Although parasitic copepods of the genus Ergasilus von Nordmann, 1832 are globally distributed parasites of fish, their phylogenetic relationships with other Copepoda are not clear, and the characteristics of their mitochondrial genomes (mitogenomes) are not thoroughly understood. The objective of this study was to address these knowledge gaps by sequencing the complete mitogenome of Ergasilus tumidus Markevich, 1940. The complete mitogenome (GenBank Acc. No. OQ596537) was 14,431 bp long and it comprised 13 protein-coding genes (PCGs), 22 tRNAs, two tRNAs, and two control regions (CRs). Phylogenetic analyses, conducted using concatenated nucleotide and amino acid sequences of 13 protein-coding genes, produced two partially incongruent topologies. While the order Calanoida was consistently resolved as the sister lineage to the other three orders, topological instability was observed in the relationships of the orders Cyclopoida, Siphonostomatoida and Harpacticoida. Siphonostomatoida clustered with Cyclopoida in the nucleotide-based phylogeny, but with Harpacticoida in the amino acid-based phylogeny. The latter topology conforms to the widely accepted relationships, but we speculate that the former topology is more likely to be the correct one. Our study provides a complete mitogenome sequence of E. tumidus, which helps us better understand the molecular evolution of the genus Ergasilus. Additionally, we suggest a different perspective on the controversial phylogenetic relationships among Siphonostomatoida, Cyclopoida and Harpacticoida, diverging from previously accepted views.

Department of Pathogenic Biology School of Medicine Jianghan University Wuhan China

Hubei Key Laboratory of Cognitive and Affective Disorders Institute of Biomedical Sciences School of Medicine Jianghan University Wuhan China

State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences Wuhan China

Zobrazit více v PubMed

Abdullah M., Khairurrijal K. 2009: A simple method for determining surface porosity based on SEM images using OriginPro software. Indones. J. Phys. 20: 37-40. DOI

Avise J.C., Arnold J., Ball R.M., Bermingham E., Lamb T., Neigel J.E., Reeb C.A., Saunders N.C. 1987: Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu. Rev. Ecol. Syst. 18: 489-522. DOI

Benson G. 1999: Tandem repeats finder: a program to analyze DNA sequences. Nucl. Acids Res. 27: 573-580. DOI

Bernot J.P., Boxshall G.A., Crandall K.A. 2021: A synthesis tree of the Copepoda: integrating phylogenetic and taxonomic data reveals multiple origins of parasitism. PeerJ. 9: e12034. DOI

Bernt M., Donath A., Jühling F., Externbrink F., Florentz C., Fritzsch G., Pütz J., Middendorf M., Stadler P.F. 2013: MITOS: improved de novo metazoan mitochondrial genome annotation. Mol. Phylogen. Evol. 69: 313-319. DOI

Boore J.L. 1999: Animal mitochondrial genomes. Nucl. Acids Res. 27: 1767-1780. DOI

Boxshall G.A., Defaye D. 2007: Global diversity of copepods (Crustacea: Copepoda) in freshwater. Hydrobiologia 595: 195-207. DOI

Boxshall G.A., Jaume D. 2000: Making waves: the repeated colonization of fresh water by copepod crustaceans. Adv. Ecol. Res. 31: 61-79. DOI

Delgado P.M., Delgado J.P.M., Arenas J.V., Orbe R.I. 2011: Massive infestation by Perulernaea gamitanae (Crustacea: Cyclopoida: Lernaidae) in juvenile gamitana, cultured in the Peruvian Amazon. Vet. Mex. 42: 59-64.

