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Hao CL, Yang YY, Wei NW, Liu YJ, Shi CX, Wang JP, Zhang L, Xia SZ, Yue C. Complete mitochondrial genomes of Dactylogyrus crucifer and Dactylogyrus zandti reveal distinct patterns of codon usage within Dactylogyrus. Gene 2024; 933:148935. [PMID: 39255859 DOI: 10.1016/j.gene.2024.148935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/24/2024] [Accepted: 09/06/2024] [Indexed: 09/12/2024]
Abstract
Monogeneans of the genus Dactylogyrus Diesing, 1850, the largest genus in the family Dactylogyridae, mostly parasitize the gills of cyprinoid hosts; however, only 3 Dactylogyrus' mitochondrial genomes (mitogenomes) are studied so far. The aim of this research is to extend our understanding of the mitogenomes of Dactylogyrus. We sequenced the mitogenomes of D. crucifer and D. zandti isolated from Rutilus rutilus and Abramis brama orientalis in northwest China, and then we compared these mitogenomes with other monogeneans. We used Illumina NovaSeq to sequence the entire mitochondrial genomes of D. crucifer and D. zandti and characterized the mitogenomes to understand the gene structure, gene identity, the secondary structures of the 22 tRNA genes, and relative synonymous codon usage. We used the analytic Bayesian Information and Maximum Likelihood methods to determine their associated phylogenetic trees. The mitogenomes of D. crucifer and D. zandti were 14,403 and 18,584 bp, respectively. Organization and positioning of these genes were in accordance with Dactylogyrus lamellatus and Dactylogyrus tuba. The nucleotide composition of Dactylogyridae was different from other families of Monogenea, and the A+T count of genus Dactylogyrus (54 - 58.4 %) was lower than other genus species of the family Dactylogyridea (63.9 - 78.4 %) in protein-coding genes. Dactylogyrus members displayed a codon usage bias. The relative synonymous codon used by Dactylogyrus was not conserved and was lower than other monogeneans. The codon use patterns of closely-related species isolated from closely-related hosts were identical. Phylogenetic analyses using mitogenomic dataset produced Dactylogyrus isolated from host subfamily Leuciscinae formed a sister-group. Our results contributed significantly to an increased database of mitogenomes, more than 50 %, for Dactylogyrus that may help future studies of mitochondrial genes and codon uses for the analysis of monogenean phylogenetics.
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Affiliation(s)
- Cui-Lan Hao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China; Xinjiang Key Laboratory of New Drug Study and Creation for Herbivorous Animals, China.
| | - Yuan-Yuan Yang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Nian-Wen Wei
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Yan-Jun Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Cai-Xia Shi
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Jin-Pu Wang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Li Zhang
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Shen-Zhen Xia
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
| | - Cheng Yue
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
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Gastineau R, Bouguerche C, Tazerouti F, Justine JL. Morphological and molecular characterisation of Tristoma integrum Diesing, 1850 (Monogenea, Capsalidae), including its complete mitogenome. Parasite 2023; 30:16. [PMID: 37191588 DOI: 10.1051/parasite/2023016] [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: 02/27/2023] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
Capsalids are monopisthocotylean monogenean parasites found on the skin and gills of fish. Capsalines (subfamily Capsalinae) are large-sized capsalids, parasitic on highly prized gamefish, and species of Tristoma parasitise only the gills of swordfish (Xiphias gladius). We obtained specimens of Tristoma integrum Diesing, 1850 from swordfish collected off Algeria in the Mediterranean Sea. Here, we describe the specimens, including the key systematics characters of dorsolateral body sclerites. One specimen was used for a next generation sequencing analysis but a part of it, including the sclerites, was mounted on a permanent slide, drawn, and deposited in a curated collection. We characterised the complete mitogenome, the ribosomal cluster (including 18S and 28S) and additional genes such as Elongation factor 1 alpha (EF1α) and Histone 3. We also retrieved molecular information from the host tissue present in the gut of the monogenean and provide the sequence of the complete rRNA cluster of the host, X. gladius. The mitogenome of T. integrum is 13 968 bp in length and codes for 12 protein, 2 rRNA and 22 tRNA. Phylogenies of capsalids were generated from 28S sequences and concatenated mitochondrial protein-coding genes, respectively. In the 28S phylogeny, most subfamilies based on morphology were not found to be monophyletic, but the Capsalinae were monophyletic. In both phylogenies, the closest member to Tristoma spp. was a member of the Capsaloides. In an Appendix, we report the complex nomenclatural history of Tristoma Cuvier, 1817 and its species.
