OJGen  Vol.3 No.3 , September 2013
Characterization of randomly amplified polymorphic DNA (RAPD) fragments revealing clonal variability in cercariae of avian schistosome Trichobilharzia szidati (Trematoda: Schistosomatidae)
ABSTRACT

Recently we applied randomly amplified polymorphic DNA (RAPD) fingerprinting to detect clonal variability among individual cercariae within daughter sporocysts and rediae of 10 digenean trematodes (Platyhelminthes: Trematoda). The most variable RAPD patterns were obtained for Schistosomatidae representative-avian schistosome Trichobilharzia szidati. In this work, 50 polymorphic DNA fragments of approximately 300-1500 bp from RAPD patterns of individual T. szidati cercariae were cloned and sequenced. As a result genomic DNA sequences (total length of approximately 41,000 bp) revealing clonal variability in T. szidati cercariae were obtained and analyzed. The analysis indicated that these sequences contained tandem, inverted and dispersed repeats as well as regions homological to retroelements of two human parasites, Schistosoma mansoni and S. japonicum. Tandem and inverted repeats constituted 8.9% and 22.1% respectively, while the percentage of dispersed repeats was 21.0%. The average content of these components was 41.7% with the average AT content being 59.0%. About 40% of sequences included regions ranging in length from 96 to 1005 bp which displayed amino acid homology with open reading frame pol products of S. mansoni and S. japonicum retroelements: non-long terminal repeat retrotransposons (nLTRs, 76%), long terminal repeat retrotransposons (LTRs, 14%), and Penelope-like elements (PLEs, 10%). Most of these regions (86.4%) contained frameshifts, gaps, and stop-codons. The largest portion of them was homological to nLTRs of the RTE clade (67%). The number of sequences homologous to the members of CR1 lineage was 7 times smaller (9%). Homology with LTRs of Gypsy/Ty3 and BEL clades was revealed in 5% and 9% of cases respectively. We assume that the repetitive elements including retroelement-like sequences described in the current study may serve as the source of clonal variability detected previously in T. szidati and other digenean trematodes. Such genome regions rapidly accumulate mutations and thus may play an important functional role in the life history of the species.


Cite this paper
Korsunenko, A. , Chrisanfova, G. , Arifov, A. , Ryskov, A. and Semyenova, S. (2013) Characterization of randomly amplified polymorphic DNA (RAPD) fragments revealing clonal variability in cercariae of avian schistosome Trichobilharzia szidati (Trematoda: Schistosomatidae). Open Journal of Genetics, 3, 141-158. doi: 10.4236/ojgen.2013.33017.
References
[1]   Bell, G. (1982) The masterpiece of nature: The evolution and genetics of sexuality. University of California Press, Berkeley.

[2]   Galaktionov, K. and Dobrovolskij, A. (1998) The origin and evolution of trematode life cycles. Nauka, Saint-Petersburg.

[3]   Galaktionov, K. and Dobrovolskij, A. (2003) The biology and evolution of trematodes. Kluwer Academic Publishers, Boston, Dordrecht, London.

[4]   Cort, W.W., Ameel, D.J. and Van Der Woude, A. (1954) Germinal development in the sporocysts and rediae of the digenetic trematodes. Experimental Parasitology, 3, 185-225. doi:10.1016/0014-4894(54)90008-9

[5]   Lushai, G. and Loxdale, H.D. (2002) The biological improbability of a clone. Genetics Research, 79, 1-9. doi:10.1017/S0016672301009582

[6]   Bayne, C.J. and Grevelding, C.G. (2003) Cloning of Schistosoma mansoni sporocysts in vitro and detection of genetic heterogeneity among individuals within clones. Journal of Parasitology, 89, 1056-1060. doi:10.1645/GE-3186RN

[7]   Grevelding, C.G. (1999) Genomic instability in Schistosoma mansoni. Molecular and Biochemical Parasitology, 101, 207-216. doi:10.1016/S0166-6851(99)00078-X

[8]   Gower, C.M., Shrivastava, J., Lamberton, P.H., et al. (2007) Development and application of an ethically and epidemiologically advantageous assay for the multi-locus microsatellite analysis of Schistosoma mansoni. Parasitology, 134, 523-536. doi:10.1017/S0031182006001685

[9]   Yin, M., Hu, W., Mo, X., et al. (2008) Multiple near-identical genotypes of Schistosoma japonicum can occur in snails and have implications for population-genetic analyses. International Journal for Parasitology, 38, 1681-1691. doi:10.1016/j.ijpara.2008.05.015

[10]   Khalturin, K.V., Mikhailova, N.A. and Granovich, A.I. (2000) Genetic heterogeneity in natural populations of Microphallus piriformes and M. pygmaeus parthenites (Trematoda: Microphallidae). Parazitologiia, 34, 486-501.

