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Hua CJ, Huang Y, Li HQ, Feng JM, Qiao JL, Hu S, Liu W, Shu XJ. Characterization of the complete mitochondrial genome of Ergasilus anchoratus Markevich, 1946 (Ergasilidae) and phylogeny of Copepoda. Syst Parasitol 2024; 101:33. [PMID: 38647718 DOI: 10.1007/s11230-023-10140-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/11/2023] [Indexed: 04/25/2024]
Abstract
The mitochondrial (mt) genome can provide data for phylogenetic analyses and evolutionary biology. Herein, we sequenced and annotated the complete mt genome of Ergasilus anchoratus. This mt genome was 13852 bp long and comprised 13 protein-coding genes (PCGs), 22 tRNAs and 2 rRNAs. All PCGs used the standard ATN start codons and complete TAA/TAG termination codons. A majority of tRNA genes exhibited standard cloverleaf secondary structures, with the exception of one tRNA that lacked the TψC arm (trnC), and three tRNAs that lacked the DHU arm (trnR, trnS1 and trnS2). Phylogenetic analyses conducted using Bayesian inference (BI) and maximum likelihood (ML) methods both supported Ergasilidae as a monophyletic family forming a sister group to Lernaea cyprinacea and Paracyclopina nana. It also supported the monophyly of orders Calanoida, Cyclopoida, and Siphonostomatoida; and the monophyly of families Harpacticidae, Ergasilidae, Diaptomidae, and Calanidae. The gene orders of E. anchoratus and Sinergasilus undulatus were identical, which represents the first instance of two identical gene orders in copepods. More mt genomes are needed to better understand the phylogenetic relationships within Copepoda in the future.
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Affiliation(s)
- Cong-Jie Hua
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Yan Huang
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Hui-Quan Li
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Jin-Mei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Jia-Lu Qiao
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Song Hu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Wei Liu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Xi-Ji Shu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China.
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He J, Zhou Z, Huang Y, Feng J, Li W, Wang G, Hua C. Evolutionary Rates, Divergence Rates, and Performance of Individual Mitochondrial Genes Based on Phylogenetic Analysis of Copepoda. Genes (Basel) 2023; 14:1496. [PMID: 37510402 PMCID: PMC10379994 DOI: 10.3390/genes14071496] [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: 06/22/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Copepoda is a large and diverse group of crustaceans, which is widely distributed worldwide. It encompasses roughly 9 orders, whose phylogeny remains unresolved. We sequenced the complete mitochondrial genome (mitogenome) of Sinergasilus major (Markevich, 1940) and used it to explore the phylogeny and mitogenomic evolution of Copepoda. The mitogenome of S. major (14,588 bp) encodes the standard 37 genes as well as a putative control region, and molecular features are highly conserved compared to other Copepoda mitogenomes. Comparative analyses indicated that the nad2 gene has relatively high nucleotide diversity and evolutionary rate, as well as the largest amount of phylogenetic information. These results indicate that nad2 may be a better marker to investigate phylogenetic relationships among closely related species in Copepoda than the commonly used cox1 gene. The sister-group relationship of Siphonostomatoida and Cyclopoida was recovered with strong support in our study. The only topological ambiguity was found within Cyclopoida, which might be caused by the rapid evolution and sparse taxon sampling of this lineage. More taxa and genes should be used to reconstruct the Copepoda phylogeny in the future.
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Affiliation(s)
- Junzong He
- School of Life Science, Jianghan University, Wuhan 430056, China
| | - Zhihao Zhou
- School of Life Science, Jianghan University, Wuhan 430056, China
| | - Yan Huang
- School of Life Science, Jianghan University, Wuhan 430056, China
| | - Jinmei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Wenxiang Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430056, China
| | - Guitang Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430056, China
| | - Congjie Hua
- Wuhan Institutes of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan 430056, China
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Yeom J, Lee W. A new species of the genus SarsamphiascusHuys, 2009 (Copepoda: Harpacticoida: Miraciidae) from a sublittoral zone of Hawaii. PeerJ 2020; 8:e8506. [PMID: 32095348 PMCID: PMC7017794 DOI: 10.7717/peerj.8506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 01/03/2020] [Indexed: 11/22/2022] Open
Abstract
A new species of SarsamphiascusHuys, 2009 was collected from sandy sediments of Hawaii at 12 –18 m depth. While the new species, Sarsamphiascus hawaiiensis sp. nov., is morphologically most closely related to S. kawamurai (Ueda & Nagai, 2005), the two species can be distinguished by the combination of the following morphological characteristics: elongated segments of the antennule in the new species, type of outer setae of the P5 exopod (bare in S. kawamurai), position of the inner seta of the P5 exopod in both sexes (more proximal in S. kawamurai), length and type of the setae of female P6 (shorter and bare in S. kawamurai). This is the first species of Sarsamphiascus from Hawaii to be discovered. Molecular analyses of mitochondrial cytochrome c oxidase subunit I (mtCOI) and nuclear 18S ribosomal RNA (18S rRNA) genes confirmed that S. hawaiiensis and S. kawamurai are distinct species.
