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Investigation of nuclear and mitochondrial DNA polymorphism in closely related species of endemic Baikal sponges

  • Animal Genetics
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Abstract

In order to investigate the phylogenetic relationships among endemic Baikal sponges of the family Lubomirskiidae and to clarify their taxonomy, the sequence variation at the silicatein-encoding gene and the mtDNA intergenic region was examined. Phylogenetic analysis of the silicatein α1 gene exonic regions in six freshwater sponge species revealed considerable interspecific variability of this region. The analysis performed did not support the monophyly of the genera Lubomirskia and Baikalospongia. The mtDNA region between the COX2 and ATP6 genes was examined in five species from the Lubomirskiidae family, including multiple samples for analyzing intraspecific variations. According to the data obtained, the genus Baikalospongia was paraphyletic with respect to Lubomirskia, while B. bacilifera and B. recta did not form monophyletic groups. Molecular data indicate that taxonomy of Lubomirskiidae should be revised. It was demonstrated that, in endemic Baikal sponges, the accelerated evolution was accompanied by an increase in the length of the non-coding regions in both mitochondrial and nuclear genes.

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References

  1. Li, C.W., Chen, J.Y., and Hua, T.E., Precambrian sponges with cellular structures, Science, 1998, vol. 249, pp. 879–882.

    Article  Google Scholar 

  2. Hooper, J.N.A. and van Soest, R.W.M., Systema Porifera: A Guide to the Classification of Sponges, Dordrecht: Kluwer, 2002.

    Book  Google Scholar 

  3. Manconi, R. and Pronzato, R., Suborder Spongillina subord. nov.: Freshwater sponges, Systema Porifera: A Guide to the Classification of Sponges, Hooper, J.N.A. and van Soest, R.W.M., Eds., Dordrecht: Kluwer, 2002, pp. 921–1020.

    Chapter  Google Scholar 

  4. Efremova, S.M., Sponges, Annotirovannyi spisok fauny ozera Baikal i ego vodosbornogo basseina (An Annotated List of the Fauna of Lake Baikal and Its Catchment Area), Timoshkin, O.A., et al., Eds., Novosibirsk: Nauka, 2001, vol. 1, pp. 177–190.

    Google Scholar 

  5. Efremova, S.M., New genus and new species of sponges from family Lubomirskiidae Rezvoj, 1936, Annotirovannyi spisok fauny ozera Baikal i ego vodosbornogo basseina (An Annotated List of the Fauna of Lake Baikal and Its Catchment Area), Timoshkin, O.A., et al., Eds., Novosibirsk: Nauka, 2004, vol. 1, book 2, pp. 1261–1278.

    Google Scholar 

  6. Masuda, Y., Studies on the taxonomy and distribution of freshwater sponges in Lake Baikal, Prog. Mol. Subcell. Biol., 2009, vol. 47, pp. 81–110.

    Article  PubMed  Google Scholar 

  7. Addis, J.S. and Peterson, K.J., Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18SrDNA, COI mtDNA, and ITS2 rDNA sequences, Zool. Scripta, 2005, vol. 34, pp. 549–557.

    Article  Google Scholar 

  8. Meixner, M.J., Luter, C., Eckert, C., et al., Phylogenetic analysis of freshwater sponges provide evidence for endemism and radiation in ancient lakes, Mol. Phylogenet. Evol., 2007, vol. 45, pp. 875–886.

    Article  PubMed  CAS  Google Scholar 

  9. Itskovich, V., Gontcharov, A., Masuda, Y., et al., Molecular phylogeny of freshwater sponges (Porifera) based on ITS1 and ITS2 sequences of ribosomal DNA, J. Mol. Evol., 2008, vol. 67, pp. 608–620.

    Article  PubMed  CAS  Google Scholar 

  10. Harcet, M., Bilandzija, H., Bruvo-Madari, B., et al., Taxonomic position of Eunapius subterraneus (Porifera, Spongillidae) inferred from molecular data-a revised classification needed? Mol. Phylogenet. Evol., 2010, vol. 54, pp. 1021–1027.