Eyun S.I. 2017: Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies. BMC Evol. Biol. 17: 23. DOI

Hadfield K.A., Smit N.J. 2019: Parasitic Crustacea as vectors. In N.J. Smit, N.L.Bruce and K.A. Hadfield (Eds.), Parasitic Crustacea. State of Knowledge and Future Trends. Springer, Cham, pp. 331-342. DOI

Hu F., Lin Y., Tang J. 2014: MLGO: phylogeny reconstruction and ancestral inference from gene-order data. BMC Bioinformatics 15: 354. DOI

Hua C.J., Zhang D., Zou H., Li M., Jakovlić I., Wu S.G., Wang G.T., Li W.X. 2019: Morphology is not a reliable taxonomic tool for the genus Lernaea: molecular data and experimental infection reveal that L. cyprinacea and L. cruciata are conspecific. Parasit. Vectors 12: 579. DOI

Huelsenbeck J.P., Hillis D.M. 1993: Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42: 247-264. DOI

Huys R., Llewellyn-Hughes J., Conroy-Dalton S., Olson P.D., Spinks J.N., Johnston D.A. 2007: Extraordinary host switching in siphonostomatoid copepods and the demise of the Monstrilloida: integrating molecular data, ontogeny and antennulary morphology. Mol. Phylogen. Evol. 43: 368-378. DOI

Huys R., Llewellyn-Hughes J., Olson P.D., Nagasawa K. 2006: Small subunit rDNA and Bayesian inference reveal Pectenophilus ornatus (Copepoda incertae sedis) as highly transformed Mytilicolidae, and support assignment of Chondracanthidae and Xarifiidae to Lichomolgoidea (Cyclopoida). Biol. J. Linn. Soc. 87: 403-425. DOI

Jakovlić I., Zou H., Zhao X.-M., Zhang J., Wang G.-T., Zhang D. 2021: Evolutionary history of inversions in directional mutational pressures in crustacean mitochondrial genomes: implications for evolutionary studies. Mol. Phylogen. Evol. 164: 107288. DOI

Jung S.-O., Lee Y.-M., Park T.-J., Park H.G., Hagiwara A., Leung K.M.Y., Dahms H.-U., Lee W., Lee J.-S. 2006: Thecomplete mitochondrial genome of the intertidal copepod Tigriopus sp. (Copepoda, Harpactidae) from Korea and phylogenetic considerations. J. Exp. Mar. Biol. Ecol. 333: 251-262. DOI

Kabata Z. 1979: Parasitic Copepoda of British Fishes. The Ray Society, British Museum, London, 468 pp.

Katoh K., Standley D.M. 2013: MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30: 772-780. DOI

Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S., Duran C. 2012: Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647-1649. DOI

Kilpert F., Podsiadlowski L. 2006: The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features. BMC Genomics 7: 241. DOI

Kim J., Kern E., Kim T., Sim M., Kim J., Kim Y., Park C., Nadler S.A., Park J.-K. 2017: Phylogenetic analysis of two Plectus mitochondrial genomes (Nematoda: Plectida) supports a sister group relationship between Plectida and Rhabditida within Chromadorea. Mol. Phylogen. Evol. 107: 90-102. DOI

Kuang P., Qian J. 1991: Economic Fauna of China: Parasitic Crustacea of Freshwater Fishes. Science Press, Beijing, 203 pp.

Kumar S., Stecher G., Li M., Knyaz C., Tamura K. 2018: MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol. Biol. Evol. 35: 1547. DOI

Lanfear R., Frandsen P.B., Wright A.M., Senfeld T., Calcott B. 2017: PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. 34: 772-773. DOI

Lester R.J., Hayward C.J. 2006: Phylum Arthropoda. In P.T.K. Woo (Ed.), Fish Diseases and Disorders. Volume 1: Protozoan and Metazoan Infections. CABI, Wallingford, pp. 466-565. DOI

Letunic I., Bork P. 2019: Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucl. Acids. Res. 47: W256-W259. DOI

Librado P., Rozas J. 2009: DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452. DOI

Lohse M., Drechsel O., Bock R. 2007: OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr. Genet. 52: 267-274. DOI

Lowe T.M., Eddy S.R. 1997: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl. Acids Res. 25: 955-964. DOI