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Affiliation(s)
- Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, 70-383 Szczecin, Poland
| | - Chahinez Bouguerche
- Department of Zoology, Swedish Museum of Natural History Naturhistoriska riksmuseet, Stockholm, Sweden
| | - Fadila Tazerouti
- Université des Sciences et de la Technologie Houari Boumédiène, Faculté des Sciences Biologiques, Laboratoire de Biodiversité et Environnement: Interactions - Génomes, BP 32, El Alia Bab Ezzouar, Alger, Algérie
| | - Jean-Lou Justine
- Institut Systématique Évolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005 Paris, France
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3
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Yang C, Shan B, Liu Y, Wang L, Wu Q, Luo Z, Sun D. Complete Mitochondrial Genome of Two Ectoparasitic Capsalids (Platyhelminthes: Monogenea: Monopisthocotylea): Gene Content, Composition, and Rearrangement. Genes (Basel) 2022; 13:genes13081376. [PMID: 36011287 PMCID: PMC9407395 DOI: 10.3390/genes13081376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 12/10/2022] Open
Abstract
The capsalid monogeneans are important pathogens that generally infect marine fishes and have a substantial impact on fish welfare in aquaculture systems worldwide. However, the current mitogenome information on capsalids has received little attention, limiting the understanding of their evolution and phylogenetic relationships with other monogeneans. This paper reports the complete mitochondrial genomes of Capsala katsuwoni and Capsala martinieri for the first time, which we obtained using a next-generation sequencing method. The mitogenomes of C. katsuwoni and C. martinieri are 13,265 and 13,984 bp in length, respectively. Both species contain the typical 12 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. The genome compositions show a moderate A+T bias (66.5% and 63.9% for C. katsuwoni and C. martinieri, respectively) and exhibit a negative AT skew but a positive GC skew in both species. One gene block rearrangement was found in C. katsuwoni in comparison with other capsalid species. Instead of being basal to the Gyrodactylidea and Dactylogyridea or being clustered with Dactylogyridea, all species of Capsalidea are grouped into a monophyletic clade. Our results clarify the gene rearrangement process and evolutionary status of Capsalidae and lay a foundation for further phylogenetic studies of monogeneans.
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Affiliation(s)
- Changping Yang
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Binbin Shan
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
| | - Yan Liu
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
| | - Liangming Wang
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
| | - Qiaer Wu
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
| | - Zhengli Luo
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
- School of Fisheries of Zhejiang Ocean University, Zhoushan 316022, China
| | - Dianrong Sun
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou 510300, China; (C.Y.); (B.S.); (Y.L.); (L.W.); (Q.W.); (Z.L.)
- Correspondence:
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Vorel J, Cwiklinski K, Roudnický P, Ilgová J, Jedličková L, Dalton JP, Mikeš L, Gelnar M, Kašný M. Eudiplozoon nipponicum (Monogenea, Diplozoidae) and its adaptation to haematophagy as revealed by transcriptome and secretome profiling. BMC Genomics 2021; 22:274. [PMID: 33858339 PMCID: PMC8050918 DOI: 10.1186/s12864-021-07589-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/05/2021] [Indexed: 12/12/2022] Open
Abstract
Background Ectoparasites from the family Diplozoidae (Platyhelminthes, Monogenea) belong to obligate haematophagous helminths of cyprinid fish. Current knowledge of these worms is for the most part limited to their morphological, phylogenetic, and population features. Information concerning the biochemical and molecular nature of physiological processes involved in host–parasite interaction, such as evasion of the immune system and its regulation, digestion of macromolecules, suppression of blood coagulation and inflammation, and effect on host tissue and physiology, is lacking. In this study, we report for the first time a comprehensive transcriptomic/secretome description of expressed genes and proteins secreted by the adult stage of Eudiplozoon nipponicum (Goto, 1891) Khotenovsky, 1985, an obligate sanguivorous monogenean which parasitises the gills of the common carp (Cyprinus carpio). Results RNA-seq raw reads (324,941 Roche 454 and 149,697,864 Illumina) were generated, de novo assembled, and filtered into 37,062 protein-coding transcripts. For 19,644 (53.0%) of them, we determined their sequential homologues. In silico functional analysis of E. nipponicum RNA-seq data revealed numerous transcripts, pathways, and GO terms responsible for immunomodulation (inhibitors of proteolytic enzymes, CD59-like proteins, fatty acid binding proteins), feeding (proteolytic enzymes cathepsins B, D, L1, and L3), and development (fructose 1,6-bisphosphatase, ferritin, and annexin). LC-MS/MS spectrometry analysis identified 721 proteins secreted by E. nipponicum with predominantly immunomodulatory and anti-inflammatory functions (peptidyl-prolyl cis-trans isomerase, homolog to SmKK7, tetraspanin) and ability to digest host macromolecules (cathepsins B, D, L1). Conclusions In this study, we integrated two high-throughput sequencing techniques, mass spectrometry analysis, and comprehensive bioinformatics approach in order to arrive at the first comprehensive description of monogenean transcriptome and secretome. Exploration of E. nipponicum transcriptome-related nucleotide sequences and translated and secreted proteins offer a better understanding of molecular biology and biochemistry of these, often neglected, organisms. It enabled us to report the essential physiological pathways and protein molecules involved in their interactions with the fish hosts. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07589-z.
