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Ellison CI, Frey MR, Sanford E, Maslakova S. Ribbon worms (phylum Nemertea) from Bodega Bay, California: A largely undescribed diversity. Zookeys 2024; 1204:15-64. [PMID: 38873218 PMCID: PMC11167275 DOI: 10.3897/zookeys.1204.117869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/25/2024] [Indexed: 06/15/2024] Open
Abstract
The diversity of nemerteans along the Pacific coast of the United States is regarded as well characterized, but there remain many cryptic, undescribed, and "orphan" species (those known only in their larval form). Recent sampling of nemerteans in Oregon and Washington has begun to fill in these taxonomic gaps, but nemertean diversity in California has received relatively little attention over the past 60 years. During the summers of 2019 and 2020, nemertean specimens were collected from 20 locations in the Bodega Bay region of northern California, USA, including rocky intertidal shores, sandy beaches, mudflats, and other habitats. Based on morphological assessment and DNA sequence analysis (partial Cytochrome Oxidase I and 16S rRNA genes), our surveys identified 34 nemertean species. Only 13 of these (38%) can be confidently assigned to described species. Another 11 represent species that are new to science, including members of the genera Riserius, Nipponnemertes, Poseidonemertes, Zygonemertes, Nemertellina, Oerstedia, and three species of uncertain affiliation. The remaining ten species include undescribed or cryptic species of uncertain status that have been found previously along the Pacific Coast of North America. Our surveys also document extensions of known geographic ranges for multiple species, including the first records in California of Antarctonemertesphyllospadicola, Cephalothrixhermaphroditica, and Maculauraoregonensis. This is the first report of the genus Nemertellina in the northeast Pacific and Riserius in California. Overall, our findings highlight how much remains to be learned about the diversity and distribution of nemerteans in the northeast Pacific.
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Affiliation(s)
- Christina I. Ellison
- Department of Biology, Oregon Institute of Marine Biology, University of Oregon, Charleston, OR, USAUniversity of OregonCharlestonUnited States of America
| | - Madeline R. Frey
- Bodega Marine Laboratory, Bodega Bay, CA 94923, USABodega Marine LaboratoryBodega BayUnited States of America
| | - Eric Sanford
- Bodega Marine Laboratory, Bodega Bay, CA 94923, USABodega Marine LaboratoryBodega BayUnited States of America
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USAUniversity of CaliforniaDavisUnited States of America
| | - Svetlana Maslakova
- Department of Biology, Oregon Institute of Marine Biology, University of Oregon, Charleston, OR, USAUniversity of OregonCharlestonUnited States of America
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Shen CY, Xue W, Pang C, Alireza A, Mao X, Han J, Chen H, Fu C. Characterization of the complete mitochondrial genome of Quasilineus sinicus Gibson, 1990 (Nemertea: Heteronemertea) and its phylogenetic implications. Mitochondrial DNA B Resour 2022; 7:1749-1751. [PMID: 36213866 PMCID: PMC9542323 DOI: 10.1080/23802359.2022.2126287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In this study, we sequenced and characterized the complete mitochondrial genome (mitogenome) of Quasilineus sinicus Gibson, 1990 (Heteronemertea, Nemertea) using Illumina sequencing technology. The circular mitogenome was 16,358 bp in length and comprised 22 transfer RNA genes, 13 protein-coding genes, and two ribosomal RNA genes. Its overall base composition included 20.82% A, 41.06% T, 26.68% G, and 11.44% C; in fact, the mitogenome had a high A + T content of 61.88%. Furthermore, our phylogenetic analysis demonstrated that Paleonemertea, Pilidiophora, and Hoplonemertea were monophyletic groups, and Q. sinicus was most closely related to Iwatanemertes piperata.
