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Lee GH, Min GS. The complete mitochondrial genome of a marine polychaete, Prionospio cf. japonica (Annelida: Spionidae). Mitochondrial DNA B Resour 2023; 8:985-988. [PMID: 37746033 PMCID: PMC10515661 DOI: 10.1080/23802359.2023.2241696] [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: 11/30/2022] [Accepted: 07/21/2023] [Indexed: 09/26/2023] Open
Abstract
Prionospio Malmgren 1867 is one of the abundant genera of the family Spionidae Grube, 1850. Despite its rich diversity, information on their complete mitochondrial genome has remained unknown. In this study, we determined the complete mitochondrial genome of a spionid polychaete, Prionospio cf. japonica Okuda 1935. The specimen was collected from the fine sand in the intertidal zone of South Korea. The mitogenome consists of 15,267 base pairs, harboring 13 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs. The maximum-likelihood phylogenetic tree based on the 11 PCGs showed that Prionospio cf. japonica grouped with other spionid polychaetes and formed a monophyletic group. Also, the mtDNA of P. cf. japonica was more closely related to that of non-polydorin spionid, Marenzelleria neglecta, than polydorin spionids. The molecular data will be valuable for studying evolutionary relationships among annelids.
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Affiliation(s)
- Geon Hyeok Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, Korea
- Department of Biological Sciences, Inha University, Incheon, Korea
| | - Gi-Sik Min
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, Korea
- Department of Biological Sciences, Inha University, Incheon, Korea
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Cejp B, Ravara A, Aguado MT. First mitochondrial genomes of Chrysopetalidae (Annelida) from shallow-water and deep-sea chemosynthetic environments. Gene 2022; 815:146159. [PMID: 34995739 DOI: 10.1016/j.gene.2021.146159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023]
Abstract
Among Annelida, Chrysopetalidae is an ecologically and morphologically diverse group, which includes shallow-water, deep-sea, free-living, and symbiotic species. Here, the four first mitochondrial genomes of this group are presented and described. One of the free-living shallow-water species Chrysopetalum debile (Chrysopetalinae), one of the yet undescribed free-living deep-sea species Boudemos sp., and those of the two deep-sea bivalve endosymbionts Craseoschema thyasiricola and Iheyomytilidicola lauensis (Calamyzinae). An updated phylogeny of Chrysopetalidae is performed, which supports previous phylogenetic hypotheses within Chrysopetalinae and indicates a complex ecological evolution within Calamyzinae. Additionally, analyses of natural selection pressure in the four mitochondrial genomes and additional genes from the two shallow-water species Bhawania goodei and Arichlidon gathofi were performed. Relaxed selection pressure in the mitochondrion of deep-sea and symbiotic species was found, with many sites under selection identified in the COX3 gene of deep-sea species.
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Affiliation(s)
- Benjamin Cejp
- Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, 37073, Germany.
| | - Ascensão Ravara
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
| | - M Teresa Aguado
- Animal Evolution and Biodiversity, Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology, Georg-August-University Göttingen, 37073, Germany.
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Alves PR, Halanych KM, Santos CSG. The phylogeny of Nereididae (Annelida) based on mitochondrial genomes. ZOOL SCR 2020. [DOI: 10.1111/zsc.12413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paulo Ricardo Alves
- Programa de Pós‐Graduação em Biologia Marinha e Ambientes Costeiros Laboratório de Sistemática e Ecologia de Polychaeta Departamento de Biologia Marinha Universidade Federal Fluminense Niterói Brasil
| | - Kenneth M. Halanych
- Molette Laboratory for Environmental and Climate Change Studies Department of Biological Sciences Auburn University Auburn AL USA
| | - Cinthya Simone Gomes Santos
- Programa de Pós‐Graduação em Biologia Marinha e Ambientes Costeiros Laboratório de Sistemática e Ecologia de Polychaeta Departamento de Biologia Marinha Universidade Federal Fluminense Niterói Brasil
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Chen XH, Yang S, Yang W, Si YY, Xu RW, Fan B, Wang L, Meng ZN. First genetic assessment of brackish water polychaete Tylorrhynchus heterochaetus: mitochondrial COI sequences reveal strong genetic differentiation and population expansion in samples collected from southeast China and north Vietnam. Zool Res 2020; 41:61-69. [PMID: 31709784 PMCID: PMC6956720 DOI: 10.24272/j.issn.2095-8137.2020.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/29/2019] [Indexed: 11/10/2022] Open
Abstract