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Affiliation(s)
- Jiří Vorel
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
| | - Krystyna Cwiklinski
- Molecular Parasitology Laboratory, Centre for One Health, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Pavel Roudnický
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jana Ilgová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Lucie Jedličková
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.,Department of Zoology and Fisheries, Centre of Infectious Animal Diseases, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Prague, Czech Republic
| | - John P Dalton
- Molecular Parasitology Laboratory, Centre for One Health, Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Libor Mikeš
- Department of Parasitology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Milan Gelnar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Martin Kašný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
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Yang C, Liu Y, Shan B, Zhang G, Zhao Y, Sun D, Yu W. The complete mitochondrial genome of the Capsaloides cristatus (Platyhelminthes, Monogenea), a pathogen of the sailfish ( Istiophorus platypterus). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1053-1055. [PMID: 33796735 PMCID: PMC7995904 DOI: 10.1080/23802359.2021.1899077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This study reports the complete mitochondrial genome of the Capsaloides cristatus (Monogenea: Capsalidae) collected from the gill lamella of Istiophorus platypterus. The total length of the mitogenome was 13,948 bp, containing 12 typical platyhelminthic protein-coding genes, 22 tRNA genes, 2 rRNA genes and a putative non-coding region, with the atp8 gene being absent. The total A + T content was 65.99%, which was significantly higher than that of the C + G content (34.01%). There were two kinds of start codons (ATG and GTG) and three kinds of terminated codons (TAA, TAG and TGA) in the 12 protein-coding genes. Phylogentic analysis revealed close relationships among the genera Capsaloides, Capsala, Benedenia and Neobenedenia with high bootstrap value supported. This study will provide useful molecular data for a better understanding of the species identification and phylogenetic position of C. cristatus.
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Affiliation(s)
- Changping Yang
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China.,Key Laboratory of South China Sea Fishery Resources Exploration & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, China.,Key Laboratory of Fishery Ecology and Environment, Guangdong Province, Guangzhou, China
| | - Yan Liu
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China.,Key Laboratory of South China Sea Fishery Resources Exploration & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, China.,Key Laboratory of Fishery Ecology and Environment, Guangdong Province, Guangzhou, China
| | - Binbin Shan
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China.,Key Laboratory of South China Sea Fishery Resources Exploration & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, China.,Key Laboratory of Fishery Ecology and Environment, Guangdong Province, Guangzhou, China
| | - Gongjun Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China.,College of Aquatic products, Tianjin Agriculture University, Tianjin, China
| | - Yu Zhao
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China.,College of Aquatic products, Tianjin Agriculture University, Tianjin, China
| | - Dianrong Sun
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China.,Key Laboratory of South China Sea Fishery Resources Exploration & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, China.,Key Laboratory of Fishery Ecology and Environment, Guangdong Province, Guangzhou, China
| | - Wei Yu
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China.,Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen, China
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Roudnický P, Potěšil D, Zdráhal Z, Gelnar M, Kašný M. Laser capture microdissection in combination with mass spectrometry: Approach to characterization of tissue-specific proteomes of Eudiplozoon nipponicum (Monogenea, Polyopisthocotylea). PLoS One 2020; 15:e0231681. [PMID: 32555742 PMCID: PMC7299319 DOI: 10.1371/journal.pone.0231681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Eudiplozoon nipponicum (Goto, 1891) is a hematophagous monogenean ectoparasite which inhabits the gills of the common carp (Cyprinus carpio). Heavy infestation can lead to anemia and in conjunction with secondary bacterial infections cause poor health and eventual death of the host. This study is based on an innovative approach to protein localization which has never been used in parasitology before. Using laser capture microdissection, we dissected particular areas of the parasite body without contaminating the samples by surrounding tissue and in combination with analysis by mass spectrometry obtained tissue-specific proteomes of tegument, intestine, and parenchyma of our model organism, E. nipponicum. We successfully verified the presence of certain functional proteins (e.g. cathepsin L) in tissues where their presence was expected (intestine) and confirmed that there were no traces of these proteins in other tissues (tegument and parenchyma). Additionally, we identified a total of 2,059 proteins, including 72 peptidases and 33 peptidase inhibitors. As expected, the greatest variety was found in the intestine and the lowest variety in the parenchyma. Our results are significant on two levels. Firstly, we demonstrated that one can localize all proteins in one analysis and without using laboratory animals (antibodies for immunolocalization of single proteins). Secondly, this study offers the first complex proteomic data on not only the E. nipponicum but within the whole class of Monogenea, which was from this point of view until recently neglected.
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Affiliation(s)
- Pavel Roudnický
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- * E-mail:
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Milan Gelnar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin Kašný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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Yang C, Shan B, Liu Y, Zhao Y, Sun D. Next-generation sequencing yields the complete mitochondrial genome of the Capsala pricei Hidalgo, 1959 (Platyhelminthes: Monogenea) from South China Sea. MITOCHONDRIAL DNA PART B 2020. [DOI: 10.1080/23802359.2020.1756479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Changping Yang
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