[11]   Welsh, J. and McClelland, M. (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research, 18, 7213-7218. doi:10.1093/nar/18.24.7213

[12]   Williams, J.G., Kubelik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18, 6531-6535. doi:10.1093/nar/18.22.6531

[13]   Zarlenga, D.S. and Higgins, J. (2001) PCR as a diagnostic and quantitative technique in veterinary parasitology. Veterinary Parasitology, 101, 215-230. doi:10.1016/S0304-4017(01)00568-4

[14]   Korsunenko, A.V., Chrisanfova, G.G., Ryskov, A.P., Movsessian, S.O., Vasilyev, V.A. and Semyenova, S.K. (2010) Detection of European Trichobilharzia schistosomes (T. franki, T. szidati, and T. regenti) based on novel genome sequences. Journal of Parasitology, 96, 802-806. doi:10.1645/GE-2297.1

[15]   Semyenova, S.K., Khrisanfova, G.G., Korsunenko, A.V., et al. (2007) Multilocus variation in cercariae, parthenogenetic progeny of different species of the class Trematoda. Doklady Biological Sciences, 414, 235-238. doi:10.1134/S0012496607030192

[16]   Dvorak, J., Vanacova, S., Hampl, V., Flegr, J. and Horak, P. (2002) Comparison of European Trichobilharzia species based on ITS1 and ITS2 sequences. Parasitology, 124, 307-313.

[17]   Korsunenko, A., Chrisanfova, G., Lopatkin, A., Beer, S. A., Voronin, M., Ryskov, A.P. and Semyenova, S.K. (2012) Genetic differentiation of cercariae infrapopulations of the avian schistosome Trichobilharzia szidati based on RAPD markers and mitochondrial cox1 gene. Parasitology Research, 110, 833-841. doi:10.1007/s00436-011-2562-6

[18]   Benson, G. (1999) Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Research, 27, 573-580. doi:10.1093/nar/27.2.573

[19]   Warburton, P.E., Giordano, J., Cheung, F., Gelfand, Y. and Benson, G. (2004) Inverted repeat structure of the human genome: The X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. Genome Research, 14, 1861-1869. doi:10.1101/gr.2542904

[20]   DeMarco, R., Machado, A.A., Bisson-Filho, A.W. and Verjovski-Almeida, S. (2005) Identification of 18 new transcribed retrotransposons in Schistosoma mansoni. Biochemical and Biophysical Research Communications, 333, 230-240. doi:10.1016/j.bbrc.2005.05.080

[21]   Venancio, T.M., Wilson, R.A., Verjovski-Almeida, S. and DeMarco, R. (2010) Bursts of transposition from non-long terminal repeat retrotransposon families of the RTE clade in Schistosoma mansoni. International Journal for Parasitology, 40, 743-749. doi:10.1016/j.ijpara.2009.11.013

[22]   Berriman, M., Haas, B.J., LoVerde, P.T., et al. (2009) The genome of the blood fluke Schistosoma mansoni. Nature, 460, 352-358. doi:10.1038/nature08160

[23]   Young, N.D., Jex, A.R., Li, B., et al. (2012) Whole-genome sequence of Schistosoma haematobium. Nature Genetics, 44, 221-225. doi:10.1038/ng.1065

[24]   Zhou, Y., Zheng, H., Chen, Y., et al. (2009). The Schistosoma japonicum genome reveals features of host-parasite interplay. Nature, 460, 345-351. doi:10.1038/nature08140

[25]   Berg, D. and Howe, M. (1989). Mobile DNA. American Society of Microbiology, Washington DC.

