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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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Wang L, Hu Z, Wang Z, Zhu P, Wei G, Fan X, Huang J, Wang R, Wang H, Xie Y. Complete Mitogenome sequencing of the fish louse Argulus japonicus (Crustacea: Branchiura): Comparative analyses and phylogenetic implications. Front Vet Sci 2024; 11:1376898. [PMID: 38590542 PMCID: PMC10999652 DOI: 10.3389/fvets.2024.1376898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/05/2024] [Indexed: 04/10/2024] Open
Abstract
The fish louse Argulus japonicus, a branchiuran crustacean of the Argulidae family, is attracting increasing attention because of its parasitic tendencies and significant health threats to global fish farming. The mitogenomes can yield a foundation for studying epidemiology, genetic diversity, and molecular ecology and therefore may be used to assist in the surveillance and control of A. japonicus. In this study, we sequenced and assembled the complete mitogenome of A. japonicus to shed light on its genetic and evolutionary blueprint. Our investigation indicated that the 15,045-bp circular genome of A. japonicus encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs) with significant AT and GC skews. Comparative genomics provided an evolutionary scenario for the genetic diversity of 13 PCGs: all were under purifying selection, with cox1 and nad6 having the lowest and highest evolutionary rates, respectively. Genome-wide phylogenetic trees established a close relationship between species of the families Argulidae (Arguloida) and Armilliferidae (Porocephalida) within Crustacea, and further, A. japonicus and Argulus americanus were determined to be more closely related to each other than to others within the family Argulidae. Single PCG-based phylogenies supported nad1 and nad6 as the best genetic markers for evolutionary and phylogenetic studies for branchiuran crustaceans due to their similar phylogenetic topologies with those of genome-based phylogenetic analyses. To sum up, these comprehensive mitogenomic data of A. japonicus and related species refine valuable marker resources and should contribute to molecular diagnostic methods, epidemiological investigations, and ecological studies of the fish ectoparasites in Crustacea.
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Affiliation(s)
- Lidan Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zun Hu
- Department of Food Technology and Science, College of Food Science, Shanghai Ocean University, Shanghai, China
| | - Zhao Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Pengchen Zhu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Guoshan Wei
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinyi Fan
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jiali Huang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ruixi Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Hui Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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Smolina I, Espinasse M, Amundsen CR, Espinasse B. The complete mitochondrial genome of the southern calanoid copepod Calanus simillimus Giesbrecht, 1902. Mitochondrial DNA B Resour 2022; 7:1260-1262. [PMID: 35837496 PMCID: PMC9275497 DOI: 10.1080/23802359.2022.2093678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
The complete mitochondrial genome of Calanus simillimus is 27,876 bp in length (GenBank accession OK500294) and containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 transfer RNA genes. The gene order is novel compared to other Calanus species and copepods with sequenced mitogenomes. Phylogenetic analysis suggests that C. simillimus represent a fourth group within Calanus genus in addition to C. hyperboreus, C. finmarchicus and C. helgolandicus groups. The complete mitochondrial genome of C. simillimus will be useful for species identification, population genetics, phylogenetic and evolutionary studies among copepods.
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Affiliation(s)
- Irina Smolina
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Marina Espinasse
- Ecosystem processes Research Group, Institute of Marine Research, Tromsø, Norway
| | | | - Boris Espinasse
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
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Back J, Kim H, Lee SH, Lee SH, Shin MH, Lim BJ. The complete mitochondrial genome of Undinula vulgaris (Dana, 1849) (Crustacea: Calanoida: Calanidae). Mitochondrial DNA B Resour 2019; 4:4035-4036. [PMID: 33366305 PMCID: PMC7707735 DOI: 10.1080/23802359.2019.1688724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The present study reports, for the first time, the complete mitochondrial genome (mitogenome) of Undinula vulgaris. The total mitogenome length of U. vulgaris was 15,303 bp with 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and 1 non-coding region. Phylogenetic analysis showed that U. vulgaris belonged to the same family. This is the second report of the complete mitogenome sequence of the family Calanidae.
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Affiliation(s)
- Jinwook Back
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea, Janghang-eup, Republic of Korea
| | - Hana Kim
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea, Janghang-eup, Republic of Korea
| | - Sang-Hwa Lee
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea, Janghang-eup, Republic of Korea
| | - Sang-Hui Lee
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea, Janghang-eup, Republic of Korea
| | - Myung-Hwa Shin
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea, Janghang-eup, Republic of Korea
| | - Byung-Jin Lim
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea, Janghang-eup, Republic of Korea
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Jooste CM, Emami-Khoyi A, Gan HM, Wasserman RJ, Dalu T, Teske PR. The complete mitochondrial genome of Africa's largest freshwater copepod, Lovenula raynerae. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1555013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Candice M. Jooste
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, South Africa
| | - Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, South Africa
| | - Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Ryan J. Wasserman
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
- South African Institute for Aquatic Biodiversity (SAIAB), Grahamstown, South Africa
| | - Tatenda Dalu
- Department of Ecology and Resource Management, University of Venda, Thohoyandou, South Africa
| | - Peter R. Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, South Africa
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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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Choquet M, Alves Monteiro HJ, Bengtsson-Palme J, Hoarau G. The complete mitochondrial genome of the copepod Calanus glacialis. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:506-507. [PMID: 33473877 PMCID: PMC7799568 DOI: 10.1080/23802359.2017.1361357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Calanus glacialis, a marine planktonic copepod, is a keystone species in the Arctic Ocean. In this study, we shotgun sequenced the total DNA of one C. glacialis individual, using the NextSeq® Illumina platform, in order to determine its mitochondrial genome sequence. We successfully assembled and annotated this 20,674 bp long sequence, which included 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. Common gene-coding regions of 19 other species were used to reconstruct a phylogenetic tree, using mitogenomes of the phylogenetically closest copepods available. The new resource described here constitutes a tool of interest for better understanding the structure and dynamics of C. glacialis populations.