- Key Laboratory of South China Sea Fishery Resources Exploration & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Fishery Ecology and Environment, Guangdong Province, Guangzhou, China
| | - Binbin Shan
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
- Key Laboratory of South China Sea Fishery Resources Exploration & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Fishery Ecology and Environment, Guangdong Province, Guangzhou, China
| | - Yan Liu
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
- Key Laboratory of South China Sea Fishery Resources Exploration & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Fishery Ecology and Environment, Guangdong Province, Guangzhou, China
| | - Yu Zhao
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
- Fisheries College, Tianjin Agriculture University, Tianjin, China
| | - Dianrong Sun
- South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, China
- Key Laboratory of South China Sea Fishery Resources Exploration & Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- Key Laboratory of Fishery Ecology and Environment, Guangdong Province, Guangzhou, China
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Zhang D, Zou H, Wu SG, Li M, Jakovlić I, Zhang J, Chen R, Li WX, Wang GT. Evidence for Adaptive Selection in the Mitogenome of a Mesoparasitic Monogenean Flatworm Enterogyrus malmbergi. Genes (Basel) 2019; 10:genes10110863. [PMID: 31671638 PMCID: PMC6896049 DOI: 10.3390/genes10110863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/26/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023] Open
Abstract
Whereas a majority of monogenean flatworms are ectoparasitic, i.e., parasitize on external surfaces (mainly gills) of their fish hosts, Enterogyrus species (subfamily Ancyrocephalinae) are mesoparasitic, i.e., parasitize in the stomach of the host. As there are numerous drastic differences between these two environments (including lower oxygen availability), we hypothesized that this life-history innovation might have produced adaptive pressures on the energy metabolism, which is partially encoded by the mitochondrial genome (OXPHOS). To test this hypothesis, we sequenced mitochondrial genomes of two Ancyrocephalinae species: mesoparasitic E. malmbergi and ectoparasitic Ancyrocephalus mogurndae. The mitogenomic architecture of E. malmbergi is mostly standard for monogeneans, but that of A. mogurndae exhibits some unique features: missing trnL2 gene, very low AT content (60%), a non-canonical start codon of the nad2 gene, and exceptionally long tandem-repeats in the non-coding region (253 bp). Phylogenetic analyses produced paraphyletic Ancyrocephalinae (with embedded Dactylogyrinae), but with low support values. Selective pressure (PAML and HYPHY) and protein structure analyses all found evidence for adaptive evolution in cox2 and cox3 genes of the mesoparasitic E. malmbergi. These findings tentatively support our hypothesis of adaptive evolution driven by life-history innovations in the mitogenome of this species. However, as only one stomach-inhabiting mesoparasitic monogenean was available for this analysis, our findings should be corroborated on a larger number of mesoparasitic monogeneans and by physiological studies.
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Affiliation(s)
- Dong Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100000, China.
| | - Hong Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Shan G Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100000, China.
| | - Ming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100000, China.
| | | | - Jin Zhang
- Bio-Transduction Lab, Wuhan 430075, China.
| | - Rong Chen
- Bio-Transduction Lab, Wuhan 430075, China.
| | - Wen X Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100000, China.
| | - Gui T Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100000, China.
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9
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Baeza JA, Sepúlveda FA, González MT. The complete mitochondrial genome and description of a new cryptic species of Benedenia Diesing, 1858 (Monogenea: Capsalidae), a major pathogen infecting the yellowtail kingfish Seriola lalandi Valenciennes in the South-East Pacific. Parasit Vectors 2019; 12:490. [PMID: 31623679 PMCID: PMC6798380 DOI: 10.1186/s13071-019-3711-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/11/2019] [Indexed: 01/19/2023] Open
Abstract
Background The monogenean Benedenia seriolae parasitizes fishes belonging to the genus Seriola, represents a species complex, and causes substantial impact on fish welfare in aquaculture systems worldwide. This study reports, for the first time, the complete mitochondrial genome of B. humboldti n. sp., a new cryptic species from the South-East Pacific (SEP). Methods The mitogenome of B. humboldti n. sp. was assembled from short Illumina 150 bp pair-end reads. The phylogenetic position of B. humboldti n. sp. among other closely related congeneric and confamiliar capsalids was examined using mitochondrial protein-coding genes (PCGs). Morphology of B. humboldti n. sp. was examined based on fixed and stained specimens. Results The AT-rich mitochondrial genome of B. humboldti is 13,455 bp in length and comprises 12 PCGs (atp8 was absent as in other monogenean genomes), 2 ribosomal RNA genes, and 22 transfer RNA genes. All protein-coding, ribosomal RNA, and transfer RNA genes are encoded on the H-strand. The gene order observed in the mitochondrial genome of B. humboldti n. sp. was identical to that of B. seriolae from Japan but different from that of B. seriolae from Australia. The genetic distance between B. humboldti n. sp. and B. seriolae from Japan was high. Minor but reliable differences in the shape of the penis were observed between Benedenia humboldti n. sp. and congeneric species. Conclusions Phylogenetic analyses based on PCGs in association with differences in the shape of the penis permitted us to conclude that the material from the South-East Pacific represents a new species of Benedenia infecting S. lalandi off the coast of Chile. The discovery of this parasite represents the first step to improving our understanding of infestation dynamics and to develop control strategies for this pathogen infecting the farmed yellowtail kingfish, Seriola lalandi, in the South-East Pacific.![]()
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA. .,Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, Florida, 34949, USA. .,Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
| | - Fabiola A Sepúlveda
- Laboratorio Eco-parasitologia y Epidemiologia Marina (LEPyEM), Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta, Angamos 601, Antofagasta, Chile
| | - M Teresa González
- Laboratorio Eco-parasitologia y Epidemiologia Marina (LEPyEM), Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta, Angamos 601, Antofagasta, Chile.
