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The Mitochondrial Genome of the Globally Invasive Barnacle Megabalanus coccopoma Darwin 1854 (Crustacea: Balanomorpha): Rearrangement and Phylogenetic Consideration within Balanomorpha. DIVERSITY 2023. [DOI: 10.3390/d15010117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Megabalanus coccopoma (Darwin, 1854) is a globally invasive species in Balanomorpha (Crustacea). This species is a model organism for studying marine pollution and ecology. However, its mitogenome remains unknown. The mitogenome sequencing of M. coccopoma is completed in the present study. It has a 15,098 bp in length, including 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), along with a putative regulatory area. A substantial A+T bias was observed in the genome composition (68.2%), along with a negative AT (0.82) and GC (−0.136) skew. Compared to the gene sequence of the ground model of pan-crustacea, 13 gene clusters (or genes), such as 10 tRNAs and 3 PCGs, were observed in a different order. This was in line with the previously observed large-scale gene rearrangements of Balanomorpha. Among the 37 genes, the gene cluster (M-nad2-W-cox1-L2-cox2-D-atp8-atp6-cox3-G- nad3-R-N-A-E-S1) Balanomorpha was conserved. Furthermore, phylogeny analysis indicated that the existing Balanomorpha species family was divided into nine rearrangement patterns, supporting the polyphyly of Balanoidea.
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Tian M, Chen P, Song J, He F, Shen X. The first mitochondrial genome of Capitulum mitella (Crustacea: Cirripedia) from China: revealed the phylogenetic relationship within Thoracica. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2573-2575. [PMID: 33457867 PMCID: PMC7783061 DOI: 10.1080/23802359.2020.1781564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Capitulum mitella (Crustacea: Cirripedia) is an important stalked barnacle. The first mitochondrial genome of C. mitella from China was presented, which is a circular molecule of 15,930 bp in length and AT content is 64.4%. It encodes 37 genes, including 13 PCGs, 22 tRNAs, and two rRNAs, which is consistent with most barnacles species reported. There are 15 genes encoded on the light strand and 22 genes encoded on the heavy strand. Identical to most barnacles species reported, srRNA and lrRNA genes are adjacent and separated only by trnV gene. Phylogenetic trees showed that C. mitella clustered with Pollicipes polymerus, indicating Pollicipedidae is monophyletic. However, Scalpelliformes was not monophyletic from the phylogenetic tree. From the level of order, the Lepadiformes was located at the base of the phylogenetic tree, indicating that its divergence time was earlier than Scalpelliformes. The results provided more insights into phylogenetic consideration at the genomic level within superorder Thoracica.
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Affiliation(s)
- Mei Tian
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Panpan Chen
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Jun Song
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Fuxiang He
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Jiangsu Ocean University, Lianyungang, China
| | - Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
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Lee WK, Kim SJ, Ju SJ, Hou BK. Complete mitochondrial genome of the hydrothermal vent shrimp Rimicaris variabilis (Decapoda: Caridea: Alvinocarididae) from the North Fiji basin. Mitochondrial DNA B Resour 2019; 4:3475-3476. [PMID: 33366046 PMCID: PMC7707337 DOI: 10.1080/23802359.2019.1674717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 09/25/2019] [Indexed: 12/02/2022] Open
Abstract
The family Alvinocarididae is the monophyletic taxon which lives restrictively at chemosynthesis-based environments in the deep-sea. Here, for the first time, we report the complete mitogenome of the alvinocaridid vent shrimp Rimicaris variabilis from the North Fiji Basin. The mitogenome was 15,909 bp in length, with 65.6% AT content. Its protein-coding gene organization was typical of other alvinocaridid shrimps. Based on the phylogenetic tree, R. variabilis was most closely related to Shinkaicaris leurokolos, rather than with other Rimicaris species. To resolve this incongruence between traditional morphological classification and molecular analyses, further mitogenomic analysis of undetermined alvinocaridid taxa is necessary.
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Affiliation(s)
- Won-Kyung Lee
- Genome Editing Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
| | - Se-Joo Kim
- Genome Editing Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
| | - Se-Jong Ju
- Global Ocean Research Center, Korea Institute of Ocean Science and Technology, Busan, Korea
- Marine Biology Major, University of Science & Technology, Daejeon, Korea
| | - Bo Kyeng Hou
- Genome Editing Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
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Lee WK, Mi Kang H, Chan BKK, Ju SJ, Kim SJ. Complete mitochondrial genome of the hydrothermal vent stalked barnacle Vulcanolepas fijiensis (Cirripedia, Scalpelliforms, Eolepadidae). Mitochondrial DNA B Resour 2019; 4:2725-2726. [PMID: 33365701 PMCID: PMC7706898 DOI: 10.1080/23802359.2019.1644564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 07/10/2019] [Indexed: 11/30/2022] Open
Abstract
The family Eolepadidae is the only stalked barnacle in hydrothermal vent regions. Here, we determined the mitogenome of the eolepadid Vulcanolepas fijiensis. The mitogenome was 17,374 bp long, with 76.6% AT content. Its protein-coding gene organization was identical to that of the deep-sea scalpellid Arcoscalpellum epeeum. On the mitogenomic tree, two scalpellomorphan families (Eolepadidae and Scalpellidae) were monophyletic while the other scalpellomorphan family Pollicipedidae did not form the monophyletic group with them. Further mitogenomic analysis of undetermined taxa in hydrothermal vents is required to deepen our understanding of their phylogenetic relationships.
