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Sun S, Xiao N, Sha Z. Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea. PeerJ 2022; 10:e13730. [PMID: 35919401 PMCID: PMC9339218 DOI: 10.7717/peerj.13730] [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: 04/22/2022] [Accepted: 06/23/2022] [Indexed: 01/17/2023] Open
Abstract
Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-Ser AGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-Ser AGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.
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Affiliation(s)
- Shao’e Sun
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ning Xiao
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
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2
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Yu M, Zhang D, Zhao X. Sequencing and phylogenomics of the complete mitochondrial genome of Allodiplogaster sp. (Rhabditida: Diplogasteridae): A new gene order and its phylogenetic implications. Gene 2022; 840:146761. [PMID: 35905856 DOI: 10.1016/j.gene.2022.146761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/13/2022] [Accepted: 07/24/2022] [Indexed: 11/18/2022]
Abstract
Gene order has been utilized as a phylogenetic signal for many taxa. However, its phylogenetic performance has not been evaluated in Nematoda. As there is only one nematode mitogenome available to date, in the Diplogasteridae family, we sequenced the mitogenome of Allodiplogaster sp. and constructed a phylogeny for Nematoda using this updated mitogenome dataset. We then compared this phylogeny to one constructed using gene order. The complete mitochondrial genome of Allodiplogaster sp. was 13,953 bp in size and included 22 tRNAs, two rRNAs, and 12 protein-coding genes. To assess how Allodiplogaster sp. is related to other nematode species, we used Bayesian inference and maximum likelihood algorithms to construct phylogenetic trees of the Nematoda. We found that: 1) The target species Allodiplogaster sp. is closely related to Allodiplogaster sudhausi. The topology of the mitogenome based phylogeny was nearly identical to previous phylogenies created using 18S rRNA data, except for the placement of the Strongyloididae family. 2) The maximum likelihood tree constructed using gene order was roughly consistent with the mitogenome-based tree at the family level, but not at the species level. 3) Protein-coding genes were ordered differently in Allodiplogaster sp. versus Allodiplogaster sudhausi; this represents the first report of such a reordering in the class Chromadorea in our study. Our study confirms that gene order represents useful phylogenetic information for the Nematoda: the maximum likelihood tree based on gene order provided additional support for the nematode phylogeny constructed using molecular data.
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Affiliation(s)
- Min Yu
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Dong Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Xumao Zhao
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China.
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3
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Ma B, Li Z, Lv Y, E Z, Fang J, Ren C, Luo P, Hu C. Analysis of Complete Mitochondrial Genome of Bohadschia argus (Jaeger, 1833) (Aspidochirotida, Holothuriidae). Animals (Basel) 2022; 12:ani12111437. [PMID: 35681901 PMCID: PMC9179316 DOI: 10.3390/ani12111437] [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] [Received: 04/26/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 12/04/2022] Open
Abstract
Bohadschia argu is a kind of sea cucumber with high economic value; it is the only undisputed species in the genus Bohadschia. In this study, the complete mitochondrial genome (mitogenome) of B. argus was acquired through high-throughput sequencing. The mitochondrial genome of B. argus was 15,656 bp in total length and contained a putative control region (CR) and 37 typical genes of animal mitochondrial genomes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes (tRNA). The sizes of the PCGs ranged from 168 bp to 1833 bp, and all PCGs except nad6 were encoded on the heavy chain (H). Both rrnS and rrnL were also encoded on the H chain. Twenty-two tRNA genes had positive AT skew and GC skew. All tRNAs had a typical cloverleaf secondary structure except for trnI, in which an arm of dihydrouridine was missing. B. argus shared the same gene arrangement order (the echinoderm ground pattern) as other species in Aspidochirotida. Phylogenetic analysis clearly revealed that B. argus belongs as a member of the Holothuriidae, and it is closely related to members of Actinopyga and Holothuria.
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Affiliation(s)
- Bo Ma
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuobo Li
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Lv
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou 535011, China;
| | - Zixuan E
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianxiang Fang
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
| | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- Correspondence: ; Tel.: +86-18520090836
| | - Chaoqun Hu
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
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4
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Li Z, Ma B, Li X, Lv Y, Jiang X, Ren C, Hu C, Luo P. The Complete Mitochondrial Genome of Stichopus naso (Aspidochirotida: Stichopodidae: Stichopus) and Its Phylogenetic Position. Genes (Basel) 2022; 13:genes13050825. [PMID: 35627210 PMCID: PMC9141342 DOI: 10.3390/genes13050825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 01/21/2023] Open
Abstract
The mitochondrial genome is widely used to study the molecular evolution of and perform phylogenetic analyses on animals. In this study, the complete mitochondrial genome (mitogenome) of Stichopus naso was sequenced. The mitogenome was 16,239 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The genome composition showed positive AT-skew (0.023) and negative GC-skew (−0.158). The order of the mitochondrial genes was consistent with those from the Stichopus and Isostichopus species, whereas it was different from those of other species of Aspidochirotida. The phylogenetic analysis, based on the nucleotide sequences of 13 PCGs through the methods of Bayesian inference (BI) and maximum likelihood (ML), indicated that S. naso has close relationships with S. horrens and S. monotuberculatus, and belongs to a member of Stichopodidae. Our study provides a reference mitogenome for further molecular evolution studies and phylogenetic research on sea cucumbers.
