Genetic diversity and population structure of penis fish (Urechis unicinctus) based on mitochondrial and nuclear gene markers

References

• Abe H, Sato-okoshi W, Tanaka M, Okoshi K, Teramoto W, Kondoh T, Nishitani G, Endo Y. 2014. Swimming behavior of the spoon worm Urechis unicinctus (Annelida, Echiura). Zoology (Jena). 117:216–223.
   PubMed Web of Science ®Google Scholar
• Alexander K, Procell LR, Kirby SD, Baskin SI. 1989. The inactivation of rhodanese by nitrite and inhibition by other anions in vitro. J Biochem Toxic. 4:29–33.
   PubMedGoogle Scholar
• Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16:37–48.
   PubMed Web of Science ®Google Scholar
• Beesley PL, Ross GJB, Glasby CJ. 2000. Polychaetes and allies: the southern synthesis. Collingwood: CSIRO Publishing.
   Google Scholar
• Beinert H. 2000. Iron-sulfur proteins: ancient structures, still full of surprises. J Biol Inorg Chem. 5:2–15.
   PubMed Web of Science ®Google Scholar
• Beinert H, Holm RH, Münck E. 1997. Iron-sulfur clusters: nature's modular, multipurpose structures. Science. 277:653–659.
   PubMed Web of Science ®Google Scholar
• Bi Q, Han B, Feng Y, Jiang Z, Yang Y, Liu W. 2013. Antithrombotic effects of a newly purified fibrinolytic protease from Urechis unicinctus. Thromb Res. 132:135–144.
   Web of Science ®Google Scholar
• Billington N, Hebert PDN. 1991. Mitochondrial DNA diversity in fishes and its implications for introductions. Can J Fish Aquat Sci. 48:80–94.
   Web of Science ®Google Scholar
• Biseswar R. 2012. Zoogeography of the echiuran fauna of the East Pacific Ocean (Phylum: Echiura). Zootaxa. 3479:69–76.
   Google Scholar
• Buzaleh AM, Vazquez ES, Batlle AM. 1990. The effect of cyanide intoxication on hepatic rhodanese kinetics. Gen Pharmacol-VASC S. 21:219–222.
   PubMedGoogle Scholar
• Cagianut B, Schnebli HP, Rhyner K, Furrer J. 1984. Decreased thiosulfate sulfur transferase (rhodanese) in Leber's hereditary optic atrophy. J Mol Med. 62:850–854.
   Google Scholar
• Egekeze JO, Oehme FW. 1980. Cyanides and their toxicity: a literature review. Vet Quart. 2:104–114.
   PubMed Web of Science ®Google Scholar
• Excoffier L, Laval G, Schneider S. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform. 1:47–50.
   PubMed Web of Science ®Google Scholar
• Fu W, Jack RF, Morgan TV, Dean DR, Johnson MK. 1994. nifU gene product from azotobacter vinelandii is a homodimer that contains two identical [2Fe-2S] clusters. Biochemistry. 33:13455–13463.
   PubMed Web of Science ®Google Scholar
• Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147:915–925.
   PubMed Web of Science ®Google Scholar
• Garcia SM, Zerbi A, Aliaume C, Dochi T, Lasserre G. 2003. The ecosystem approach to fisheries: Issues, terminology, principles, institutional foudations, implementation and outlook. Rome: Food and Agriculture Organization of the United Nations (FAO).
   Google Scholar
• Goto R. 2016. A comprehensive molecular phylogeny of spoon worms (Echiura, Annelida): implications for morphological evolution, the origin of dwarf males, and habitat shifts. Mol Phylogenet Evol. 99:247–260.
   PubMed Web of Science ®Google Scholar
• Guindon S, Dufayard J, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate Maximum-Likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59:307–321.
   PubMed Web of Science ®Google Scholar
• Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp. 41:95–98.
   Google Scholar
• Henmi Y, Itani G, Iwasaki K, Nishikawa T, Sato M, Sato S, Taru M, Fujita Y, Fukuda H, Kubo H, et al. 2015. The present status and problems of threatened benthic animals in the tidal flats of Japan. Japn J Benthol. 69:1–17. (in Japanese)
   Google Scholar
• Huelsenbeck JP, Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics. 17:754–755.
   PubMed Web of Science ®Google Scholar
• Jo HY, Jung WK, Kim SK. 2008. Purification and characterization of a novel anticoagulant peptide from marine echiuroid worm, Urechis unicinctus. Process Biochem. 43:179–184.