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Zhang D, Li WX, Zou H, Wu SG, Li M, Jakovlić I, Zhang J, Chen R, Wang GT. Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements. Parasit Vectors 2018; 11:601. [PMID: 30458858 PMCID: PMC6245931 DOI: 10.1186/s13071-018-3144-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 10/10/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent mitochondrial phylogenomics studies have reported a sister-group relationship of the orders Capsalidea and Dactylogyridea, which is inconsistent with previous morphology- and molecular-based phylogenies. As Dactylogyridea mitochondrial genomes (mitogenomes) are currently represented by only one family, to improve the phylogenetic resolution, we sequenced and characterized two dactylogyridean parasites, Lamellodiscus spari and Lepidotrema longipenis, belonging to a non-represented family Diplectanidae. RESULTS The L. longipenis mitogenome (15,433 bp) contains the standard 36 flatworm mitochondrial genes (atp8 is absent), whereas we failed to detect trnS1, trnC and trnG in L. spari (14,614 bp). Both mitogenomes exhibit unique gene orders (among the Monogenea), with a number of tRNA rearrangements. Both long non-coding regions contain a number of different (partially overlapping) repeat sequences. Intriguingly, these include putative tRNA pseudogenes in a tandem array (17 trnV pseudogenes in L. longipenis, 13 trnY pseudogenes in L. spari). Combined nucleotide diversity, non-synonymous/synonymous substitutions ratio and average sequence identity analyses consistently showed that nad2, nad5 and nad4 were the most variable PCGs, whereas cox1, cox2 and cytb were the most conserved. Phylogenomic analysis showed that the newly sequenced species of the family Diplectanidae formed a sister-group with the Dactylogyridae + Capsalidae clade. Thus Dactylogyridea (represented by the Diplectanidae and Dactylogyridae) was rendered paraphyletic (with high statistical support) by the nested Capsalidea (represented by the Capsalidae) clade. CONCLUSIONS Our results show that nad2, nad5 and nad4 (fast-evolving) would be better candidates than cox1 (slow-evolving) for species identification and population genetics studies in the Diplectanidae. The unique gene order pattern further suggests discontinuous evolution of mitogenomic gene order arrangement in the Class Monogenea. This first report of paraphyly of the Dactylogyridea highlights the need to generate more molecular data for monogenean parasites, in order to be able to clarify their relationships using large datasets, as single-gene markers appear to provide a phylogenetic resolution which is too low for the task.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Wen X. Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Shan G. Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Jin Zhang
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Rong Chen
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Gui T. Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
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Zhang D, Zou H, Wu SG, Li M, Jakovlić I, Zhang J, Chen R, Li WX, Wang GT. Three new Diplozoidae mitogenomes expose unusual compositional biases within the Monogenea class: implications for phylogenetic studies. BMC Evol Biol 2018; 18:133. [PMID: 30176801 PMCID: PMC6122551 DOI: 10.1186/s12862-018-1249-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 08/20/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND As the topologies produced by previous molecular and morphological studies were contradictory and unstable (polytomy), evolutionary relationships within the Diplozoidae family and the Monogenea class (controversial relationships among the Discocotylinea, Microcotylinea and Gastrocotylinea suborders) remain unresolved. Complete mitogenomes carry a relatively large amount of information, sufficient to provide a much higher phylogenetic resolution than traditionally used morphological traits and/or single molecular markers. However, their implementation is hampered by the scarcity of available monogenean mitogenomes. Therefore, we sequenced and characterized mitogenomes belonging to three Diplozoidae family species, and conducted comparative genomic and phylogenomic analyses for the entire Monogenea class. RESULTS Taxonomic identification was inconclusive, so two of the species were identified merely to the genus level. The complete mitogenomes of Sindiplozoon sp. and Eudiplozoon sp. are 14,334 bp and 15,239 bp in size, respectively. Paradiplozoon opsariichthydis (15,385 bp) is incomplete: an approximately 2000 bp-long gap within a non-coding region could not be sequenced. Each genome contains the standard 36 genes (atp8 is missing). G + T content and the degree of GC- and AT-skews of these three mitogenome (and their individual elements) were higher than in other monogeneans. nad2, atp6 and nad6 were the most variable PCGs, whereas cox1, nad1 and cytb were the most conserved. Mitochondrial phylogenomics analysis, conducted using concatenated amino acid sequences of all PCGs, indicates that evolutionary relationships of the three genera are: (Eudiplozoon, (Paradiplozoon, Sindiplozoon)); and of the three suborders: (Discocotylinea, (Microcotylinea, Gastrocotylinea)). These intergeneric relationships were also supported by the skewness and principal component analyses. CONCLUSIONS Our results show that nad2, atp6 and nad6 (fast-evolving) would be better candidates than cox1 (slow-evolving) for species identification and population genetics studies in Diplozoidae. Nucleotide bias and codon and amino acid usage patterns of the three diplozoid mitogenomes are more similar to cestodes and trematodes than to other monogenean flatworms. This unusual mutational bias was reflected in disproportionately long branches in the phylogram. Our study offsets the scarcity of molecular data for the subclass Polyopisthocotylea to some extent, and might provide important new insights into the evolutionary history of the three genera and three suborders.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Shan G. Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Jin Zhang
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Rong Chen
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Wen X. Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Gui T. Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
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Vanhove MPM, Briscoe AG, Jorissen MWP, Littlewood DTJ, Huyse T. The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae). BMC Genomics 2018; 19:520. [PMID: 29973152 PMCID: PMC6032552 DOI: 10.1186/s12864-018-4893-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to offer genetic resources for work on African monogeneans by providing mitogenomic data of four species (two belonging to Gyrodactylidae, two to Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective. RESULTS Using Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). Complete nuclear ribosomal operons were also retrieved, as molecular vouchers. The start codon TTG is new for Gyrodactylus and for Dactylogyridae, as is the incomplete stop codon TA for Dactylogyridae. Especially the nad2 gene is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, instead of the supposedly 'primitive' African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines. CONCLUSIONS The amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available.