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Affiliation(s)
- Zhuobo Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Ma
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Lv
- Marin College, Beibu Gulf University, Qinzhou 535011, China;
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
| | - Chaoqun Hu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
| | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology (LMB), Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology Chinese Academy of Sciences, Guangzhou 510301, China; (Z.L.); (B.M.); (X.L.); (X.J.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- Correspondence:
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5
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Sun JJ, Sun ZH, Wei JL, Ding J, Song J, Chang YQ. Identification and functional analysis of foxl2 and nodal in sea cucumber, Apostichopus japonicus. Gene Expr Patterns 2022; 44:119245. [PMID: 35381371 DOI: 10.1016/j.gep.2022.119245] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/24/2022] [Accepted: 03/19/2022] [Indexed: 11/28/2022]
Abstract
Sea cucumber (Apostichopus japonicus) is an important mariculture species in China. To date, the mechanisms of sex determination and differentiation in sea cucumber remain unclear. Identifying sex-specific molecular markers is an effective method for revealing the genetic basis of sex determination and sex differentiation. In this study, foxl2 and nodal homologous genes were identified in A. japonicus. Foxl2 exhibited dynamic and sexually dimorphic expression patterns in the gonads, with prominent expression in the ovaries and minimal expression in the testis according to real-time quantitative PCR (RT-qPCR) study. As nodal was specifically expressed in the ovary, it could serve as an ovary-specific marker in sea cucumber. Additionally, knockdown of foxl2 or nodal using RNA interference (RNAi) led to the down-regulation of piwi, germ cell-less, and dmrt1, suggesting that foxl2 and nodal may play important roles in gonad maintenance of sea cucumber. Overall, this study adds to our understanding of the roles of foxl2 and nodal in the gonadal development of A. japonicus, which provides further insight into the mechanisms of sea cucumber sex determination and differentiation.
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Affiliation(s)
- Juan-Juan Sun
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Zhi-Hui Sun
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Jin-Liang Wei
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Ya-Qing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
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Sun S, Sha Z, Xiao N. The first two complete mitogenomes of the order Apodida from deep-sea chemoautotrophic environments: New insights into the gene rearrangement, origin and evolution of the deep-sea sea cucumbers. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100839. [PMID: 33933835 DOI: 10.1016/j.cbd.2021.100839] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
The deep-sea ecosystem is considered as the largest and most remote biome of the world. It is meaningful and important to elucidate the life origins by exploring the origin and adaptive genetic mechanisms of the large deep-sea organisms. Sea cucumbers (Holothuroidea) are abundant and economically important group of echinoderms, living from the shallow-waters to deep-sea. In this study, we present the mitochondrial genomes of the sea cucumber Chiridota heheva and Chiridota sp. collected from the deep-sea cold seep and hydrothermal vent, respectively. This is the first reported mitochondrial genomes from the order Apodida. The mitochondrial genomes of C. heheva (17,200 bp) and Chiridota sp. (17,199 bp) display novel gene arrangements with the first protein-coding gene rearrangements in the class Holothuroidea. Bases composition analysis showed that the A + T content of deep-sea holothurians were significantly higher than that of the shallow-water groups. We compared the arrangement of genes from the 24 available holothurian mitogenomes and found that the transposition, reverse transposition and tandem-duplication-random-losses (TDRL) may be involved in the evolution of mitochondrial gene arrangements in Holothuroidea. Phylogenetic analysis revealed that the Apodida clustered with Elasipodida, forming two basal deep-sea holothurian clades. The divergence between the deep-sea and shallow-water holothurians was located at 386.93 Mya, during the Late Devonian. Mitochondrial protein-coding genes of deep-sea holothurians underwent relaxed purifying selection. There are 57 positive selected amino acids sites for some mitochondrial genes of the three deep-sea clades, implying they may involve in the adaption of deep-sea sea cucumbers.