   Web of Science ®Google Scholar
• Kang K. 1999. Sediment preference and burrow shape of spoon worm, Urechis unicinctus in laboratory culture. Korea J Aquac. 12:193–196.
   Google Scholar
• Kang KH, Min KJ, Chun SS. 2010. Effects of Urechis unicinctus juveniles on chemical characteristics of organically contaminated coastal sediment. Chin J Oceanol Limn. 9:48–52.
   Google Scholar
• Katsares V, Tsiora A, Galinou-Mitsoudi S, Imsiridou A. 2008. Genetic structure of the endangered species Pinna nobilis (Mollusca: Bivalvia) inferred from mtDNA sequences. Biologia. 63:412–417.
   Web of Science ®Google Scholar
• Kazama M, Tamai K, Nishikawa T, Moriyama R, Hino A. 2014. Monophyletic possibility in Japanese and Chinese groups of Echiuran worm, Urechis unicinctus. Sci J Kanagawa Univ. 25:99–105. (in Japanese)
   Google Scholar
• Knowlton N, Weigt LA. 1998. New dates and new rates for divergence across the Isthmus of Panama. P Roy Soc B-Biol Sci. 265:2257–2263.
   Web of Science ®Google Scholar
• Li FL, Wang W, Zhou H. 1994. Study of echiuroid worms (Echiura) about Yellow and Bohai Sea. J Ocean Univ China. 24:2–8. (in Chinese)
   Google Scholar
• Li N, Song S. 1998. Urechis unicinctus. Bull Biol. 8:12–14. (in Chinese)
   Google Scholar
• Li N, Wang B. 1997. Reproductive biology of Urechis unicinctus along the coast of Shandong province. Acta Zool Sin. 43:433–435. (in Chinese)
   Google Scholar
• Li Y, Wang B, Wang W, Dong J. 2016. Genetic diversity analysis of Jellyfish rhopilema esculentumin Liaodong Bay based on the COI sequence. Fish Sci. 35:404–409. (in Chinese)
   Google Scholar
• Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452.
   PubMed Web of Science ®Google Scholar
• Liu X, Zhang L, Zhang Z, Ma X, Liu J. 2015. Transcriptional response to sulfide in the Echiuran worm Urechis unicinctus by digital gene expression analysis. BMC Genomics. 16:829
   PubMed Web of Science ®Google Scholar
• Liu Z, Cordes JF. 2004. DNA marker technologies and their applications in aquaculture genetics. Aquaculture. 238:1–37.
   Web of Science ®Google Scholar
• Ma YB, Zhang ZF, Shao MY, Kang KH, Tan Z, Li JL. 2011. Sulfide:quinone oxidoreductase from Echiuran worm Urechis unicinctus. Mar Biotechnol. 13:93–107.
   PubMed Web of Science ®Google Scholar
• Ma ZJ, Bao Z, Kang KH, Li YU, Zhang Z. 2005. The changes of three components in coelomic fluid of Urechis unicinctus exposed to different concentrations of sulfide. Chin J Oceanol Limn. 23:104–109.
   Google Scholar
• Markert JA, Champlin DM, Gutjahrgobell RE, Grear JS, Kuhn A, Mcgreevy TG, Roth AC, Bagley MJ, Nacci DE. 2010. Population genetic diversity and fitness in multiple environments. Bmc Evol Biol. 10:1–13.
   PubMed Web of Science ®Google Scholar
• Miller PA, Elliott NG, Koutoulis A, Kube PD, Vaillancourt RE. 2012. Genetic diversity of cultured, naturalized, and native pacific oysters, crassostrea gigas, determined from multiplexed microsatellite markers. J Shellfish Res. 31:611–617.
   Web of Science ®Google Scholar
• Murina GVV, Adrianov AV, Chernyshev AV. 2007. Dedicated to the memory of edward cutler. Russ J Mar Biol. 33:137–138.
   Web of Science ®Google Scholar
• Nei M, Koehn RK. 1983. Evolution of genes and proteins. Sunderland: Sinauer Associates Inc.
   Google Scholar
• Nishikawa T. 1995. Some historical considerations on the Japanese ethnobiological nomenclature of the echiurans (Phylum Echiura). Aquabiology. 17:512–517.
   Google Scholar
• Perezlosada M, Nolte MJ, Crandall KA, Shaw PW. 2007. Testing hypotheses of population structuring in the Northeast Atlantic Ocean and Mediterranean Sea using the common cuttlefish Sepia officinalis. Mol Ecol. 16:2667–2679.
   PubMed Web of Science ®Google Scholar
• Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics. 14:817–818.
