level (immunomodulation, feeding, and development). Comparison between the newly assembled E. nipponicum mitochondrial genome (length of 17,038 bp) and other diplozoid monogeneans confirms the existence of two distinct Eudiplozoon species infecting different fish hosts: Cyprinus carpio and Carassius spp. CONCLUSIONS Although the amount of sequencing data and characterised molecules of monogenean parasites has recently increased, a better insight into their molecular biology is needed. The E. nipponicum nuclear genome presented here, currently the largest described genome of any monogenean parasite, represents a milestone in the study of monogeneans and their molecules but further omics research is needed to understand these parasites' biological nature.
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Affiliation(s)
- Jiří Vorel
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic.
| | - Nikol Kmentová
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Agoralaan Gebouw D, Diepenbeek, B-3590, Belgium
| | - Christoph Hahn
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, A-8010, Austria
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Martin Kašný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
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Bachmann L, Beermann J, Brey T, de Boer HJ, Dannheim J, Edvardsen B, Ericson PGP, Holston KC, Johansson VA, Kloss P, Konijnenberg R, Osborn KJ, Pappalardo P, Pehlke H, Piepenburg D, Struck TH, Sundberg P, Markussen SS, Teschke K, Vanhove MPM. The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022. ZOOL SCR 2023. [DOI: 10.1111/zsc.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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Monnens M, Halajian A, Littlewood DTJ, Briscoe AG, Artois T, Vanhove MP. Can avian flyways reflect dispersal barriers of clinostomid parasites? First evidence from the mitogenome of Clinostomum complanatum. Gene X 2023; 851:146952. [DOI: 10.1016/j.gene.2022.146952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 09/08/2022] [Accepted: 10/03/2022] [Indexed: 11/04/2022] Open
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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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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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