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Affiliation(s)
- Marvin Choquet
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Williams ST, Foster PG, Hughes C, Harper EM, Taylor JD, Littlewood DTJ, Dyal P, Hopkins KP, Briscoe AG. Curious bivalves: Systematic utility and unusual properties of anomalodesmatan mitochondrial genomes. Mol Phylogenet Evol 2017; 110:60-72. [PMID: 28274686 DOI: 10.1016/j.ympev.2017.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/26/2017] [Accepted: 03/02/2017] [Indexed: 11/29/2022]
Abstract
Mitogenomic trees for Bivalvia have proved problematic in the past, but several highly divergent lineages were missing from these analyses and increased representation of these groups may yet improve resolution. Here, we add seven new sequences from the Anomalodesmata and one unidentified semelid species (Bryopa lata, Euciroa cf. queenslandica, Laternula elliptica, Laternula truncata, Lyonsia norwegica, Myadora brevis, Tropidomya abbreviata, "Abra" sp.). We show that relationships in a mitogenomic tree for the Class are improved by the addition of seven anomalodesmatans from this highly divergent clade, but are still not completely consistent with relationships recovered in studies of nuclear genes. We suggest that some anomalous relationships (for instance the non-monophyly of Bivalvia) may be partially explained by compositional heterogeneity in the mitogenome and suggest that the addition of more taxa may help resolve both this effect and possible instances of long branch attraction. We also identify several curious features about anomalodesmatan mitogenomes. For example, many protein-coding gene boundaries are poorly defined in marine bivalves, but particularly so in anomalodesmatans, primarily due to non-conserved boundary sequences. The use of transcriptomic and genomic data together enabled better definition of gene boundaries, the identification of possible pseudogenes and suggests that most genes are translated monocistronically, which contrasts with many other studies. We also identified a possible case of gene duplication of ND5 in Myadora brevis (Myochamidae). Mitogenome size in the Anomalodesmata ranges from very small compact molecules, with the smallest for Laternula elliptica (Laternulidae) only 14,622bp, to Bryopa lata (Clavagellidae) which is at least 31,969bp long and may be >40,000bp. Finally, sampled species show a high degree of sequence divergence and variable gene order, although intraspecific variation in Laternula elliptica is very low.
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Affiliation(s)
- S T Williams
- Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom.
| | - P G Foster
- Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom
| | - C Hughes
- Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom
| | - E M Harper
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, United Kingdom
| | - J D Taylor
- Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom
| | - D T J Littlewood
- Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom
| | - P Dyal
- Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom
| | - K P Hopkins
- Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom; Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, United Kingdom(1)
| | - A G Briscoe
- Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom
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Shen X, Tsang LM, Chu KH, Achituv Y, Chan BKK. Mitochondrial genome of the intertidal acorn barnacle Tetraclita serrata Darwin, 1854 (Crustacea: Sessilia): Gene order comparison and phylogenetic consideration within Sessilia. Mar Genomics 2015; 22:63-9. [PMID: 25907711 DOI: 10.1016/j.margen.2015.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 04/09/2015] [Accepted: 04/09/2015] [Indexed: 01/11/2023]
Abstract
The complete mitochondrial genome of the intertidal barnacle Tetraclita serrata Darwin, 1854 (Crustacea: Maxillopoda: Sessilia) is presented. The genome is a circular molecule of 15,200 bp, which encodes 13 PCGs, 2 ribosomal RNA genes, and 22 transfer RNA genes. All non-coding regions are 591 bp in length, with the longest one speculated as the control region (389 bp), which is located between srRNA and trnK. The overall A+T content of the mitochondrial genome of T. serrata is 65.4%, which is lowest among all the eight mitochondrial genomes reported from sessile barnacles. There are variations of initiation and stop codons in the reported sessile barnacle mitochondrial genomes. Large-scale gene rearrangements are found in these genomes as compared to the pancrustacean ground pattern. ML and Bayesian analyses of all 15 complete mitochondrial genomes available from Maxillopoda lead to identical phylogenies. The phylogenetic tree based on mitochondrial PCGs shows that Argulus americanus (Branchiura) cluster with Armillifer armillatus (Pentastomida), distinct from all ten species from Cirripedia. Within the order Sessilia, Amphibalanus amphitrite (Balanidae) clusters with Striatobalanus amaryllis (Archaeobalanidae), and Nobia grandis (Pyrgomatidae). However, the two Megabalanus (Balanidae) are separated from the above grouping, resulting in non-monophyly of the family Balanidae. Moreover, the two Megabalanus have large-scale rearrangements as compared to the gene order shared by former three species. Therefore, both phylogenetic analysis using PCG sequences and gene order comparison suggest that Balanidae is not a monophyletic group. Given the limited taxa and moderate support values of the internal branches, the non-monophyly of the family Balanidae requires further verification.
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Affiliation(s)
- Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science/Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China; Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Ling Ming Tsang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 202, Taiwan
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
| | - Yair Achituv
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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Easton EE, Darrow EM, Spears T, Thistle D. The mitochondrial genomes of Amphiascoides atopus and Schizopera knabeni (Harpacticoida: Miraciidae) reveal similarities between the copepod orders Harpacticoida and Poecilostomatoida. Gene 2014; 538:123-37. [DOI: 10.1016/j.gene.2013.12.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 12/24/2013] [Indexed: 12/15/2022]
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