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Affiliation(s)
- Jisu Yeom
- Department of Life Science, Hanyang University, Seoul, South Korea
| | - Wonchoel Lee
- Department of Life Science, Hanyang University, Seoul, South Korea
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Weydmann A, Przyłucka A, Lubośny M, Walczyńska KS, Serrão EA, Pearson GA, Burzyński A. Mitochondrial genomes of the key zooplankton copepods Arctic Calanus glacialis and North Atlantic Calanus finmarchicus with the longest crustacean non-coding regions. Sci Rep 2017; 7:13702. [PMID: 29057900 PMCID: PMC5651803 DOI: 10.1038/s41598-017-13807-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/03/2017] [Indexed: 11/19/2022] Open
Abstract
We determined the nearly complete mitochondrial genomes of the Arctic Calanus glacialis and its North Atlantic sibling Calanus finmarchicus, which are key zooplankton components in marine ecosystems. The sequenced part of C. glacialis mitogenome is 27,342 bp long and consists of two contigs, while for C. finmarchicus it is 29,462 bp and six contigs, what makes them the longest reported copepod mitogenomes. The typical set of metazoan mitochondrial genes is present in these mitogenomes, although the non-coding regions (NCRs) are unusually long and complex. The mitogenomes of the closest species C. glacialis and C. finmarchicus, followed by the North Pacific C. sinicus, are structurally similar and differ from the much more typical of deep-water, Arctic C. hyperboreus. This evolutionary trend for the expansion of NCRs within the Calanus mitogenomes increases mitochondrial DNA density, what resulted in its similar density to the nuclear genome. Given large differences in the length and structure of C. glacialis and C. finmarchicus mitogenomes, we conclude that the species are genetically distinct and thus cannot hybridize. The molecular resources presented here: the mitogenomic and rDNA sequences, and the database of repetitive elements should facilitate the development of genetic markers suitable in pursuing evolutionary research in copepods.
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Affiliation(s)
- Agata Weydmann
- Institute of Oceanology, Polish Academy of Sciences, Sopot, 81-712, Poland.
- University of Gdansk, Institute of Oceanography, Gdynia, 81-378, Poland.
| | | | - Marek Lubośny
- Institute of Oceanology, Polish Academy of Sciences, Sopot, 81-712, Poland
| | | | - Ester A Serrão
- University of Algarve, CCMAR, CIMAR, Faro, 8005-139, Portugal
| | | | - Artur Burzyński
- Institute of Oceanology, Polish Academy of Sciences, Sopot, 81-712, Poland
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Easton EE, Thistle D. Do some deep‐sea, sediment‐dwelling species of harpacticoid copepods have 1000‐km‐scale range sizes? Mol Ecol 2016; 25:4301-18. [DOI: 10.1111/mec.13744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/19/2016] [Accepted: 06/22/2016] [Indexed: 11/29/2022]
Affiliation(s)
- E. E. Easton
- Department of Earth, Ocean and Atmospheric Science Florida State University Tallahassee FL 32306‐4320 USA
| | - D. Thistle
- Department of Earth, Ocean and Atmospheric Science Florida State University Tallahassee FL 32306‐4320 USA
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Castro-romero R, Montes MM, Martorelli SR, Sepulveda D, Tapia S, Martínez-aquino A. Integrative taxonomy of Peniculus, Metapeniculus, and Trifur (Siphonostomatoida: Pennellidae), copepod parasites of marine fishes from Chile: species delimitation analyses using DNA barcoding and morphological evidence. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1158213] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Raúl Castro-romero
- Universidad de Antofagasta, Facultad Ciencias del Mar, Depto. Ciencias Acuáticas y Ambientales, Antofagasta, Chile
| | - Martín M. Montes
- CEPAVE, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | | | - Diego Sepulveda
- Universidad de Antofagasta, Depto. Biomédico, Antofagasta, Chile
| | - Silvia Tapia
- Universidad de Antofagasta, Facultad Ciencias del Mar, Depto. Ciencias Acuáticas y Ambientales, Antofagasta, Chile
- Universidad de Antofagasta, Depto. Biomédico, Antofagasta, Chile
| | - Andrés Martínez-aquino
- División Zoología Invertebrados, Museo de La Plata, FCNyM, UNLP, Paseo del Bosque s/n, 1900 La Plata, Argentina
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Karanovic T, Djurakic M, Eberhard SM. Cryptic Species or Inadequate Taxonomy? Implementation of 2D Geometric Morphometrics Based on Integumental Organs as Landmarks for Delimitation and Description of Copepod Taxa. Syst Biol 2015; 65:304-27. [PMID: 26608965 DOI: 10.1093/sysbio/syv088] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/13/2015] [Indexed: 12/16/2022] Open
Abstract