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Affiliation(s)
- Shao'e Sun
- Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Zhongli Sha
- Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Xiao
- Institute of Oceanology, Chinese Academy of Science, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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7
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Liao M, Li B, Xiao N, Kong M, Wang Y, Wang J, Rong X, Zhang Z, Yu Y. Complete sequence of mitochondrial DNA of a deep-sea holothurian species of the genus Synallactes (Synallactida: Synallactidae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2699-2700. [PMID: 33457910 PMCID: PMC7782141 DOI: 10.1080/23802359.2020.1787266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
One complete mitochondrial genome (mitogenome) was determined for a deep-sea holothurian species of the genus Synallactes (Synallactida: Synallactidae). The mitochondrial genome size of the sea cucumber was 15,920 bp. The sequence contains 2 ribosomal RNA genes (12S and 16S), 22 transfer RNA genes, and 13 protein-coding genes, as found in most previously determined holothurian mitogenomes. The A + T content of the complete mitochondrial genome sequence was 64.45%. The base composition showed a tendency of AT. The resulted maximum likelihood (ML) tree of Holothuroidea supported that Synallactes sp. is a species of Synallactida.
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Affiliation(s)
- Meijie Liao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Bin Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Ning Xiao
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Miao Kong
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Yingeng Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Jinjin Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Xiaojun Rong
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Zheng Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
| | - Yongxiang Yu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao, China
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8
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Yang F, Zhou C, Tran NT, Sun Z, Wu J, Ge H, Lu Z, Zhong C, Zhu Z, Yang Q, Lin Q. Comparison of the complete mitochondrial genome of Phyllophorus liuwutiensis (Echinodermata: Holothuroidea: Phyllophoridae) to that of other sea cucumbers. FEBS Open Bio 2020; 10:1587-1600. [PMID: 32573974 PMCID: PMC7396427 DOI: 10.1002/2211-5463.12914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 05/31/2020] [Accepted: 06/17/2020] [Indexed: 12/25/2022] Open
Abstract
Sea cucumber species are abundant (>1400 species) and widely distributed globally. mtDNA sequencing is frequently used to identify the phylogenetic and evolutionary relationships among species. However, there are no reports on the mitochondrial genome of Phyllophorus liuwutiensis. Here, we performed mtDNA sequencing of P. liuwutiensis to examine its phylogenetic relationships with other echinoderms. Its mitochondrial genome (15 969 bp) contains 37 coding genes, including 13 protein‐coding genes, 22 tRNA genes and 2 rRNA genes. Except for one protein‐coding gene (nad6) and five tRNA genes encoded on the negative strand, all other genes were encoded on the positive strand. The mitochondrial bases of P. liuwutiensis were composed of 29.55% T, 22.16% C, 35.64% A and 12.64% G. The putative control region was 703 bp in length. Seven overlapping regions (1–10 bp) were found. The noncoding region between the genes ranged from 1 to 130 bp in length. One putative control region has been found in the P. liuwutiensis mitogenome. All of the tRNA genes were predicted to fold into a cloverleaf structure. In addition, we compared the gene arrangements of six echinoderms, revealing that the gene order of P. liuwutiensis was a new arrangement.
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Affiliation(s)
- Fuyuan Yang
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,College of Fisheries and Life Science, Shanghai Ocean University, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Ngoc Tuan Tran
- Institute of Marine Sciences, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, China
| | - Zaiqiao Sun
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Hui Ge
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhen Lu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Chenhui Zhong
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhihuang Zhu
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Qiuhua Yang
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,College of Fisheries and Life Science, Shanghai Ocean University, China
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9
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Zhong S, Liu Y, Zhao Y, Huang G. The complete mitochondrial genome of sea cucumber Stichopus monotuberculatus (aspidochirotida: Stichopodidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3305-3306. [PMID: 33365967 PMCID: PMC7707201 DOI: 10.1080/23802359.2019.1673244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The sea cucumber, Stichopus monotuberculatus, is an economically important holothuroid in China due to its larger body size and valuable nutrition. However, the taxonomic revision studies of Stichopodidae have been one of the most controversial issues in recent years. Moreover, there remain considerable doubts about a complex of cryptic species within S. monotuberculatus. In this study, we report the complete mitochondrial genome of S. monotuberculatus. The mitogenome has 16,274 base pairs (60.4% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study adds one more available complete mitogenomes of Stichopus and will provide useful genetic information for future evolutionary and taxonomic classification of Stichopodidae.
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Affiliation(s)
- Shengping Zhong
- Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Yonghong Liu
- Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Yanfei Zhao
- Key Laboratory of Marine Biotechnology, Guangxi Institute of Oceanology, Beihai, China
| | - Guoqiang Huang
- Institute of marine drugs, Guangxi University of Chinese Medicine, Nanning, China
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Yang Q, Lin Q, Wu J, Yang F, Ge H, Qiu D, Li Z, Lu Z, Li S, Zhou C. The complete mitochondrial genome sequence of Stichopus variegatus (Echinodermata: Holothuroidea) and phylogenetic studies of Echinodermata. Mitochondrial DNA B Resour 2019; 4:3244-3245. [PMID: 33365938 PMCID: PMC7707333 DOI: 10.1080/23802359.2019.1669502] [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: 07/11/2019] [Accepted: 08/16/2019] [Indexed: 11/16/2022] Open
Abstract
At present, there exist some confusing issues on the species classification and phylogeny in Echinodermata. In this study, we first determined and described the complete mitochondrial genome of Stichopus variegatus. The complete mitogenome sequence had a circular mapping molecular with the total length of 16,315 bp and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. To further validate the newly determined sequences, phylogenetic trees involving all the Holothuroidea and other Echinodermata species available in GenBank Database were constructed. These results would be used for the species identification and further phylogenetic studies of Echinodermata.
