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Particle and Fibre Toxicology Volume 7 ,Issue 1 , ,2014-06-19
Complete mitochondrial genome sequences of two parasitic/commensal nemerteans, Gononemertes parasita and Nemertopsis tetraclitophila (Nemertea: Hoplonemertea)
Wen-Yan Sun 1 Dong-Li Xu 1 Hai-Xia Chen 2 Wei Shi 3 Per Sundberg 2 Malin Strand 4 Shi-Chun Sun 1
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DOI:10.1186/1756-3305-7-273
Received 2014-04-20, accepted for publication 2014-06-14, Published 2014-06-14
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摘要

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.

关键词

Phylogeny; Mitochondrial genome; Parasitic/Commensal; Nemertopsis tetraclitophila; Gononemertes parasita;Nemertea

授权许可

2014 Sun et al.; licensee BioMed Central Ltd.
http://creativecommons.org/licenses/by/2.0/

图表

Figure 1. Map of the mitochondrial genomes of Gononemertes parasita and Nemertopsis tetraclitophila. Genes coded on the coding strand are arranged clockwise; those on the other strand are counter-clockwise. Thirteen protein-coding genes are shown in blue and two ribosomal RNA genes in pink. Transfer RNA genes are labeled by their single letter of corresponding amino acids. Major non-coding regions (mNCR) are represented in grey.

Figure 2. Scatter plot of AT- and GC-skews in 14 nemertean species. Values were calculated for the coding strand of the overall mitogenome sequences (▲) and the major non-coding region (Cephalothrix sp. not included because the major non-coding region of this species is incomplete) (●). AT-skew = (A-T)/(A + T); GC-skew = (G-C)/(G + C). Af = Amphiporus formidabilis, Ch = Cephalothrix hongkongiensis, Csp = Cephalothrix sp., Eg = Emplectonema gracile, Ip = Iwatanemertes piperata, Gp = Gononemertes parasita, Lv = Lineus viridis, La = Lineus alborostratus, Nt = Nemertopsis tetraclitophila, Np = Nipponnemertes punctatula, Nm = Nectonemertes cf. mirabilis, Ps = Prosadenoporus spectaculum, Pp = Paranemertes cf. peregrina, Zr = Zygeupolia rubens.

Figure 3. Length comparisons of protein-coding genes (A) and ribosomal RNA genes (B) among 14 nemertean mitogenomes. Abbreviations of species names see Figure 2.

Figure 4. Phylogenetic trees resulting from maximum likelihood and Bayesian inference. A. Nucleotide sequences (3rd codon position removed)/amino acid sequences of 13 protein-coding genes (same tree topology obtained from the both datasets). B. Nucleotide sequences (3rd codon position removed) of protein-coding genes, rRNA and tRNA sequences. Numbers at the nodes correspond to posterior probabilities (left) and bootstrap proportions (right) (in tree A, the upper values are those of the nucleotide tree and the lower ones are those of the amino acid tree). Capital letters (A to K) in tree B correspond to the nodes for which Bremer support values were calculated (see Table 3).

Table 1.

Table 2.

Table 3.

通讯作者

Shi-Chun Sun. Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China .sunsc@ouc.edu.cn

推荐引用方式

Wen-Yan Sun,Dong-Li Xu,Hai-Xia Chen,Wei Shi,Per Sundberg,Malin Strand,Shi-Chun Sun. Complete mitochondrial genome sequences of two parasitic/commensal nemerteans, Gononemertes parasita and Nemertopsis tetraclitophila (Nemertea: Hoplonemertea). Particle and Fibre Toxicology ,Vol.7, Issue 1(2014) : .