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Affiliation(s)
- Maarten P. M. Vanhove
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O.Box 17, FI-00014 Helsinki, Finland
- Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
- Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
| | - Andrew G. Briscoe
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Michiel W. P. Jorissen
- Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
- Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
| | - D. Tim J. Littlewood
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Tine Huyse
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven, Belgium
- Biology Department, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium
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Justine JL, Poddubnaya LG. Spermiogenesis and spermatozoon ultrastructure in basal polyopisthocotylean monogeneans, Hexabothriidae and Chimaericolidae, and their significance for the phylogeny of the Monogenea. Parasite 2018; 25:7. [PMID: 29436366 PMCID: PMC5811217 DOI: 10.1051/parasite/2018007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/24/2018] [Indexed: 11/14/2022] Open
Abstract
Sperm ultrastructure provides morphological characters useful for understanding phylogeny; no study was available for two basal branches of the Polyopisthocotylea, the Chimaericolidea and Diclybothriidea. We describe here spermiogenesis and sperm in Chimaericola leptogaster (Chimaericolidae) and Rajonchocotyle emarginata (Hexabothriidae), and sperm in Callorhynchocotyle callorhynchi (Hexabothriidae). Spermiogenesis in C. leptogaster and R. emarginata shows the usual pattern of most Polyopisthocotylea with typical zones of differentiation and proximo-distal fusion of the flagella. In all three species, the structure of the spermatozoon is biflagellate, with two incorporated trepaxonematan 9 + "1" axonemes and a posterior nucleus. However, unexpected structures were also seen. An alleged synapomorphy of the Polyopisthocotylea is the presence of a continuous row of longitudinal microtubules in the nuclear region. The sperm of C. leptogaster has a posterior part with a single axoneme, and the part with the nucleus is devoid of the continuous row of microtubules. The spermatozoon of R. emarginata has an anterior region with membrane ornamentation, and posterior lateral microtubules are absent. The spermatozoon of C. callorhynchi has transverse sections with only dorsal and ventral microtubules, and its posterior part shows flat sections containing a single axoneme and the nucleus. These findings have important implications for phylogeny and for the definition of synapomorphies in the Neodermata. We point out a series of discrepancies between actual data and interpretation of character states in the matrix of a phylogeny of the Monogenea. Our main conclusion is that the synapomorphy "lateral microtubules in the principal region of the spermatozoon" does not define the Polyopisthocotylea but is restricted to the Mazocraeidea.
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Affiliation(s)
- Jean-Lou Justine
- Institut Systématique Évolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE,
57 rue Cuvier, CP 51,
75005
Paris France
| | - Larisa G. Poddubnaya
- I. D. Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences,
152742
Borok, Yaroslavl Russia
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Bachmann L, Fromm B, Patella de Azambuja L, Boeger WA. The mitochondrial genome of the egg-laying flatworm Aglaiogyrodactylus forficulatus (Platyhelminthes: Monogenoidea). Parasit Vectors 2016; 9:285. [PMID: 27188228 PMCID: PMC4869361 DOI: 10.1186/s13071-016-1586-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/11/2016] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The rather species-poor oviparous gyrodactylids are restricted to South America. It was suggested that they have a basal position within the otherwise viviparous Gyrodactylidae. Accordingly, it was proposed that the species-rich viviparous gyrodactylids diversified and dispersed from there. METHODS The mitochondrial genome of Aglaiogyrodactylus forficulatus was bioinformatically assembled from next-generation illumina MiSeq sequencing reads, annotated, and compared to previously published mitochondrial genomes of other monogenoidean flatworm species. RESULTS The mitochondrial genome of A. forficulatus consists of 14,371 bp with an average A + T content of 75.12 %. All expected 12 protein coding, 22 tRNA, and 2 rRNA genes were identified. Furthermore, there were two repetitive non-coding regions essentially consisting of 88 bp and 233 bp repeats, respectively. Maximum Likelihood analyses placed the mitochondrial genome of A. forficulatus in a well-supported clade together with the viviparous Gyrodactylidae species. The gene order differs in comparison to that of other monogenoidean species, with rearrangements mainly affecting tRNA genes. In comparison to Paragyrodactylus variegatus, four gene order rearrangements, i.e. three transpositions and one complex tandem-duplication-random-loss event, were detected. CONCLUSION Mitochondrial genome sequence analyses support a basal position of the oviparous A. forficulatus within Gyrodactylidae, and a sister group relationship of the oviparous and viviparous forms.
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Affiliation(s)
- Lutz Bachmann
- Natural History Museum, University of Oslo, PO Box 1172, Blindern, 0318, Oslo, Norway.
| | - Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium, Hospital, Oslo University Hospital, PO Box 4950, Nydalen, 0424, Oslo, Norway
| | - Luciana Patella de Azambuja
- Laboratório de Ecologia Molecular e Parasitologia Evolutiva-LEMPE, Universidade, Federal do Paraná-UFPR, Curitiba, Brazil
| | - Walter A Boeger
- Laboratório de Ecologia Molecular e Parasitologia Evolutiva-LEMPE, Universidade, Federal do Paraná-UFPR, Curitiba, Brazil
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Solà E, Álvarez-Presas M, Frías-López C, Littlewood DTJ, Rozas J, Riutort M. Evolutionary analysis of mitogenomes from parasitic and free-living flatworms. PLoS One 2015; 10:e0120081. [PMID: 25793530 PMCID: PMC4368550 DOI: 10.1371/journal.pone.0120081] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/19/2015] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial genomes (mitogenomes) are useful and relatively accessible sources of molecular data to explore and understand the evolutionary history and relationships of eukaryotic organisms across diverse taxonomic levels. The availability of complete mitogenomes from Platyhelminthes is limited; of the 40 or so published most are from parasitic flatworms (Neodermata). Here, we present the mitogenomes of two free-living flatworms (Tricladida): the complete genome of the freshwater species Crenobia alpina (Planariidae) and a nearly complete genome of the land planarian Obama sp. (Geoplanidae). Moreover, we have reanotated the published mitogenome of the species Dugesia japonica (Dugesiidae). This contribution almost doubles the total number of mtDNAs published for Tricladida, a species-rich group including model organisms and economically important invasive species. We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection. Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels. Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.
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Affiliation(s)
- Eduard Solà
- Institut de Recerca de la Biodiversitat and Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain
| | - Marta Álvarez-Presas
- Institut de Recerca de la Biodiversitat and Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain
| | - Cristina Frías-López
- Institut de Recerca de la Biodiversitat and Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain
| | | | - Julio Rozas
- Institut de Recerca de la Biodiversitat and Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain
| | - Marta Riutort
- Institut de Recerca de la Biodiversitat and Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain
- * E-mail: (MR)
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The complete mitochondrial genome of Neobenedenia melleni (Platyhelminthes: Monogenea): mitochondrial gene content, arrangement and composition compared with two Benedenia species. Mol Biol Rep 2014; 41:6583-9. [PMID: 25024046 DOI: 10.1007/s11033-014-3542-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 06/20/2014] [Indexed: 10/25/2022]
Abstract
The complete mitochondrial (mt) genome sequences of Neobenedenia melleni were determined and compared with those of Benedenia seriolae and B. hoshinai. This circular genome comprises 13,270 bp and includes all 36 typical mt genes found in flatworms. Total AT content of N. melleni is 75.9 %. ATG is the most common start codon, while nad4L is initiated by GTG. All protein-coding genes are predicted to terminate with TAG and TAA. N. melleni has the trnR with a TCG anticodon, which is the same to B. seriolae but different from B. hoshinai (ACG). The mt gene arrangement of N. melleni is similar to that of B. seriolae and B. hoshinai with the exception of three translocations (trnF, trnT and trnG). The overlapped region between nad4L and nad4 was found in the N. melleni mt genome, which was also reported for the published Gyrodactylus species, but it was not found in those of B. seriolae and B. hoshinai, which are non-coding regions instead. The present study provides useful molecular characters for species or strain identification and systematic studies of this parasite.
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Zhang J, Wu X, Li Y, Xie M, Li A. The complete mitochondrial genome of Tetrancistrum nebulosi (Monogenea: Ancyrocephalidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:22-3. [PMID: 24438309 DOI: 10.3109/19401736.2013.867441] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The first complete mitochondrial (mt) genome of Ancyrocephalidae is reported herein. The mt genome of Tetrancistrum nebulosi was 13,392 bp in length containing 12 protein-coding genes (lacking atp8), 22 tRNA genes and 2 rRNA genes. The longest non-coding region was located between nad5 and trnG, and the A + T content was 72.4%. All tRNAs had the typical clover-leaf secondary structure except for trnS1((AGN)), trnR, trnF and trnQ. The rrnL and rrnS subunits were separated by trnC, as documented in the monopisthocotylean groups (Benedenia and Gyrodactylus species), while they were adjacent to each other in the polyopisthocotylean species (Microcotyle sebastis, Polylabris halichoeres and Pseudochauhanea macrorchis).
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Affiliation(s)
- Juan Zhang
- a National Testing Center of Food Quality Supervision (Guangdong), Guangdong Testing Institute for Product Quality Supervision , Foshan , PR China .,b Key Laboratory for Aquatic Products Safety of Ministry of Education/State Key Laboratory of Biocontrol , School of Life Sciences, Sun Yat-sen University , Guangzhou , PR China , and
| | - Xiangyun Wu
- c Key Laboratory of Marine Bio-resource Sustainable Utilization, Department of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , PR China
| | - Yanwei Li
- b Key Laboratory for Aquatic Products Safety of Ministry of Education/State Key Laboratory of Biocontrol , School of Life Sciences, Sun Yat-sen University , Guangzhou , PR China , and
| | - Mingquan Xie
- b Key Laboratory for Aquatic Products Safety of Ministry of Education/State Key Laboratory of Biocontrol , School of Life Sciences, Sun Yat-sen University , Guangzhou , PR China , and
| | - Anxing Li
- b Key Laboratory for Aquatic Products Safety of Ministry of Education/State Key Laboratory of Biocontrol , School of Life Sciences, Sun Yat-sen University , Guangzhou , PR China , and
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Vanhove MPM, Tessens B, Schoelinck C, Jondelius U, Littlewood DTJ, Artois T, Huyse T. Problematic barcoding in flatworms: A case-study on monogeneans and rhabdocoels (Platyhelminthes). Zookeys 2013:355-79. [PMID: 24453567 PMCID: PMC3890687 DOI: 10.3897/zookeys.365.5776] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 12/02/2013] [Indexed: 11/12/2022] Open
Abstract
Some taxonomic groups are less amenable to mitochondrial DNA barcoding than others. Due to the paucity of molecular information of understudied groups and the huge molecular diversity within flatworms, primer design has been hampered. Indeed, all attempts to develop universal flatworm-specific COI markers have failed so far. We demonstrate how high molecular variability and contamination problems limit the possibilities for barcoding using standard COI-based protocols in flatworms. As a consequence, molecular identification methods often rely on other widely applicable markers. In the case of Monogenea, a very diverse group of platyhelminth parasites, and Rhabdocoela, representing one-fourth of all free-living flatworm taxa, this has led to a relatively high availability of nuclear ITS and 18S/28S rDNA sequences on GenBank. In a comparison of the effectiveness in species assignment we conclude that mitochondrial and nuclear ribosomal markers perform equally well. In case intraspecific information is needed, rDNA sequences can guide the selection of the appropriate (i.e. taxon-specific) COI primers if available.