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Affiliation(s)
- Qiuhua Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, Guangdong, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Fuyuan Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Hui Ge
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Denggao Qiu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Zhongqin Li
- Fisheries College, Engineering Research Center on Eel Modern Industrial Technology of Ministry of Education, Jimei University, Xiamen, Fujian, China
| | - Zhen Lu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, Guangdong, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, Fujian, China
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Yang Q, Lin Q, Yang F, Wu J, Lu Z, Li S, Zhou C. Characterization of the complete mitochondrial genome of a holothurians species: Holothuria hilla (Holothuroidea: Holothuriidae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2847-2848. [PMID: 33365756 PMCID: PMC7706501 DOI: 10.1080/23802359.2019.1660267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Mitochondrial genome sequence is a great potential method to both resolve disputed taxonomic issues and to infer phylogenetic relationships among holothurians. In this study, we present the complete mitochondrial genome of Holothuria hilla which was 15,744 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. The gene content and arrangement were typical for Holothuroidea ground pattern. The overall base composition was 32.43% A, 27.20% T, 24.35% C and 16.02% G, showing a bias toward A + T (59.63%). The maximum-likelihood tree based on the concatenated 13 protein-coding genes revealed the phylogenetic relationships among the Holothuroidea species.
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Affiliation(s)
- Qiuhua Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Fuyuan Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhen Lu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
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Yang Q, Lin Q, Wu J, Tran NT, Huang R, Sun Z, Zhu Z, Lu Z, Li S, Zhou C. Complete mitochondrial genome of Holothuria leucospilata (Holothuroidea, Holothuriidae) and phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2751-2752. [PMID: 33365713 PMCID: PMC7706471 DOI: 10.1080/23802359.2019.1644226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The complete Holothuria leucospilata mitochondrial genome was determined and analyzed in this work. It had a circular mapping molecular with a total length of 15,904 bp and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 putative control region. Phylogenetic analysis showed that H. leucospilata clustered together with Holothuria scabra and Holothuria forskali. The complete mitochondrial genome provided in this work would be used for elucidation of Holothuroidea conservation genetics and evolutionary relationships.
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Affiliation(s)
- Qiuhua Yang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China.,Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Qi Lin
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Jianshao Wu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Ngoc Tuan Tran
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Ruifang Huang
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zaiqiao Sun
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhihuang Zhu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Zhen Lu
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Marine Biology Institute, Shantou University, Shantou, China
| | - Chen Zhou
- Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Fisheries Research Institute of Fujian, Xiamen, China
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Mu W, Liu J, Zhang H. Complete mitochondrial genome of Benthodytes marianensis (Holothuroidea: Elasipodida: Psychropotidae): Insight into deep sea adaptation in the sea cucumber. PLoS One 2018; 13:e0208051. [PMID: 30500836 PMCID: PMC6267960 DOI: 10.1371/journal.pone.0208051] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/09/2018] [Indexed: 01/01/2023] Open
Abstract
Complete mitochondrial genomes play important roles in studying genome evolution, phylogenetic relationships, and species identification. Sea cucumbers (Holothuroidea) are ecologically important and diverse members, living from the shallow waters to the hadal trench. In this study, we present the mitochondrial genome sequence of the sea cucumber Benthodytes marianensis collected from the Mariana Trench. To our knowledge, this is the first reported mitochondrial genome from the genus Benthodytes. This complete mitochondrial genome is 17567 bp in length and consists of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes (duplication of two tRNAs: trnL and trnS). Most of these genes are coded on the positive strand except for one protein-coding gene (nad6) and five tRNA genes which are coded on the negative strand. Two putative control regions (CRs) have been found in the B. marianensis mitogenome. We compared the order of genes from the 10 available holothurian mitogenomes and found a novel gene arrangement in B. marianensis. Phylogenetic analysis revealed that B. marianensis clustered with Peniagone sp. YYH-2013, forming the deep-sea Elasipodida clade. Positive selection analysis showed that eleven residues (24 S, 45 S, 185 S, 201 G, 211 F and 313 N in nad2; 108 S, 114 S, 322 C, 400 T and 427 S in nad4) were positively selected sites with high posterior probabilities. We predict that nad2 and nad4 may be the important candidate genes for the further investigation of the adaptation of B. marianensis to the deep-sea environment.