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Affiliation(s)
- Chun-Yang Shen
- Department of Biology, Chengde Medical University, Chengde, Hebei Province, China
| | - Wei Xue
- Department of Chemical Engineering, Hebei Petroleum University of Technology, Chengde, Hebei Province, China
| | - Chong Pang
- Department of Pharmacology, Chengde Medical University, Chengde, Hebei Province, China
| | - Asem Alireza
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, Hainan Province, China
| | - Xiaonan Mao
- Department of Biology, Chengde Medical University, Chengde, Hebei Province, China
| | - Jiahui Han
- Department of Biology, Chengde Medical University, Chengde, Hebei Province, China
| | - Haonan Chen
- Department of Biology, Chengde Medical University, Chengde, Hebei Province, China
| | - Chunzheng Fu
- Institute of Sericulture, Chengde Medical University, Chengde, Hebei Province, China
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Kutyumov VA, Predeus AV, Starunov VV, Maltseva AL, Ostrovsky AN. Mitochondrial gene order of the freshwater bryozoan Cristatella mucedo retains ancestral lophotrochozoan features. Mitochondrion 2021; 59:96-104. [PMID: 33631347 DOI: 10.1016/j.mito.2021.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022]
Abstract
Bryozoans are aquatic colonial suspension-feeders abundant in many marine and freshwater benthic communities. At the same time, the phylum is under studied on both morphological and molecular levels, and its position on the metazoan tree of life is still disputed. Bryozoa include the exclusively marine Stenolaemata, predominantly marine Gymnolaemata and exclusively freshwater Phylactolaemata. Here we report the mitochondrial genome of the phylactolaemate bryozoan Cristatella mucedo. This species has the largest (21,008 bp) of all currently known bryozoan mitogenomes, containing a typical metazoan gene compendium as well as a number of non-coding regions, three of which are longer than 1500 bp. The trnS1/trnG/nad3 region is presumably duplicated in this species. Comparative analysis of the gene order in C. mucedo and another phylactolaemate bryozoan, Pectinatella magnifica, confirmed their close relationships, and revealed a stronger similarity to mitogenomes of phoronids and other lophotrochozoan species than to marine bryozoans, indicating the ancestral nature of their gene arrangement. We suggest that the ancestral gene order underwent substantial changes in different bryozoan cladesshowing mosaic distribution of conservative gene blocks regardless of their phylogenetic position. Altogether, our results support the early divergence of Phylactolaemata from the rest of Bryozoa.
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Affiliation(s)
- Vladimir A Kutyumov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia.
| | - Alexander V Predeus
- Bioinformatics Institute, Kantemirovskaya 2A, 197342 Saint Petersburg, Russia
| | - Viktor V Starunov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Arina L Maltseva
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia
| | - Andrew N Ostrovsky
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; Department of Palaeontology, Faculty of Geography, Geology and Astronomy, University of Vienna, Althanstr. 14, 1090 Vienna, Austria.
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4
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Nam SE, Rhee JS. Characterization and phylogenetic analysis of the complete mitochondrial genome of the marine ribbon worm Cephalothrix species (nemertea: Palaeonemertea). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1756967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Sang-Eun Nam
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, Republic of Korea
| | - Jae-Sung Rhee
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, Republic of Korea
- Research Institute of Basic Sciences, Incheon National University, Incheon, Republic of Korea
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Lee SY, Lee HJ, Kim YK. Comparative analysis of complete mitochondrial genomes with Cerithioidea and molecular phylogeny of the freshwater snail, Semisulcospira gottschei (Caenogastropoda, Cerithioidea). Int J Biol Macromol 2019; 135:1193-1201. [PMID: 31176862 DOI: 10.1016/j.ijbiomac.2019.06.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/19/2019] [Accepted: 06/05/2019] [Indexed: 11/26/2022]
Abstract
In this study, we determined the complete mitochondrial genome (mt genome) of Semisulcospira gottschei for the first time and then compared it with the mt genome of species belonging to Cerithioidea. The mt genome consists of 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and non-coding region with a total length of 16,101 bp. The type of constitutive genes and the direction of the coding strand which appeared in the mt genome were the same as the ones observed in Cerithioidea except for the tRNA-Q and tRNA-R positions. The S. gottschei mt genome had a non-coding region with an AT-rich loop between tRNA-F and tRNA-C regions. In regard to molecular phylogeny, two types of analysis were performed to confirm the introgressive hybridization of S. gottschei and to identify the phylogenetic location among the species in Caenogastropoda. As a result, S. gottschei used in this study belonged to the same clade as other non-introgressed S. gottschei. As for the molecular phylogenic analysis of species belonging to Caenogastropoda, S. gottschei was found to be the closest to S. coreana taxonomically and to be included in Cerithioidea.
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Affiliation(s)
- Sang Yoon Lee
- The East Coast Research Institute of Life Science, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Hwa Jin Lee
- Department of Marine Biotechnology, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Yi Kyung Kim
- The East Coast Research Institute of Life Science, Gangneung-Wonju National University, Gangneung 25457, South Korea; Department of Marine Biotechnology, Gangneung-Wonju National University, Gangneung 25457, South Korea.