   PubMed Web of Science ®Google Scholar
• Rabaoui L, Mejri R, Tlig-Zouari S, Bahri L, Hassine OKB, Tsigenopoulos CS. 2011. Genetic variation among populations of the endangered fan mussel Pinna nobilis (Mollusca: Bivalvia) along the Tunisian coastline. Hydrobiologia. 678:99–111.
   Web of Science ®Google Scholar
• Reed DH, Frankham R. 2003. Correlation between fitness and genetic diversity. Conserv Biol. 17:230–237.
   Web of Science ®Google Scholar
• Ren G, Ma H, Ma C, Wang W, Chen W, Ma L. 2016. Genetic diversity and population structure of Portunus sanguinolentus (Herbst, 1783) revealed by mtDNA COI sequences. Mitochondr DNA Part A. 28:1.
   PubMed Web of Science ®Google Scholar
• Rouse GW, Fauchald K. 1995. The articulation of Annelids. Zool Scr. 24:269–301.
   Web of Science ®Google Scholar
• Saito H, Niwa N, Kawai K, Imabayashi H. 2011. Current state of aquatic animals sold as sport fishing bait in western Japan. Hiroshima: Hiroshima University. 3:45–57. (in Japanese)
   Google Scholar
• Schulze A. 2006. Phylogeny and genetic diversity of Palolo worms (Palola, Eunicidae) from the Tropical North Pacific and the Caribbean. Biol Bull. 210:25–37.
   PubMed Web of Science ®Google Scholar
• Slatkin M, Hudson RR. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. 129:555–562.
   PubMed Web of Science ®Google Scholar
• Smit JDG, Urbanska KM. 1986. Rhodanese activity in Lotus corniculatus s.l. J Nat Hist. 20:1467–1476.
   Web of Science ®Google Scholar
• Struck TH, Paul C, Hill N, Hartmann S, Hosel C, Kube M, Lieb B, Meyer A, Tiedemann R, Purschke G. 2011. Phylogenomic analyses unravel annelid evolution. Nature. 471:95–98.
   PubMed Web of Science ®Google Scholar
• Sung WS, Park SH, Dong GL. 2008. Antimicrobial effect and membrane-active mechanism of Urechis tachykinins, neuropeptides derived from Urechis unicinctus. Febs Lett. 582:2463–2466.
   PubMed Web of Science ®Google Scholar
• Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:585–595.
   PubMed Web of Science ®Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. Mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731–2739.
   PubMed Web of Science ®Google Scholar
• Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876–4882.
   PubMed Web of Science ®Google Scholar
• Wang S, Zhang Z, He C, Kang KH, Ma ZJ. 2010. The effect of toxic sulfide exposure on oxygen consumption and oxidation products in Urechis unicinctus (Echiura:Urechidae). Chin J Oceanol Limn. 9:157–161.
   Google Scholar
• Wright S. 1972. Evolution and the genetics of populations. J Bio Sci. 4:253–256.
   Google Scholar
• Wu Z, Shen X, Sun MA, Ren J, Wang Y, Huang Y, Liu B. 2009. Phylogenetic analyses of complete mitochondrial genome of Urechis unicinctus (Echiura) support that echiurans are derived annelids. Mol Phylogenet Evol. 52:558–562.
   PubMed Web of Science ®Google Scholar
• Xu X, Huo W, Meng X, Chen Y. 2016. The artificial nursing and cultivation techniques of Urechis unicinctus. Ocean and Fishery. 2:53–55. (in Chinese)
   Google Scholar
• Yang G, An L, Sun Z. 1999. Analysis of nutrient composition in Urechis uncinctus. Mar Sci. 6:13–14. (in Chinese)
   Google Scholar
• Zhang L, Liu X, Liu J, Zhang Z. 2013. Characteristics and function of sulfur dioxygenase in Echiuran worm Urechis unicinctus. PLoS One. 8:81885.
   Web of Science ®Google Scholar
• Zhang L, Liu X, Qin Z, Liu J, Zhang Z. 2016. Expression characteristics of sulfur dioxygenase and its function adaption to sulfide in echiuran worm Urechis unicinctus. Gene. 593:334–341.
   PubMed Web of Science ®Google Scholar
• Zhang R, Leng P, Wang X, Zhang Z. 2017. Molecular analysis and genetic diversity of Aedes albopictus (Diptera, Culicidae) from China. Mitochondr DNA Part A. 13:1–6.
   Web of Science ®Google Scholar
• Zhang XM, Li KJ. 2011. Research progress on biology and physiology of Urechis uniconctus. J Henan Agri Sci. 40:26–29. (in Chinese)
   Google Scholar