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Affiliation(s)
- Wendan Mu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- * E-mail:
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Shen X, Sun S, Zhao FQ, Zhang GT, Tian M, Tsang LM, Wang JF, Chu KH. Phylomitogenomic analyses strongly support the sister relationship of the Chaetognatha and Protostomia. ZOOL SCR 2015. [DOI: 10.1111/zsc.12140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology/Co-Innovation Center of Jiangsu Marine Bio-industry Technology; Huaihai Institute of Technology; Lianyungang 222005 China
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing 100101 China
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Shatin Hong Kong China
| | - Song Sun
- KLMEES and JBMERS; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
| | - Fang Qing Zhao
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing 100101 China
| | - Guang Tao Zhang
- KLMEES and JBMERS; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
| | - Mei Tian
- Jiangsu Key Laboratory of Marine Biotechnology/Co-Innovation Center of Jiangsu Marine Bio-industry Technology; Huaihai Institute of Technology; Lianyungang 222005 China
| | - Ling Ming Tsang
- Institute of Marine Biology; National Taiwan Ocean University; Keelung 20224 Taiwan
| | - Jin Feng Wang
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing 100101 China
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Shatin Hong Kong China
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15
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Zhang Z, Bao X, Dong Y, Gao X, Gao L, Li S, Liu W, Hou H, Shi J, Pu H. Complete mitochondrial genome of Parastichopus californicus (Aspidochirotida: Stichopodidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3569-70. [PMID: 26260176 DOI: 10.3109/19401736.2015.1074222] [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
In this study, we first determined and described the complete mitogenome sequence of Parastichopus californicus, which was 16 727 bp in length. The mitochondrial genome had the canonical mitochondrial gene content, including 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. The overall base composition of the heavy-strand was 31.5% A, 18 % G, 20.6% C and 29.9% T, with a high A + T content of 61.4%. ML phylogenetic tree indicated that P. californicus and P. nigripunctatus were clustered in one branch belonging to the genus Parastichopus. This conclusion was identical to the former result by the methods of morphological taxonomy.
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Affiliation(s)
- Zhenyu Zhang
- a School of Food Science and Technology, Dalian Polytechnic University , Dalian , Liaoning , P.R. China and
| | - Xiangbo Bao
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Ying Dong
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Xianggang Gao
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Lei Gao
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Shilei Li
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Weidong Liu
- b Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute , Dalian , Liaoning , P.R. China
| | - Hongman Hou
- a School of Food Science and Technology, Dalian Polytechnic University , Dalian , Liaoning , P.R. China and
| | - Jingyun Shi
- a School of Food Science and Technology, Dalian Polytechnic University , Dalian , Liaoning , P.R. China and
| | - Hongshaung Pu
- a School of Food Science and Technology, Dalian Polytechnic University , Dalian , Liaoning , P.R. China and
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Xia J, Ren C, Yu Z, Wu X, Qian J, Hu C. Complete mitochondrial genome of the sandfish Holothuria scabra (Holothuroidea, Holothuriidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4174-4175. [PMID: 25629485 DOI: 10.3109/19401736.2014.1003899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mitogenome) sequence of Holothuria scabra, an economically and ecologically important tropical sea cucumber, was first sequenced and annotated. The mitochondrial DNA is 15,779 bp in length and contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a 456 bp putative control region, of which gene order is identical to the echinoderm ground pattern. Comparative analyses between H. scabra and other holothurians revealed three new findings: (1) the mitogenome of H. scabra is highly compact having five regions with overlapping genes and least intergenic nucleotides among the sequenced holothurians, only accounting for 3.58% of its mitogenome; (2) the genus Holothuria mitogenomes show a pattern of high interspecies divergence at the 13 PCGs, and the genetic p-distance reaches 25.68% between H. scabra and H. forskali; (3) the incomplete stop codon T of cox2 shared with H. forskali may be a common feature in the genus Holothuria.