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Hao Y, Kajihara H, Chernyshev AV, Okazaki RK, Sun SC. DNA Taxonomy of Paranemertes (Nemertea: Hoplonemertea) with Spirally Fluted Stylets. Zoolog Sci 2016; 32:571-8. [PMID: 26654040 DOI: 10.2108/zs140275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Of the 14 nominal species that are now or have ever been assigned to the genus Paranemertes Coe, 1901 , four have been reported to have stylets with a spirally fluted or braided appearance. Although differentiation in color patterns has been documented among species/populations, these nemerteans share similar external characters. Using the sequence datasets of mitochondrial cytochrome c oxidase subunit I (COI), 16S rRNA, and nuclear 28S rRNA genes of specimens from 14 localities of Canada, USA, Russia, Japan, and China, we analyzed the genetic differentiation and reconstructed the phylogenetic trees for these nemerteans. In conjunction with the external characters, we discuss their taxonomy and species delimitation. An analysis based on COI dataset showed high genetic variations among populations and even among worms from the same geographic area. The analyzed 111 individuals were assigned into seven networks by statistical parsimony analysis. The inter-network uncorrected p-distances ranged from 0.044 to 0.172 and the mean intra-network uncorrected p-distances varied from 0.001 to 0.005. With the exception of two networks that contain specimens from the East China Sea, all networks were well-supported by the results of Bayesian and neighbor-joining analyses on the COI data. Phylogenetic trees based on 16S rRNA and 28S rRNA datasets were basically similar to the COI trees, but specimens in some networks were merged into larger clades. Present molecular analyses support the validity of P. sanjuanensis and the synonymization of P. cylindracea with P. peregrina. Nemerteans previously recorded as P. peregrina may contain several species and sympatric speciation might have been occurred in this nemertean group.
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Affiliation(s)
- Yue Hao
- 1 institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Hiroshi Kajihara
- 2 Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Alexei V Chernyshev
- 3 A.V. Zhirmunsky Institute of Marine Biology, Vladivostok 690041, Russia.,4 Far Eastern Federal University, Vladivostok, Russia
| | - Robert K Okazaki
- 5 Department of Zoology, Weber State University, 1415 Edvalson Street, Dept 2505, Ogden, UT 84408-2505, USA
| | - Shi-Chun Sun
- 1 institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
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7
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Evolution of mitochondrial gene order in Annelida. Mol Phylogenet Evol 2016; 94:196-206. [DOI: 10.1016/j.ympev.2015.08.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 07/30/2015] [Accepted: 08/05/2015] [Indexed: 01/08/2023]
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Shen C, Shi-Chun S. Mitochondrial genome of Micrura bella (Nemertea: Heteronemertea), the largest mitochondrial genome known to phylum Nemertea. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2899-900. [PMID: 26155969 DOI: 10.3109/19401736.2015.1060429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome (mitogenome) of Micrura bella was sequenced and analyzed. Being the largest mitogenome known to phylum Nemertea, the genome is 16 847 bp in length. It encodes 37 genes typical to metazoan mitogenomes and has the same gene arrangement with the other Heteronemertea mitogenomes sequenced to date. The genome has the maximal number of non-coding nucleotides (2037 bp at 25 sites) in Nemertea mitogenomes, among which two large non-coding regions were found (507 and 508 bp, respectively).