    Article  PubMed  Google Scholar 

  11. Erpenbeck, D., Weier, T., De Voogd, N.J., et al., Insights into the evolution of freshwater sponges (Porifera: Demospongiae: Spongillina): Barcoding and phylogenetic data from lake Tanganyika endemics indicate multiple invasions and unsettle existing taxonomy, Mol. Phylogenet. Evol., 2011, vol. 61, pp. 231–235.

    Article  PubMed  Google Scholar 

  12. Shimizu, K., Cha, J., Stucky, G.D., et al., Silicatein alpha: Cathepsin L-like protein in sponge biosilica, Proc. Natl. Acad. Sci. U.S.A., 1998, vol. 95, pp. 6234–6238.

    Article  PubMed  CAS  Google Scholar 

  13. Kaluzhnaya, O.V., Belikov, S.I., Schröder, H.C., et al., Dynamics of skeleton formation in the Lake Baikal sponge Lubomirskia baicalensis: 2. Molecular biological studies, Naturwissenschaften, 2005, vol. 92, pp. 128–133.

    Article  PubMed  CAS  Google Scholar 

  14. Funayama, N., Nakatsukasa, M., Kuraku, S., et al., Isolation of Ef silicatein and Ef lectin as molecular markers for sclerocytes and cells involved in innate immunity in the freshwater sponge Ephydatia fluviatilis, Zool. Sci., 2005, vol. 22, pp. 1113–1122.

    Article  PubMed  CAS  Google Scholar 

  15. Mohri, K., Nakatsukasa, M., Masuda, Y., et al., Toward understanding the morphogenesis of siliceous spicules in freshwater sponge: Differential mRNA expression of spicule type specific silicatein genes in Ephydatia fluviatilis, Dev. Dyn., 2008, vol. 273, pp. 3024–3039.

    Article  Google Scholar 

  16. Kaluzhnaya, O.V., Belikova, A.S., Podol’skaia, E.P., et al., Silicateins identification of the freshwater sponge L. baicalensis, Mol. Biol. (Moskow), 2007, vol. 41, no. 4, pp. 616–623.

    Article  Google Scholar 

  17. Kalyuzhnaya, O.V., Kras’ko, A.G., Grebeniuk, V.A., et al., Freshwater sponge silicateins: Comparison of sequences and exon-intron structure of genes, Mol. Biol. (Moskow), 2011, vol. 45, no. 4, pp. 617–626.

    Google Scholar 

  18. Erpenbeck, D., Voigt, O., Adamski, M., et al., Mitochondrial diversity of early-branching metazoa is revealed by the complete mt genome of a haplosclerid demosponge, Mol. Biol. Evol., 2007, vol. 24, no. 1, pp. 19–22.

    Article  PubMed  CAS  Google Scholar 

  19. Watkins, R.F. and Beckenbach, A.T., Partial sequence of a sponge mitochondrial genome reveals sequence similarity to Cnidaria in cytochrome oxidase subunit II and the large ribosomal RNA subunit, J. Mol. Evol., 1999, vol. 48, no. 5, pp. 542–54.

    Article  PubMed  CAS  Google Scholar 

  20. Itskovich, V., Belikov, S., Efremova, S., et al., Monophyletic origin of freshwater sponges in ancient lakes based on partial structures of COXI gene, Hydrobiologia, 2006, vol. 568, pp. 155–159.

    Article  Google Scholar 

  21. Lavrov, D.V., Maikova, O.O., Pett, W., et al., Small inverted repeats drive mitochondrial genome evolution in Lake Baikal sponges, Gene, 2012, vol. 15, no. 505(1), pp. 91–99.