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参考文献
[1] Bremer K: Branch support and tree stability. Cladistics 1994, 10:295-304.
[2] Kajihara H, Chernyshev AV, Sun S-C, Sundberg P, Crandall FB: Checklist of nemertean genera and species published between 1995–2007. Species Div 2008, 13:245-274.
[3] Turbeville JM, Field KG, Raff RA: Phylogenetic position of phylum Nemertini, inferred from 18S rRNA sequences: molecular data as a test of morphological character homology. Mol Biol Evol 1992, 9:235-249.
[4] Passamaneck Y, Halanych KM: Lophotrochozoan phylogeny assessed with LSU and SSU data: evidence of lophophorate polyphyly. Mol Phylogenet Evol 2006, 40:20-28.
[5] Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sørensen MV, Haddock SH, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G: Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452:745-749.
[6] Podsiadlowski L, Braband A, Struck TH, von Dohren J, Bartolomaeus T: Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea. BMC Genomics 2009, 10:364. BioMed Central Full Text
[7] Turbeville JM: An ultrastructural analysis of coelomogenesis in the hoplonemertine Prosorhochmus americanus and the polychaete Magelona sp. J Morphol 1986, 187:51-60.
[8] Sundberg P, Turbeville JM, Lindh S: Phylogenetic relationships among higher Nemertean (Nemertea) Taxa inferred from 18S rDNA sequences. Mol Phylogenet Evol 2001, 20:327-334.
[9] Thollesson M, Norenburg JL: Ribbon worm relationships: a phylogeny of the phylum Nemertea. Proc Biol Sci 2003, 270:407-415.
[10] Andrade SCS, Strand M, Schwartz M, Chen HX, Kajihara H, Von Döhren J, Sun SC, Junoy J, Thiele M, Norenburg JL, Turbeville JM, Giribet G, Sundberg P: Disentangling ribbon worm relationships: multi-locus analysis supports traditional classification of the phylum Nemertea. Cladistics 2012, 28:141-159.
[11] Strand M, Samuelsson H, Sundberg P: Nationalnyckeln till Sveriges flora och fauna. Stjärnmaskar − slemmaskar. Sipuncula − Nemertea. Uppsala: ArtDatabanken, SLU; 2010.
[12] Gibson R: The macrobenthic nemertean fauna of Hong Kong. In Proceedings of the Second International Marine Biological Workshop: the Marine Flora and Fauna of Hong Kong and Southern China, 1986. Volume 1. Edited by Morton B. Hong Kong: Hong Kong University Press; 1990:33-212.
[13] Bergendal D: Über ein Paar sehr eigenthümliche nordische Nemertinen. Zoologischer Anzeiger 1900, 23:313-328.
[14] Roe P: Ecological implications of the reproductive biology of symbiotic nemerteans. Hydrobiologia 1988, 156:13-22.
[15] Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964.
[16] Denman RB: Using RNAFOLD to predict the activity of small catalytic RNAs. Biotechniques 1993, 15:1090-1095.
[17] Grant JR, Stothard P: The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res 2008, 36:W181-W184.
[18] Xia X: DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Mol Biol Evol 2013, 30:1720-1728.
[19] Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25:4876-4882.
[20] Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739.
[21] Golombek A, Tobergte S, Nesnidal MP, Purschke G, Struck TH: Mitochondrial genomes to the rescue - diurodrilidae in the myzostomid trap. Mol Phylogenet Evol 2013, 68:312-326.
[22] Stöger I, Schrodl M: Mitogenomics does not resolve deep molluscan relationships (yet?). Mol Phylogenet Evol 2013, 69:376-392.
[23] Talavera G, Castresana J: Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007, 56:564-577.
[24] Posada D, Crandall KA: MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
[25] Nylander JAA: MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University; 2004. [http://www.abc.se/ webcite]
[26] Abascal F, Zardoya R, Posada D: ProtTest: selection of best-fit models of protein evolution. Bioinformatics 2005, 21:2104-2105.
[27] Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O: New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010, 59:307-321.
[28] Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
[29] Swofford DL: PAUP* – Phylogenetic Analysis Using Parsimony (*and Other Methods). Ver. 4.0. [Computer software and manual]. Sunderland, MA: Sinauer Associates. In Book PAUP* – Phylogenetic Analysis Using Parsimony (*and Other Methods). Ver. 4.0. [Computer software and manual]. Sunderland, MA: Sinauer Associates; 1999.
[30] TreeRot version 3 [http://people.bu.edu/msoren/TreeRot.html webcite]
[31] Bremer K: The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 1988, 42:795-803.
[32] Hassanin A, Leger N, Deutsch J: Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences. Syst Biol 2005, 54:277-298.
[33] Riepsamen AH, Gibson T, Rowe J, Chitwood DJ, Subbotin SA, Dowton M: Poly(T) variation in heteroderid nematode mitochondrial genomes is predominantly an artefact of amplification. J Mol Evol 2011, 72:182-192.
[34] Gibson T, Farrugia D, Barrett J, Chitwood DJ, Rowe J, Subbotin S, Dowton M: The mitochondrial genome of the soybean cyst nematode, Heterodera glycines. Genome 2011, 54:565-574.
[35] Nesnidal MP, Helmkampf M, Bruchhaus I, Hausdorf B: The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships. BMC Genomics 2011, 12:572. BioMed Central Full Text
[36] Ojala D, Montoya J, Attardi G: tRNA punctuation model of RNA processing in human mitochondria. Nature 1981, 290:470-474.
[37] McMahon DP, Hayward A, Kathirithamby J: The mitochondrial genome of the ‘twisted-wing parasite’ Mengenilla australiensis (Insecta, Strepsiptera): a comparative study. BMC Genomics 2009, 10:603. BioMed Central Full Text
[38] 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. BioMed Central Full Text
[39] Chen HX, Sundberg P, Wu HY, Sun SC: The mitochondrial genomes of two nemerteans, Cephalothrix sp. (Nemertea: Palaeonemertea) and Paranemertes cf. peregrina (Nemertea: Hoplonemertea). Mol Biol Rep 2011, 38:4509-4525.
[40] Gasser RB, Jabbar A, Mohandas N, Hoglund J, Hall RS, Littlewood DT, Jex AR: Assessment of the genetic relationship between Dictyocaulus species from Bos taurus and Cervus elaphus using complete mitochondrial genomic datasets. Parasit Vectors 2012, 5:241. BioMed Central Full Text
[41] Sun WY, Sun SC: A description of the complete mitochondrial genomes of Amphiporus formidabilis. Mol Biol Rep, in press: Prosadenoporus spectaculum and Nipponnemertes punctatula (Nemertea: Hoplonemertea: Monostilifera); doi:10.1007/s11033-014-3438-5
[42] Arnason E, Rand DM: Heteroplasmy of short tandem repeats in mitochondrial DNA of Atlantic cod, Gadus morhua. Genetics 1992, 132:211-220.
[43] Kumazawa Y, Nishida M: Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J Mol Evol 1993, 37:380-398.
[44] Sundberg P, Chernyshev AV, Kajihara H, Kanneby T, Strand M: Character-matrix based descriptions of two new nemertean (Nemertea) species. Zool J Linn Soc 2009, 157:264-294.
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