Discovery of cryptic species using molecular tools has become common in many animal groups but it is rarely accompanied by morphological revision, creating ongoing problems in taxonomy and conservation. In copepods, cryptic species have been discovered in most groups where fast-evolving molecular markers were employed. In this study at Yeelirrie in Western Australia we investigate a subterranean species complex belonging to the harpacticoid genus Schizopera Sars, 1905, using both the barcoding mitochondrial COI gene and landmark-based two-dimensional geometric morphometrics. Integumental organs (sensilla and pores) are used as landmarks for the first time in any crustacean group. Complete congruence between DNA-based species delimitation and relative position of integumental organs in two independent morphological structures suggests the existence of three distinct evolutionary units. We describe two of them as new species, employing a condensed taxonomic format appropriate for cryptic species. We argue that many supposedly cryptic species might not be cryptic if researchers focus on analyzing morphological structures with multivariate tools that explicitly take into account geometry of the phenotype. A perceived supremacy of molecular methods in detecting cryptic species is in our view a consequence of disparity of investment and unexploited recent advancements in morphometrics among taxonomists. Our study shows that morphometric data alone could be used to find diagnostic morphological traits and gives hope to anyone studying small animals with a hard integument or shell, especially opening the door to assessing fossil diversity and rich museum collections. We expect that simultaneous use of molecular tools with geometry-oriented morphometrics may yield faster formal description of species. Decrypted species in this study are a good example for urgency of formal descriptions, as they display short-range endemism in small groundwater calcrete aquifers in a paleochannel, where their conservation may be threatened by proposed mining.
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Affiliation(s)
- Tomislav Karanovic
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, Korea; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia;
| | - Marko Djurakic
- Department of Biology and Ecology, Faculty of Science, University of Novi Sad, Trg Dositeja Obradovića 2, Novi Sad 21000, Serbia
| | - Stefan M Eberhard
- Subterranean Ecology Pty Ltd, Coningham, Tasmania 7054, Australia; and Connected Waters Initiative Research Centre, University of New South Wales, Sydney 2052, Australia
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Doublet V, Ubrig E, Alioua A, Bouchon D, Marcadé I, Maréchal-Drouard L. Large gene overlaps and tRNA processing in the compact mitochondrial genome of the crustacean Armadillidium vulgare. RNA Biol 2015; 12:1159-68. [PMID: 26361137 DOI: 10.1080/15476286.2015.1090078] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
A faithful expression of the mitochondrial DNA is crucial for cell survival. Animal mitochondrial DNA (mtDNA) presents a highly compact gene organization. The typical 16.5 kbp animal mtDNA encodes 13 proteins, 2 rRNAs and 22 tRNAs. In the backyard pillbug Armadillidium vulgare, the rather small 13.9 kbp mtDNA encodes the same set of proteins and rRNAs as compared to animal kingdom mtDNA, but seems to harbor an incomplete set of tRNA genes. Here, we first confirm the expression of 13 tRNA genes in this mtDNA. Then we show the extensive repair of a truncated tRNA, the expression of tRNA involved in large gene overlaps and of tRNA genes partially or fully integrated within protein-coding genes in either direct or opposite orientation. Under selective pressure, overlaps between genes have been likely favored for strong genome size reduction. Our study underlines the existence of unknown biochemical mechanisms for the complete gene expression of A. vulgare mtDNA, and of co-evolutionary processes to keep overlapping genes functional in a compacted mitochondrial genome.
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Affiliation(s)
- Vincent Doublet
- a Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions , UMR CNRS 7267, Poitiers , France
| | - Elodie Ubrig
- b Institut de biologie moléculaire des plantes; associated with the University of Strasbourg , Strasbourg , France
| | - Abdelmalek Alioua
- b Institut de biologie moléculaire des plantes; associated with the University of Strasbourg , Strasbourg , France
| | - Didier Bouchon
- a Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions , UMR CNRS 7267, Poitiers , France
| | - Isabelle Marcadé
- a Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions , UMR CNRS 7267, Poitiers , France
| | - Laurence Maréchal-Drouard
- b Institut de biologie moléculaire des plantes; associated with the University of Strasbourg , Strasbourg , France
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Karanovic T, Kim K, Grygier MJ. A new species ofSchizopera(Copepoda: Harpacticoida) from Japan, its phylogeny based on the mtCOI gene and comments on the genusSchizoperopsis. J NAT HIST 2015. [DOI: 10.1080/00222933.2015.1028112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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