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Affiliation(s)
- Maarten P M Vanhove
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Leuven, Belgium ; Present address: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Bart Tessens
- Research Group Zoology: Biodiversity & Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | | | - Ulf Jondelius
- Department of Invertebrate Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - D Tim J Littlewood
- Division of Parasites & Vectors, Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Tom Artois
- Research Group Zoology: Biodiversity & Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Tine Huyse
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, University of Leuven, Leuven, Belgium ; Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium
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Tian SQ, Cui P, Fang SF, Liu GH, Wang CR, Zhu XQ. The complete mitochondrial genome sequence ofEimeria magna(Apicomplexa: Coccidia). ACTA ACUST UNITED AC 2013; 26:714-5. [DOI: 10.3109/19401736.2013.843088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Abstract
SUMMARY From hundreds of independent transitions from a free-living existence to a parasitic mode of life, separate parasite lineages have converged over evolutionary time to share traits and exploit their hosts in similar ways. Here, we first summarize the evidence that, at a phenotypic level, eukaryotic parasite lineages have all converged toward only six general parasitic strategies: parasitoid, parasitic castrator, directly transmitted parasite, trophically transmitted parasite, vector-transmitted parasite or micropredator. We argue that these strategies represent adaptive peaks, with the similarities among unrelated taxa within any strategy extending to all basic aspects of host exploitation and transmission among hosts and transcending phylogenetic boundaries. Then, we extend our examination of convergent patterns by looking at the evolution of parasite genomes. Despite the limited taxonomic coverage of sequenced parasite genomes currently available, we find some evidence of parallel evolution among unrelated parasite taxa with respect to genome reduction or compaction, and gene losses or gains. Matching such changes in parasite genomes with the broad phenotypic traits that define the convergence of parasites toward only six strategies of host exploitation is not possible at present. Nevertheless, as more parasite genomes become available, we may be able to detect clear trends in the evolution of parasitic genome architectures representing true convergent adaptive peaks, the genomic equivalents of the phenotypic strategies used by all parasites.
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Yan HB, Wang XY, Lou ZZ, Li L, Blair D, Yin H, Cai JZ, Dai XL, Lei MT, Zhu XQ, Cai XP, Jia WZ. The mitochondrial genome of Paramphistomum cervi (Digenea), the first representative for the family Paramphistomidae. PLoS One 2013; 8:e71300. [PMID: 23990943 PMCID: PMC3750040 DOI: 10.1371/journal.pone.0071300] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/26/2013] [Indexed: 11/27/2022] Open
Abstract
We determined the complete mitochondrial DNA (mtDNA) sequence of a fluke, Paramphistomum cervi (Digenea: Paramphistomidae). This genome (14,014 bp) is slightly larger than that of Clonorchis sinensis (13,875 bp), but smaller than those of other digenean species. The mt genome of P. cervi contains 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (NCRs), a complement consistent with those of other digeneans. The arrangement of protein-coding and ribosomal RNA genes in the P. cervi mitochondrial genome is identical to that of other digeneans except for a group of Schistosoma species that exhibit a derived arrangement. The positions of some transfer RNA genes differ. Bayesian phylogenetic analyses, based on concatenated nucleotide sequences and amino-acid sequences of the 12 protein-coding genes, placed P. cervi within the Order Plagiorchiida, but relationships depicted within that order were not quite as expected from previous studies. The complete mtDNA sequence of P. cervi provides important genetic markers for diagnostics, ecological and evolutionary studies of digeneans.
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Affiliation(s)
- Hong-Bin Yan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
| | - Xing-Ye Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shanxi Province, PR China
| | - Zhong-Zi Lou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
| | - Li Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
| | - David Blair
- School of Marine and Tropical Biology, James Cook University, Queensland, Australia
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
| | - Jin-Zhong Cai
- Laboratory of Plateau Veterinary Parasitology, Veterinary Research Institute, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, Qinghai Province, PR China
| | - Xue-Ling Dai
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
| | - Meng-Tong Lei
- Laboratory of Plateau Veterinary Parasitology, Veterinary Research Institute, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, Qinghai Province, PR China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
| | - Xue-Peng Cai
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
- * E-mail: (WZJ); (XPC)
| | - Wan-Zhong Jia
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Key Laboratory of Veterinary Public Health of Agriculture Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, PR China
- * E-mail: (WZJ); (XPC)
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