Tylorrhynchus heterochaetus is a widespread benthic polychaete worm found in coastal brackish waters of the west Pacific. It has high ecological and economic value as a biomarker of water quality and as a high-quality feed in aquaculture and fisheries and is considered a delicacy in some areas of Asia. However, it has experienced a marked reduction in recent years due to overexploitation as well as changes in the environment and climate. Here, to comprehensively understand its genetic background and thus provide insights for better conservation and utilization of this species, we assessed the genetic variability and demographic history of T. heterochaetus individuals sampled from eight locations along the coasts of southeast China and north Vietnam based on mitochondrial cytochrome c oxidase I ( COI) sequences. We observed high haplotype diversity ( Hd), with an average of 0.926, but relatively low nucleotide diversity ( π), with a mean of 0.032 across all samples. A total of 94 polymorphic sites and 85 haplotypes were identified among 320 individuals. The pairwise genetic distances among haplotypes ranged from 0.001 to 0.067, with the high intraspecific divergence possibly reflecting geographic isolation and gene pool fragmentation. Significant genetic structures were revealed among the studied locations; specifically, the eight locations could be treated as six genetically different populations based on pairwise Φ ST results (0.026-0.951, P<0.01). A significant pattern of isolation-by-distance was detected between the genetic and geographic distances ( r=0.873, P=0.001). Three geographic lineages were defined based on phylogenetic tree and network analyses of COI haplotypes. AMOVA results indicated that genetic variations mainly occurred among the three lineages (89.96%). Tests of neutrality and mismatch distribution suggested that T. heterochaetus underwent recent population expansion. These results provide the first report on the genetic status of T. heterochaetus and will be valuable for the management of genetic resources and better understanding of the ecology and evolution in this species.
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Affiliation(s)
- Xing-Han Chen
- Department of Food and Environmental Engineering, Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang City, Yangjiang Polytechnic, Yangjiang, Guangdong 529500, China
| | - Sen Yang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong 520175, China
| | - Wei Yang
- Department of Food and Environmental Engineering, Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang City, Yangjiang Polytechnic, Yangjiang, Guangdong 529500, China
| | - Yuan-Yuan Si
- Department of Food and Environmental Engineering, Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang City, Yangjiang Polytechnic, Yangjiang, Guangdong 529500, China
| | - Rui-Wen Xu
- Department of Food and Environmental Engineering, Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang City, Yangjiang Polytechnic, Yangjiang, Guangdong 529500, China
| | - Bin Fan
- Department of Food and Environmental Engineering, Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang City, Yangjiang Polytechnic, Yangjiang, Guangdong 529500, China
| | - Le Wang
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Zi-Ning Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yet-Sen University, Guangzhou, Guangdong 510275, China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, Guangdong 519000, China. E-mail:
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Chen X, Yang W, Si Y, Li B, Xu R, Meng Z, Fan B. The complete mitochondrial genome of the polychaete, Marphysa tamurai (Eunicida, Eunicidae). MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1567277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Xinghan Chen
- Department of Food and Environmental Engineering, Yangjiang Polytechnic, and Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang, Yangjiang, China
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Wei Yang
- Department of Food and Environmental Engineering, Yangjiang Polytechnic, and Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang, Yangjiang, China
| | - Yuanyuan Si
- Department of Food and Environmental Engineering, Yangjiang Polytechnic, and Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang, Yangjiang, China
| | - Bo Li
- Department of Food and Environmental Engineering, Yangjiang Polytechnic, and Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang, Yangjiang, China
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Ruiwen Xu
- Department of Food and Environmental Engineering, Yangjiang Polytechnic, and Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang, Yangjiang, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, China
| | - Bin Fan
- Department of Food and Environmental Engineering, Yangjiang Polytechnic, and Key Laboratory for Marine Estuary Fishery Resources Protection of Yangjiang, Yangjiang, China
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Park T, Lee SH, Shin MH, Kim W. Determination of complete mitogenome sequence for Eastern Asian population of Cheilonereis cyclurus (Harrington, 1897) (Polychaeta: Nereididae). Mitochondrial DNA B Resour 2017; 2:669-671. [PMID: 33473941 PMCID: PMC7800064 DOI: 10.1080/23802359.2017.1372717] [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: 08/08/2017] [Accepted: 08/24/2017] [Indexed: 11/29/2022] Open
Abstract
Complete mitogenome sequence for eastern Asian population of Cheilonereis cyclurus (Polychaeta: Nereididae) was determined for the first time. The length of circular genome of C. cyclurus is 14,917 bp including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a non-coding region of 383 bp. The gene order of C. cyclurus is identical to that of the following four nereidid species: Hediste diadroma, Namalycastis abiuma, Paraleonnates uschakovi, Tylorrhynchus heterochaetus. The phylogenetic position of C. cyclurus compared to 16 selected polychaetes was conducted and present species is closely related to the clade containing Perinereis nuntia, P. aibuhitensis, and Platynereis dumerilii with high bootstrap value.