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Affiliation(s)
- Chunyang Shen
- a Institute of Evolution & Marine Biodiversity, Ocean University of China , Qingdao , China
| | - Sun Shi-Chun
- a Institute of Evolution & Marine Biodiversity, Ocean University of China , Qingdao , China
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9
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Osca D, Irisarri I, Todt C, Grande C, Zardoya R. The complete mitochondrial genome of Scutopus ventrolineatus (Mollusca: Chaetodermomorpha) supports the Aculifera hypothesis. BMC Evol Biol 2014; 14:197. [PMID: 25288450 PMCID: PMC4189740 DOI: 10.1186/s12862-014-0197-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/01/2014] [Indexed: 11/16/2022] Open
Abstract
Background With more than 100000 living species, mollusks are the second most diverse metazoan phylum. The current taxonomic classification of mollusks recognizes eight classes (Neomeniomorpha, Chaetodermomorpha, Polyplacophora, Monoplacophora, Cephalopoda, Gastropoda, Bivalvia, and Scaphopoda) that exhibit very distinct body plans. In the past, phylogenetic relationships among mollusk classes have been contentious due to the lack of indisputable morphological synapomorphies. Fortunately, recent phylogenetic analyses based on multi-gene data sets are rendering promising results. In this regard, mitochondrial genomes have been widely used to reconstruct deep phylogenies. For mollusks, complete mitochondrial genomes are mostly available for gastropods, bivalves, and cephalopods, whereas other less-diverse lineages have few or none reported. Results The complete DNA sequence (14662 bp) of the mitochondrial genome of the chaetodermomorph Scutopus ventrolineatus Salvini-Plawen, 1968 was determined. Compared with other mollusks, the relative position of protein-coding genes in the mitochondrial genome of S. ventrolineatus is very similar to those reported for Polyplacophora, Cephalopoda and early-diverging lineages of Bivalvia and Gastropoda (Vetigastropoda and Neritimorpha; but not Patellogastropoda). The reconstructed phylogenetic tree based on combined mitochondrial and nuclear sequence data recovered monophyletic Aplacophora, Aculifera, and Conchifera. Within the latter, Cephalopoda was the sister group of Gastropoda and Bivalvia + Scaphopoda. Conclusions Phylogenetic analyses of mitochondrial sequences showed strong among-lineage rate heterogeneity that produced long-branch attraction biases. Removal of long branches (namely those of bivalves and patellogastropods) ameliorated but not fully resolved the problem. Best results in terms of statistical support were achieved when mitochondrial and nuclear sequence data were concatenated. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0197-9) contains supplementary material, which is available to authorized users.
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Sun WY, Xu DL, Chen HX, Shi W, Sundberg P, Strand M, Sun SC. Complete mitochondrial genome sequences of two parasitic/commensal nemerteans, Gononemertes parasita and Nemertopsis tetraclitophila (Nemertea: Hoplonemertea). Parasit Vectors 2014; 7:273. [PMID: 24946714 PMCID: PMC4081467 DOI: 10.1186/1756-3305-7-273] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 06/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most nemerteans (phylum Nemertea) are free-living, but about 50 species are known to be firmly associated with other marine invertebrates. For example, Gononemertes parasita is associated with ascidians, and Nemertopsis tetraclitophila with barnacles. There are 12 complete or near-complete mitochondrial genome (mitogenome) sequences of nemerteans available in GenBank, but no mitogenomes of none free-living nemerteans have been determined so far. In the present paper complete mitogenomes of the above two parasitic/commensal nemerteans are reported. METHODS The complete mitochondrial genomes (mitogenome) of G. parasita and N. tetraclitophila were amplified by conventional and long PCR. Phylogenetic analyses of maximum likelihood (ML) and Bayesian inference (BI) were performed with both concatenated nucleotide and amino acid sequences. RESULTS Complete mitogenomes of G. parasita and N. tetraclitophila are 14742 bp and 14597 bp in size, respectively, which are within the range of published Hoplonemertea mitogenomes. Their gene orders are identical to that of published Hoplonemertea mitogenomes, but different from those of Palaeo- and Heteronemertea species. All the coding genes, as well as major non-coding regions (mNCRs), are AT rich, which is especially pronounced at the third codon position. The AT/GC skew pattern of the coding strand is the same among nemertean mitogenomes, but is variable in the mNCRs. Some slight differences are found between mitogenomes of the present species and other hoplonemerteans: in G. parasita the mNCR is biased toward T and C (contrary to other hoplonemerteans) and the rrnS gene has a unique 58-bp insertion at the 5' end; in N. tetraclitophila the nad3 gene starts with the ATT codon (ATG in other hoplonemerteans). Phylogenetic analyses of the nucleotide and amino acid datasets show early divergent positions of G. parasita and N. tetraclitophila within the analyzed Distromatonemertea species, and provide strong support for the close relationship between Hoplonemertea and Heteronemertea. CONCLUSION Gene order is highly conserved within the order Monostilifera, particularly within the Distromatonemertea, and the special lifestyle of G. parasita and N. tetraclitophila does not bring significant variations to the overall structures of their mitogenomes in comparison with free-living hoplonemerteans.