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Affiliation(s)
- Jianjun Xia
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Chunhua Ren
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Zonghe Yu
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Xiangyun Wu
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Jing Qian
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
| | - Chaoqun Hu
- a Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology , South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
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Complete mitogenome of the edible sea urchin Loxechinus albus: genetic structure and comparative genomics within Echinozoa. Mol Biol Rep 2014; 42:1081-9. [DOI: 10.1007/s11033-014-3847-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 11/25/2014] [Indexed: 10/24/2022]
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18
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Dilly GF, Gaitán-Espitia JD, Hofmann GE. Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: a molecular resource for phylogenetics, ecophysiology and global change biology. Mol Ecol Resour 2014; 15:425-36. [DOI: 10.1111/1755-0998.12316] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 06/24/2014] [Accepted: 07/21/2014] [Indexed: 11/30/2022]
Affiliation(s)
- G. F. Dilly
- Marine Science Institute; Department of Ecology, Evolution and Marine Biology; University of California; Santa Barbara CA USA
| | - J. D. Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Valdivia Chile
| | - G. E. Hofmann
- Marine Science Institute; Department of Ecology, Evolution and Marine Biology; University of California; Santa Barbara CA USA
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Gaitán-Espitia JD, Hofmann GE. Mitochondrial genome architecture of the giant red sea urchinMesocentrotus franciscanus(Strongylocentrotidae, Echinoida). ACTA ACUST UNITED AC 2014; 27:591-2. [DOI: 10.3109/19401736.2014.908359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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20
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Shen X, Chan BKK, Tsang LM. The mitochondrial genome of Nobia grandis Sowerby, 1839 (Cirripedia: Sessilia): the first report from the coral-inhabiting barnacles family Pyrgomatidae. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:339-41. [PMID: 24660915 DOI: 10.3109/19401736.2014.892106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This work presents the coral-inhabiting barnacle Nobia grandis Sowerby, 1839 complete mitochondrial genome, which is the first report from the family Pyrgomatidae (Cirripedia: Sessilia). The N. grandis mitochondrial genome is 15,032 bp in length, containing a total of 469 bp of non-coding nucleotides spreading in 11 intergenic regions (with the largest region of 376 bp). Compared with the pancrustacean ground pattern, there are not less than seven tRNAs rearranged in the N. grandis mitochondrial genome. Gene overlaps are founded in eight places. Nine PCGs (COX1-3, ATP6, ATP8, CYTB, ND2, ND3 and ND6) are encoded on the heavy strand while the remaining 4 PCGs and the two rRNAs are located on the light strand. As the first representative from the family Pyrgomatidae, the N. grandis mitochondrial genome will help us to explore the evolutionary history and molecular evolution of coral barnacles and Sessilia in future studies.
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Affiliation(s)
- Xin Shen
- a Jiangsu Key Laboratory of Marine Biotechnology , College of Marine Science, Huaihai Institute of Technology , Lianyungang , China
| | | | - Ling Ming Tsang
- c Institute of Marine Biology, National Taiwan Ocean University , Keelung , Taiwan
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Kim S, Lim BJ, Min GS, Choi HG. The complete mitochondrial genome of Arctic Calanus hyperboreus (Copepoda, Calanoida) reveals characteristic patterns in calanoid mitochondrial genome. Gene 2013; 520:64-72. [DOI: 10.1016/j.gene.2012.09.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/10/2012] [Accepted: 09/20/2012] [Indexed: 12/13/2022]
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22
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Ma H, Ma C, Li X, Xu Z, Feng N, Ma L. The complete mitochondrial genome sequence and gene organization of the mud crab (Scylla paramamosain) with phylogenetic consideration. Gene 2013; 519:120-7. [PMID: 23384716 DOI: 10.1016/j.gene.2013.01.028] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/14/2013] [Accepted: 01/17/2013] [Indexed: 11/24/2022]
Abstract
The complete mitochondrial genome is of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In the present study, we determined the complete mitochondrial genome DNA sequence of the mud crab (Scylla paramamosain) by 454 deep sequencing and Sanger sequencing approaches. The complete genome DNA was 15,824 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). Of 37 genes, twenty-three were encoded by the heavy strand (H-strand), while the other ones were encoded by light strand (L-strand). The gene order in the mitochondrial genome was largely identical to those obtained in most arthropods, although the relative position of gene tRNA(His) differed from other arthropods. Among 13 protein-coding genes, three (ATPase subunit 6 (ATP6), NADH dehydrogenase subunits 1 (ND1) and ND3) started with a rare start codon ATT, whereas, one gene cytochrome c oxidase subunit I (COI) ended with the incomplete stop codon TA. All 22 tRNAs could fold into a typical clover-leaf secondary structure, with the gene sizes ranging from 63 to 73 bp. The phylogenetic analysis based on 12 concatenated protein-coding genes showed that the molecular genetic relationship of 19 species of 11 genera was identical to the traditional taxonomy.
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Affiliation(s)
- Hongyu Ma
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
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Kondo M, Akasaka K. Current Status of Echinoderm Genome Analysis - What do we Know? Curr Genomics 2012; 13:134-43. [PMID: 23024605 PMCID: PMC3308324 DOI: 10.2174/138920212799860643] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 09/20/2011] [Accepted: 09/30/2011] [Indexed: 11/22/2022] Open
Abstract
Echinoderms have long served as model organisms for a variety of biological research, especially in the field of developmental biology. Although the genome of the purple sea urchin Strongylocentrotus purpuratus has been sequenced, it is the only echinoderm whose whole genome sequence has been reported. Nevertheless, data is rapidly accumulating on the chromosomes and genomic sequences of all five classes of echinoderms, including the mitochondrial genomes and Hox genes. This blossoming new data will be essential for estimating the phylogenetic relationships among echinoderms, and also to examine the underlying mechanisms by which the diverse morphologies of echinoderms have arisen.