Machida R.J., Miya M.U., Nishida M., Nishida S. 2004: Large-scale gene rearrangements in the mitochondrial genomes of two calanoid copepods Eucalanus bungii and Neocalanus cristatus (Crustacea), with notes on new versatile primers for the srRNA and COI genes. Gene 332: 71-78. DOI

Mathews P.D., Patta A.C., Gama G.S., Mertins O. 2018: Infestation by Ergasilus coatiarus (Copepoda: Ergasilidae) in two Amazonian cichlids with new host record from Peru: an ectoparasites natural control approach. C. R. Biol. 341: 16-19. DOI

Minxiao W., Song S., Chaolun L., Xin S. 2011: Distinctive mitochondrial genome of calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: useful molecular markers for phylogenetic and population studies. BMC Genomics 12: 73. DOI

Nguyen L.T., Schmidt H.A., Von Haeseler A., Minh B.Q. 2015: IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32: 268-274. DOI

Peng G., Gao Q., Song Y., Zhao Q., Luo Y., Nie P. 2010: Mitochondrial genes of Sinergasilus polycolpus (Copepoda, Ergasilidae) parasitizing the gills of fish. Acta. Hydrobiol. Sinica 34: 177-183. DOI

Perna N.T., Kocher T.D. 1995: Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41: 353-358. DOI

Piasecki W., Goodwin A.E., Eiras J.C., Nowak B.F. 2004: Importance of Copepoda in freshwater aquaculture. Zool. Stud. 43: 193-205.

Rand D.M. 1994: Thermal habit, metabolic rate and the evolution of mitochondrial DNA. Trends. Ecol. Evol. 9: 125-131. DOI

Reuter J.S., Mathews D.H. 2010: RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 11: 1-9. DOI

Ronquist F., Teslenko M., Van Der Mark P., Ayres D.L., Darling A., Höhna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P. 2012: MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61: 539-542. DOI

Shao R., Barker S. 2007: Mitochondrial genomes of parasitic arthropods: implications for studies of population genetics and evolution. Parasitology 134: 153-167. DOI

Song Y., Wang G. T., Yao W. J., Gao Q., Nie P. 2007: Phylogeny of freshwater parasitic copepods in the Ergasilidae (Copepoda: Poecilostomatoida) based on 18S and 28S rDNA sequences. Parasitol. Res. 102: 299-306. DOI

Staton J.L., Daehler L.L., Brown W.M. 1997: Mitochondrial gene arrangement of the horseshoe crab Limulus polyphemus L.: conservation of major features among arthropod classes. Mol. Biol. Evol. 14: 867-874. DOI

Suzuki Y., Glazko G.V., Nei M. 2002: Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99: 16138-16143. DOI

Talavera G., Castresana J. 2007: Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56: 564-577. DOI

Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013: MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30: 2725-2729. DOI

Tung C.-H., Cheng Y.-R., Lin C.-Y., Ho J.-S., Kuo C.-H., Yu J.-K., Su Y.-H. 2014: A new copepod with transformed body plan and unique phylogenetic position parasitic in the acorn worm Ptychodera flava. Biol. Bull. 226: 69-80. DOI

Walter T.C.B., G. (Ed.) 2024: World of Copepods Database. Access year: 2024. Ergasilus von Nordmann, 1832., www.marinespecies.org

Wang N., Xiang Y., Fang L., Wang Y., Xin H., Li S. 2013: Patterns of gene duplication and their contribution to expansion of gene families in grapevine. Plant. Mol. Biol. Rep. 31: 852-861. DOI

Xiang C.Y., Gao F., Jakovlić I., Lei H.P., Hu Y., Zhang H., Zou H., Wang G.T., Zhang D. 2023: Using PhyloSuite for molecular phylogeny and tree-based analyses. iMeta 2: e87. DOI

Zhang D., Li W.X., Zou H., Wu S.G., Li M., Jakovlić I., Zhang J., Chen R., Wang G. 2019: Homoplasy or plesiomorphy? Reconstruction of the evolutionary history of mitochondrial gene order rearrangements in the subphylum Neodermata. Int. J. Parasitol. 49: 819-829. DOI