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Affiliation(s)
- Wen-Yan Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Dong-Li Xu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Hai-Xia Chen
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 463, SE-405 30 Gothenburg, Sweden
| | - Wei Shi
- Key Laboratory of Marine Bio-resource Sustainable Utilization (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Per Sundberg
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 463, SE-405 30 Gothenburg, Sweden
| | - Malin Strand
- Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE 75007 Uppsala, Sweden
| | - Shi-Chun Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
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Sun WY, Sun SC. A description of the complete mitochondrial genomes of Amphiporus formidabilis, Prosadenoporus spectaculum and Nipponnemertes punctatula (Nemertea: Hoplonemertea: Monostilifera). Mol Biol Rep 2014; 41:5681-92. [PMID: 24939507 DOI: 10.1007/s11033-014-3438-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/27/2014] [Indexed: 11/30/2022]
Abstract
We sequenced the complete mitochondrial genomes (mitogenomes) of three Hoplonemertea species, Amphiporus formidabilis, Prosadenoporus spectaculum and Nipponnemertes punctatula, which are 14,616, 14,655 and 15,354 bp in length, respectively. Each of the three circular mitogenomes consists of 37 typical genes and some non-coding regions. The nucleotide composition of the coding strand is biased toward T, almost a half of total nucleotides in these mitogenomes. There are many poly-T tracts across these mitogenomes, which exhibit T-number variation within different clones of protein-coding genes, mainly resulting from false PCR amplification. The major non-coding regions have tandem repeat motifs and hairpin-like structures that may be associated with the initiation of replication or transcription. Data published to date for nemerteans show that Palaeonemertea species usually bear the largest mitogenomes, while representatives in the more recently derived Distromatonemertea clade bear the smallest ones; and that the gene arrangement of mitogenomes seems to be variable within the phylum Nemertea, but stable within either of Heteronemertea and Hoplonemertea.
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Affiliation(s)
- Wen-Yan Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
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12
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Kajihara H, Sun SC, Chernyshev AV, Chen HX, Ito K, Asakawa M, Maslakova SA, Norenburg JL, Strand M, Sundberg P, Iwata F. Taxonomic identity of a tetrodotoxin-accumulating ribbon-worm Cephalothrix simula (Nemertea: Palaeonemertea): a species artificially introduced from the Pacific to Europe. Zoolog Sci 2014; 30:985-97. [PMID: 24199864 DOI: 10.2108/zsj.30.985] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We compared the anatomy of the holotype of the palaeonemertean Cephalothrix simula ( Iwata, 1952 ) with that of the holotypes of Cephalothrix hongkongiensis Sundberg, Gibson and Olsson, 2003 and Cephalothrix fasciculus ( Iwata, 1952 ), as well as additional specimens from Fukue (type locality of C. simula) and Hiroshima, Japan. While there was no major morphological discordance between these specimens, we found discrepancies between the actual morphology and some statements in the original description of C. simula with respect to supposedly species-specific characters. Our observation indicates that these three species cannot be discriminated by the anatomical characters so far used to distinguish congeners. For objectivity of scientific names, topogenetypes of the mitochondrial cytochrome c oxidase subunit I (COI) sequences are designated for C. simula, C. hongkongiensis, and C. fasciculus. Analysis of COI sequence showed that the Hiroshima population can be identified as C. simula, which has been found in previous studies from Trieste, Italy, and also from both the Mediterranean and Atlantic coasts of the Iberian Peninsula, indicating an artificial introduction via (1) ballast water, (2) ship-fouling communities, or (3) the commercially cultured oyster Crassostrea gigas ( Thunberg, 1793 ) brought from Japan to France in 1970s. Cephalothrix simula is known to be toxic, as it contains large amounts of tetrodotoxin (TTX). We report here that the grass puffer Takifugu niphobles ( Jordan and Snyder, 1901 )-also known to contain TTX- consumes C. simula. We suggest that the puffer may be able to accumulate TTX by eating C. simula.
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Affiliation(s)
- Hiroshi Kajihara
- 1 Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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Chen H, Sun S, Norenburg JL, Sundberg P. Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea). PLoS One 2014; 9:e85631. [PMID: 24454907 PMCID: PMC3893253 DOI: 10.1371/journal.pone.0085631] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/05/2013] [Indexed: 12/14/2022] Open
Abstract
The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENc values are below it. ENc-plot suggested that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally and we propose that codons containing A or U at third position are used preferentially in nemertean species, regardless of whether corresponding tRNAs are encoded in the mitochondrial DNA. Context-dependent analysis indicated that the nucleotide at the second codon position slightly affects synonymous codon choices. These results suggested that mutational and selection forces are probably acting to codon usage bias in nemertean mitochondrial genomes.