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Affiliation(s)
- Mariko Kondo
- Misaki Marine Biological Station, Graduate School of Science, and Center for Marine Biology, The University of Tokyo, Japan
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Allele-specific PCR genotyping of the HSP70 gene polymorphism discriminating the green and red color variants sea cucumber (Apostichopus japonicus). J Genet Genomics 2011; 38:351-5. [PMID: 21867961 DOI: 10.1016/j.jgg.2011.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 06/07/2011] [Accepted: 06/12/2011] [Indexed: 11/23/2022]
Abstract
Color variation is a well-known feature of sea cucumbers (Apostichopus japonicus), which are classified into three groups based on their colors of red, green and black. It is also one of the most important traits related to how they taste, and it thereby affects their market price. Attempts were made to identify single-nucleotide polymorphisms (SNPs) and to analyze differences associated with SNP genotypes between green and red color variants using HSP70 as the target gene. The HSP70 gene, which is found universally in organisms from bacteria to humans, is one of the most evolutionarily conserved genes and the most widely studied biomarker of stress response. DNA fragments of 1074 bp covering a partial sequence of the sea cucumber HSP70 gene, were amplified from both red and green variants, and subsequently analyzed for the presence of SNPs. Twenty-seven polymorphic sites in total, including heterozygous sites, were observed. Of these, six sites were found to be significantly different SNP genotypes between green and red variants. Furthermore, PCR with an internal primer designed to include an allele-specific SNP at the 3' end (site 443) showed differentiation between the two variants, 100% and 4.2% amplification in green and red variants, respectively. The validated SNPs may serve as informative genetic markers that can be used to distinguish variants at the early developmental stage, prior to color differentiation.
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Fan S, Hu C, Wen J, Zhang L. Characterization of mitochondrial genome of sea cucumber Stichopus horrens: a novel gene arrangement in Holothuroidea. SCIENCE CHINA-LIFE SCIENCES 2011; 54:434-41. [PMID: 21574045 DOI: 10.1007/s11427-011-4168-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 02/13/2011] [Indexed: 11/26/2022]
Abstract
The complete mitochondrial DNA sequence contains useful information for phylogenetic analyses of metazoa. In this study, the complete mitochondrial DNA sequence of sea cucumber Stichopus horrens (Holothuroidea: Stichopodidae: Stichopus) is presented. The complete sequence was determined using normal and long PCRs. The mitochondrial genome of Stichopus horrens is a circular molecule 16257 bps long, composed of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes. Most of these genes are coded on the heavy strand except for one protein-coding gene (nad6) and five tRNA genes (tRNA ( Ser(UCN) ), tRNA ( Gln ), tRNA ( Ala ), tRNA ( Val ), tRNA ( Asp )) which are coded on the light strand. The composition of the heavy strand is 30.8% A, 23.7% C, 16.2% G, and 29.3% T bases (AT skew=0.025; GC skew=-0.188). A non-coding region of 675 bp was identified as a putative control region because of its location and AT richness. The intergenic spacers range from 1 to 50 bp in size, totaling 227 bp. A total of 25 overlapping nucleotides, ranging from 1 to 10 bp in size, exist among 11 genes. All 13 protein-coding genes are initiated with an ATG. The TAA codon is used as the stop codon in all the protein coding genes except nad3 and nad4 that use TAG as their termination codon. The most frequently used amino acids are Leu (16.29%), Ser (10.34%) and Phe (8.37%). All of the tRNA genes have the potential to fold into typical cloverleaf secondary structures. We also compared the order of the genes in the mitochondrial DNA from the five holothurians that are now available and found a novel gene arrangement in the mitochondrial DNA of Stichopus horrens.