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Affiliation(s)
- Taeseo Park
- Animal Resources Division, National Institute of Biological Resources, Incheon, Korea
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Sang-Hwa Lee
- Graduate Program in Cellular Biology and Genetics, Colleage of Medicine, Chungbuk National University, Cheongju, Korea
| | - Myung-Hwa Shin
- National Marine Biodiversity Institute of Korea, Seocheon, Republic of Korea
| | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul, Korea
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Park T, Lee SH, Kim W. Complete mitochondrial genome sequence of the giant mud worm Paraleonnates uschakovi Khlebovich & Wu, 1962 (Polychaeta: Nereididae). Mitochondrial DNA B Resour 2016; 1:640-642. [PMID: 33490415 PMCID: PMC7800312 DOI: 10.1080/23802359.2016.1214552] [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] [Indexed: 10/28/2022] Open
Abstract
Complete mitochondrial genome sequence of the giant mud worm Paraleonnates uschakovi (Polychaeta: Nereididae) was determined in this study for the first time. The mitogenome of P. uschakovi is 15,540 bp in length. It has 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a non-coding region. Mitogenome analysis of P. uschakovi showed inversion in the positions of three tRNAs compared to the mitogenome sequences of Perinereis aibuhitensis, P. nuntia and Platynereis dumerilii. The phylogenetic position of P. uschakovi compared to 15 selected polychaetes was investigated. P. uschakovi was grouped into the family of Nereididae. It is closely related to the clade containing Tylorrhynchus heterochaetus and Namalycastis abiuma.
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Affiliation(s)
- Taeseo Park
- Animal Resources Division, National Institute of Biological Resources, Incheon, Korea.,School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Sang-Hwa Lee
- Animal Resources Division, National Institute of Biological Resources, Incheon, Korea.,Graduate Program in Cellular Biology and Genetics, Colleage of Medicine, Chungbuk National University, Cheongju, Korea
| | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul, Korea
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Chen X, Li M, Liu H, Li B, Guo L, Meng Z, Lin H. The complete mitochondrial genome of the polychaete, Goniada japonica (Phyllodocida, Goniadidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2850-1. [PMID: 26119121 DOI: 10.3109/19401736.2015.1053124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The study determined the complete mitochondrial genome (mitogenome) of the polychaete, Goniada japonica, which was first reported in the family of Goniadidae. A total of 7162 reads were generated by Illumina HiSeq2500 platform (Illumina Inc., San Diego, CA) with an average depth of 58.41×. The mitogenome of G. japonica was 15,327 bp in size and consists of 37 typical genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and a putative control region. All the 37 genes were encoded on the heavy strand whose nucleotide compositions were 35.08% of A, 33.69% of T, 11.66% of G, and 19.57% of C, showing a lower content of G + C (31.23%). The gene order of 15 major coding genes was identical to that of the Nereididae species. Phylogenetic analysis showed that G. japonica has a closer relationship with Tylorrhynchus heterochaetus of Nereididae.
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Affiliation(s)
- Xinghan Chen
- a Life Science and Technology Department, Yangjiang Vocational and Technical College , Yangjiang , China and.,b State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University , Guangzhou , China
| | - Mingming Li
- a Life Science and Technology Department, Yangjiang Vocational and Technical College , Yangjiang , China and
| | - Heping Liu
- b State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University , Guangzhou , China
| | - Bo Li
- b State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University , Guangzhou , China
| | - Liang Guo
- a Life Science and Technology Department, Yangjiang Vocational and Technical College , Yangjiang , China and
| | - Zining Meng
- a Life Science and Technology Department, Yangjiang Vocational and Technical College , Yangjiang , China and
| | - Haoran Lin
- a Life Science and Technology Department, Yangjiang Vocational and Technical College , Yangjiang , China and
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