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Affiliation(s)
- Haixia Chen
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- * E-mail: (HXC); (PS)
| | - Shichun Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jon L. Norenburg
- Department of Invertebrate Zoology, Smithsonian's National Museum of Natural History, Washington D.C., United States of America
| | - Per Sundberg
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- * E-mail: (HXC); (PS)
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Zhang J, Wu X, Xie M, Li A. The complete mitochondrial genome of Pseudochauhanea macrorchis (Monogenea: Chauhaneidae) revealed a highly repetitive region and a gene rearrangement hot spot in Polyopisthocotylea. Mol Biol Rep 2012; 39:8115-25. [PMID: 22544610 DOI: 10.1007/s11033-012-1659-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 04/16/2012] [Indexed: 02/06/2023]
Abstract
The complete mitochondrial genome of Pseudochauhanea macrorchis was determined and compared with other monogenean mitochondrial genomes from GenBank. The circular genome was 15,031 bp in length and encoded 36 genes (12 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs) typically found in flatworms. Structures of the mitochondrial genome were mostly concordant with that known for Microcotyle sebastis and Polylabris halichoeres, but also contained two noted features-a gene rearrangement hot spot and the highly repetitive region (HRR) in major non-coding region (NCR). The gene rearrangement hot spot located between the cox3 and nad5 genes, including a cluster of tRNA genes, nad6 gene and one major NCR. The HRR seemed to be a unique feature of the polyopisthocotylean mitochondrial genomes. In conclusion, the present study provided new molecular data for future studies of the comparative mitochondrial genomics and also served as a resource of markers for the studies of species populations and monogenean phylogenetics.
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Affiliation(s)
- Juan Zhang
- Key Laboratory for Aquatic Products Safety of Ministry of Education/State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 Xingang West Road, Haizhu District, Guangzhou 510275, China
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Chen HX, Sun SC, Sundberg P, Ren WC, Norenburg JL. A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea. BMC Genomics 2012; 13:139. [PMID: 22507536 PMCID: PMC3368773 DOI: 10.1186/1471-2164-13-139] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 04/17/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mitochondrial genome is important for studying genome evolution as well as reconstructing the phylogeny of organisms. Complete mitochondrial genome sequences have been reported for more than 2200 metazoans, mainly vertebrates and arthropods. To date, from a total of about 1275 described nemertean species, only three complete and two partial mitochondrial DNA sequences from nemerteans have been published. Here, we report the entire mitochondrial genomes for two more nemertean species: Nectonemertes cf. mirabilis and Zygeupolia rubens. RESULTS The sizes of the entire mitochondrial genomes are 15365 bp for N. cf. mirabilis and 15513 bp for Z. rubens. Each circular genome contains 37 genes and an AT-rich non-coding region, and overall nucleotide composition is AT-rich. In both species, there is significant strand asymmetry in the distribution of nucleotides, with the coding strand being richer in T than A and in G than C. The AT-rich non-coding regions of the two genomes have some repeat sequences and stem-loop structures, both of which may be associated with the initiation of replication or transcription. The 22 tRNAs show variable substitution patterns in nemerteans, with higher sequence conservation in genes located on the H strand. Gene arrangement of N. cf. mirabilis is identical to that of Paranemertes cf. peregrina, both of which are Hoplonemertea, while that of Z. rubens is the same as in Lineus viridis, both of which are Heteronemertea. Comparison of the gene arrangements and phylogenomic analysis based on concatenated nucleotide sequences of the 12 mitochondrial protein-coding genes revealed that species with closer relationships share more identical gene blocks. CONCLUSION The two new mitochondrial genomes share many features, including gene contents, with other known nemertean mitochondrial genomes. The tRNA families display a composite substitution pathway. Gene order comparison to the proposed ground pattern of Bilateria and some lophotrochozoans suggests that the nemertean ancestral mitochondrial gene order most closely resembles the heteronemertean type. Phylogenetic analysis proposes a sister-group relationship between Hetero- and Hoplonemertea, which supports one of two recent alternative hypotheses of nemertean phylogeny.
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Affiliation(s)
- Hai-Xia Chen
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 463, SE-405 30 Gothenburg, Sweden
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Shi-Chun Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Per Sundberg
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 463, SE-405 30 Gothenburg, Sweden
| | - Wei-Cheng Ren
- Department of Rheumatology and Inflammation Research, Sahlgrenska Academy, University of Gothenburg, PO Box 480, SE-405 30, Sweden
| | - Jon L Norenburg
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0163, USA
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