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Affiliation(s)
- SiGang Fan
- Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
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Perseke M, Bernhard D, Fritzsch G, Brümmer F, Stadler PF, Schlegel M. Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: Insights in phylogenetic relationships of Echinodermata. Mol Phylogenet Evol 2010; 56:201-11. [DOI: 10.1016/j.ympev.2010.01.035] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 01/27/2010] [Accepted: 01/30/2010] [Indexed: 10/19/2022]
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Kan XZ, Li XF, Zhang LQ, Chen L, Qian CJ, Zhang XW, Wang L. Characterization of the complete mitochondrial genome of the Rock pigeon, Columba livia (Columbiformes: Columbidae). GENETICS AND MOLECULAR RESEARCH 2010; 9:1234-49. [PMID: 20603809 DOI: 10.4238/vol9-2gmr853] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The rock pigeon (Columba livia), or Rock dove, is a member of the bird family Columbidae. We mapped the complete mitochondrial genome of the Rock pigeon. The mitochondrial genome of this species is a circular molecule of 17,229 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus a putative control region, demonstrating a structure very similar to that of other birds. As found in other vertebrates, most of these genes are coded on the H-strand, except for NADH dehydrogenase subunit 6 (nad6) and eight tRNA genes (Gln, Ala, Asn, Cys, Tyr, Ser(UCN), Pro, Glu). The AT skew and GC skew of the whole genome, protein-coding genes, tRNA, rRNA, and the control region were calculated for the complete mitochondrial genomes of 30 avian species, representing 29 orders. All protein-coding genes initiated with ATG, except for cox1 and nad5, which began with GTG. One extra nucleotide 'C' was present in NADH dehydrogenase subunit 3 (nad3). All tRNA gene sequences have the potential to fold into typical cloverleaf secondary structures. Within the control region, conserved sequences were identified in three domains. Although the conserved blocks, such as ETAS1, ETAS2, CSB1, CSB1-like, and boxes C, D, E, and F, are readily identifiable in the C. livia control region, the typical origin of H-strand replication (O(H)), CSB2 and CSB3 could not be detected. These results provide basic information for phylogenetic analyses of birds, especially Columbiformes species.
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Affiliation(s)
- X Z Kan
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China
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Kan XZ, Li XF, Lei ZP, Wang M, Chen L, Gao H, Yang ZY. Complete mitochondrial genome of Cabot's tragopan, Tragopan caboti (Galliformes: Phasianidae). GENETICS AND MOLECULAR RESEARCH 2010; 9:1204-16. [PMID: 20589618 DOI: 10.4238/vol9-2gmr820] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cabot's tragopan, Tragopan caboti, is a globally threatened pheasant endemic to southeast China. The complete mitochondrial genome of Cabot's tragopan was sequenced. The circular genome contains 16,727 bp, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus the putative control region, a structure very similar to that of other Galliformes. As found in other vertebrates, most of these genes code on the H-strand, except for the NADH dehydrogenase subunit 6 (nad6) and eight tRNA genes (Gln, Ala, Asn, Cys, Tyr, Ser(UCN), Pro, Glu). All protein-coding genes initiated with ATG, except for cox1, which began with GTG, and had a strong skew of C vs G (GC skew = -0.29 to -0.73). One extra 'C' nucleotide was found in the NADH dehydrogenase subunit 3 (nad3). All the tRNA gene sequences have the potential to fold into typical cloverleaf secondary structures. Conserved sequences in three domains were identified within the control region (D-loop). These results provide basic information for phylogenetic analyses among Galliform birds, and especially Tragopan species.
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Affiliation(s)
- X Z Kan
- The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, College of Life Sciences, Anhui Normal University, Wuhu, China.
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Caron JB, Conway Morris S, Shu D. Tentaculate fossils from the Cambrian of Canada (British Columbia) and China (Yunnan) interpreted as primitive deuterostomes. PLoS One 2010; 5:e9586. [PMID: 20221405 PMCID: PMC2833208 DOI: 10.1371/journal.pone.0009586] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 01/20/2010] [Indexed: 12/04/2022] Open
Abstract
Molecular and morphological evidence unite the hemichordates and echinoderms as the Ambulacraria, but their earliest history remains almost entirely conjectural. This is on account of the morphological disparity of the ambulacrarians and a paucity of obvious stem-groups. We describe here a new taxon Herpetogaster collinsi gen. et sp. nov. from the Burgess Shale (Middle Cambrian) Lagerstätte. This soft-bodied vermiform animal has a pair of elongate dendritic oral tentacles, a flexible stolon with an attachment disc, and a re-curved trunk with at least 13 segments that is directed dextrally. A differentiated but un-looped gut is enclosed in a sac suspended by mesenteries. It consists of a short pharynx, a conspicuous lenticular stomach, followed by a narrow intestine sub-equal in length. This new taxon, together with the Lower Cambrian Phlogites and more intriguingly the hitherto enigmatic discoidal eldoniids (Cambrian-Devonian), form a distinctive clade (herein the cambroernids). Although one hypothesis of their relationships would look to the lophotrochozoans (specifically the entoprocts), we suggest that the evidence is more consistent with their being primitive deuterostomes, with specific comparisons being made to the pterobranch hemichordates and pre-radial echinoderms. On this basis some of the earliest ambulacrarians are interpreted as soft-bodied animals with a muscular stalk, and possessing prominent tentacles.
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Affiliation(s)
- Jean-Bernard Caron
- Department of Natural History-Palaeobiology, Royal Ontario Museum, Toronto, Ontario, Canada.
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