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Affiliation(s)
- Won-Kyung Lee
- Genome Editing Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
| | - Hyun Mi Kang
- Stem Cell Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
| | | | - Se-Jong Ju
- Global Ocean Research Center, Korea Institute of Ocean Science and Technology, Busan, Korea
- Marine Biology Major, University of Science and Technology, Daejeon, Korea
| | - Se-Joo Kim
- Genome Editing Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
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Kim RO, Chan BKK, Hou BK, Ju SJ, Kim SJ. Complete mitochondrial genome of the deep-water epibiotic stalked barnacle, Glyptelasma annandalei (Cirripedia, Lepadiformes, Poecilasmatidae). MITOCHONDRIAL DNA PART B-RESOURCES 2018. [DOI: 10.1080/23802359.2018.1536487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Ryeo-Ok Kim
- Department of Life Science, College of Natural Sciences Sangmyung University, Seoul, Korea
| | | | - Bo Kyeng Hou
- Genome Editing Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
| | - Se-Jong Ju
- Global Ocean Research Center, Korea Institute of Ocean Science and Technology, Busan, Korea
- Marine Biology Major, University of Science & Technology, Daejeon, Korea
| | - Se-Joo Kim
- Genome Editing Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
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Kim SJ, Kang HM, Corbari L, Chan BKK. First report on the complete mitochondrial genome of the deep-water scalpellid barnacle Arcoscalpellum epeeum (Cirripedia, Thoracica, Scalpellidae). Mitochondrial DNA B Resour 2018; 3:1288-1289. [PMID: 33490579 PMCID: PMC7800395 DOI: 10.1080/23802359.2018.1532844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 11/25/2022] Open
Abstract
Scalpellids are one of the largest families of Scalpelliformes and reproduce either androdioeciously or dioeciously. Here, we characterized the first mitogenome of a scalpellid barnacle (Arcoscalpellum epeeum), which was 15,593 bp in length with a 71.5% AT content. In comparison with the pollicipedids Capitulum mitella and Pollicipes polymerus, the tRNA genes of A. epeeum were rearranged between ND3 and ND5, between CYTB and ND1, and between 12S rRNA and ND2. On the mitogenomic tree, the Scalpelliformes families Pollicipedidae and Scalpellidae were not monophyletic, which concurs with previous studies.
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Affiliation(s)
- Se-Joo Kim
- Genome Editing Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
| | - Hyun Mi Kang
- Stem Cell Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
| | - Laure Corbari
- Institut de Systématique, Evolution, Biodiversité, Muséum national d'Histoire naturelle, UMR 7205 CNRS, Sorbonne Université, EPHE, Paris, France
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Chan BKK, Aguilar L, Hou BK, Kang HM, Kim SJ. Complete mitochondrial genome of the catophragmid barnacle Catomerus polymerus (Cirripedia, Thoracica, Balanomorpha, Catophragmidae). Mitochondrial DNA B Resour 2018; 3:1286-1287. [PMID: 33474495 PMCID: PMC7799505 DOI: 10.1080/23802359.2018.1532843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 11/11/2022] Open
Abstract
The family Catophragmidae is one of the lower balanomorphs from traditional and recent multiple mitochondrial and nuclear markers molecular analysis. Here, we characterized the first mitogenome of the catophragmid barnacle Catomerus polymerus, which was 15,446 bp in length with a 68.3% AT content. The mitogenome had the typical pancrustacean gene arrangement, which was identical to the mitogenome configurations of the chthamalid Octomeris sp. and pachylasmatoid Eochionelasmus ohtai. On the mitogenomic tree, the catophragmid Catomerus polymerus formed an independent branch that was basal to the members of the superfamilies Tetraclitoidea and Balanoidea, which was inconsistent with previous findings.
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Affiliation(s)
| | - Lucia Aguilar
- Institute for Conservation Biology & Environmental Management, Biological Sciences, University of Wollongong, NSW, Australia
| | - Bo Kyeng Hou
- Genome Editing Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
| | - Hyun Mi Kang
- Stem Cell Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
| | - Se-Joo Kim
- Genome Editing Research Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
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Kim SJ, Lee WK, Kim RO, Ju SJ. Complete mitochondrial genome of the hydrothermal vent barnacle Eochionelasmus ohtai (Cirripedia, Thoracica). Mitochondrial DNA B Resour 2017; 3:46-47. [PMID: 33474060 PMCID: PMC7800951 DOI: 10.1080/23802359.2017.1419089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/15/2017] [Indexed: 11/13/2022] Open
Abstract
Thoracican barnacles are common in hydrothermal vent fields. Here, we characterized the first mitogenome of a hydrothermal vent barnacle. The mitogenome of Eochionelasmus ohtai was 15,585 bp in length and had the typical pancrustacean gene arrangement. Its protein-coding genes (PCGs) were very similar in terms of length, AT content, and start and stop codons to those of other thoracican species. The phylogenetic tree constructed with 13 PCGs divided balanomorph barnacles, including E. ohtai, into two clades. This will further our understanding of the evolution of hydrothermal vent barnacles using mitogenomes, although further mitogenomic analysis of undetermined taxa is required.
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Affiliation(s)
- Se-Joo Kim
- Korean Bioinformation Center, Korea Research Institute Bioscience and Biotechnology, Daejeon, Korea
| | - Won-Kyung Lee
- Deep-sea and Seabed Mineral Resources Research Center, Korea Institute of Ocean Science & Technology, Ansan, Korea
| | - Ryeo-Ok Kim
- Department of Life Science, College of Natural Sciences, Sangmyung University, Seoul, Korea
| | - Se-Jong Ju
- Deep-sea and Seabed Mineral Resources Research Center, Korea Institute of Ocean Science & Technology, Ansan, Korea
- Department of Marine Biology, University of Science & Technology, Daejeon, Korea
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