    Article  Google Scholar 

  22. Maikova, O.O., Stepnova, G.N., and Belikov, S.I., Variations in noncoding sequences of the mitochondrial DNA in sponges from family Lubomirskiidae, Dokl. Akad. Nauk, 2012, vol. 442, nos. 1–6, pp. 1–3.

    Google Scholar 

  23. Hall, T.A., Bioedit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp., 1999, ser. 41, pp. 95–98.

    Google Scholar 

  24. Tamura, K., Peterson, D., Peterson, N., et al., MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol., 2011, vol. 28, pp. 2731–2739.

    Article  PubMed  CAS  Google Scholar 

  25. Ronquist, F. and Huelsenbeck, J.P., MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 2003, vol. 19, pp. 1572–1574.

    Article  PubMed  CAS  Google Scholar 

  26. Keane, T.M., Creevey, C.J., Pentony, M.M., et al., Assessment of methods for amino acid matrix selection and their use on empirical data shows that assumptions for choice of matrix are not justified, BMC Evol. Biol., 2006, vol. 6, p. 29.

    Article  PubMed  Google Scholar 

  27. Borchiellini, C., Chombard, C., Manuel, M., et al., Molecular phylogeny of Demospongiae: Implications for classification and scenarios of character evolution, Mol. Phylogenet. Evol., 2004, vol. 32, pp. 823–837.

    Article  PubMed  CAS  Google Scholar 

  28. Itskovich, V., Belikov, S., Efremova, S., et al., Phylogenetic relationships between freshwater and marine Haplosclerida (Porifera, Demospongiae) based on the full length 18S rRNA and partial COXI gene sequences, Porifera Research: Biodiversity, Innovation and Sustain-ability, Custidio, M.R., Hajdu, E., Lóbo-Hajdu, G., and Muricy, G., Eds., Rio de Janeiro: Museu Nacional, 2007, pp. 383–391.

    Google Scholar 

  29. Veynberg, E., Fossil sponge fauna in Lake Baikal region, Prog. Mol. Subcell. Biol., 2009, vol. 47, pp. 185–205.

    Article  PubMed  Google Scholar 

  30. Darikova, Yu.A. and Sherbakov, D.Yu., Evolution of the phosphofructokinase gene intron in gastropods of family Baicalidae, Mol. Biol. (Moscow), 2009, vol. 43, no. 5, pp. 776–782.

    Article  CAS  Google Scholar 

  31. Avise, J.C., Phylogeography: The History and Formation of Species, Cambridge: Harvard University, 2000.

    Google Scholar 

  32. Rot, C., Goldfarb, I., Ilan, M., et al., Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria, BMC Evol. Biol., 2006, vol. 6, p. 71.

    Article  PubMed  Google Scholar 

  33. Szitenberg, A., Rot, C., Ilan, M., et al., Diversity of sponge mitochondrial introns revealed by cox 1 sequences of Tetillidae, BMC Evol. Biol., 2010, vol. 10, p. 288.

    Article  PubMed  Google Scholar 

  34. Lynch, M. and Conery, J.S., The origins of genome complexity, Science, 2003, vol. 302, pp. 1401–1404.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, 664033, Russia

    V. B. Itskovich, O. V. Kaluzhnaya & S. I. Belikov

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  1. V. B. Itskovich
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  2. O. V. Kaluzhnaya
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  3. S. I. Belikov
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Correspondence to V. B. Itskovich.

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Original Russian Text © V.B. Itskovich, O.V. Kaluzhnaya, S.I. Belikov, 2013, published in Genetika, 2013, Vol. 49, No. 8, pp. 966–974.

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Itskovich, V.B., Kaluzhnaya, O.V. & Belikov, S.I. Investigation of nuclear and mitochondrial DNA polymorphism in closely related species of endemic Baikal sponges. Russ J Genet 49, 839–846 (2013). https://doi.org/10.1134/S1022795413080036

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  • DOI: https://doi.org/10.1134/S1022795413080036

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