[26]   Kidwell, M.G. and Lisch, D. (1997) Transposable elements as sources of variation in animals and plants. Proceedings of the National Academy of Sciences of the United of America, 94, 7704-7711. doi:10.1073/pnas.94.15.7704

[27]   Thomas, M.C., Macias, F., Alonso, C. and Lopez, M.C. (2010) The biology and evolution of transposable elements in parasites. Trends in Parasitology, 26, 350-362. doi:10.1016/j.pt.2010.04.001

[28]   Laten, H.M., Mogil, L.S. and Wright, L.N. (2009) A shotgun approach to discovering and reconstructing consensus retrotransposons ex novo from dense contigs of short sequences derived from Genbank Genome Survey Sequence database records. Gene, 448, 168-173. doi:10.1016/j.gene.2009.06.011

[29]   Drew, A.C., Minchella, D.J., King, L.T., Rollinson, D. and Brindley, P.J. (1999) SR2 elements, non-long terminal repeat retrotransposons of the RTE-1 lineage from the human blood fluke Schistosoma mansoni. Molecular Biology and Evolution, 16, 1256-1269. doi:10.1093/oxfordjournals.molbev.a026216

[30]   Dimitri, P., Junakovic, N. and Arca, B. (2003) Colonization of heterochromatic genes by transposable elements in Drosophila. Molecular Biology and Evolution, 20, 503-512. doi:10.1093/molbev/msg048

[31]   Mandrioli, M. (2000) Mariner-like transposable elements are interspersed within the rDNA-associated heterochromatin of the pufferfish Tetraodon fluviatilis (Osteichthyes). Chromosome Research, 8, 177-179. doi:10.1023/A:1009254805686

[32]   Sijen, T. and Plasterk, R.H. (2003) Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature, 426, 310-314. doi:10.1038/nature02107

[33]   Boyle, J.P., Wu, X.J., Shoemaker, C.B. and Yoshino, T.P. (2003) Using RNA interference to manipulate endogenous gene expression in Schistosoma mansoni sporocysts. Molecular and Biochemical Parasitology, 128, 205-215. doi:10.1016/S0166-6851(03)00078-1

[34]   Zhao, Z.R., Lei, L., Liu, M., Zhu, S.C., Ren, C.P., Wang, X.N. and Shen, J.J. (2008) Schistosoma japonicum: Inhibition of Mago nashi gene expression by shRNA-mediated RNA interference. Experimental Parasitology, 119, 379-384. doi:10.1016/j.exppara.2008.03.015

[35]   Hao, L., Cai, P., Jiang, N., Wang, H. and Chen, Q. (2010) Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicum. BMC Genomics, 11, 55. doi:10.1186/1471-2164-11-55

[36]   Wang, Z., Xue, X., Sun, J., et al. (2010) An “in-depth” description of the small non-coding RNA population of Schistosoma japonicum schistosomulum. PLoS Neglected Tropical Diseases, 4, e596. doi:10.1371/journal.pntd.0000596

[37]   Brennecke, J., Aravin, A.A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R. and Hannon, G.J. (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell, 128, 1089-1103. doi:10.1016/j.cell.2007.01.043

[38]   Betran, E. and Long, M. (2002) Expansion of genome coding regions by acquisition of new genes. Genetica, 115, 65-80. doi:10.1023/A:1016024131097

[39]   Oliver, K.R. and Greene, W.K. (2009) Transposable elements: powerful facilitators of evolution. BioEssays, 31, 703-714. doi:10.1002/bies.200800219

[40]   Helleday, T. (2003) Pathways for mitotic homologous recombination in mammalian cells. Mutation Research, 532, 103-115. doi:10.1016/j.mrfmmm.2003.08.013

[41]   Brinster, R.L., Braun, R.E., Lo, D., Avarbock, M.R., Oram, F. and Palmiter, R.D. (1989) Targeted correction of a major histocompatibility class II E alpha gene by DNA microinjected into mouse eggs. Proceedings of the National Academy of Sciences of the United of America, 86, 7087-7091. doi:10.1073/pnas.86.18.7087

[42]   Wurst, W. and Joyner, A. (1993) Production of targeted embryonic stem cell clones. In A. Joyner, Ed., Gene Targeting: A Practical Approach. Oxford University Press, New York, 33-61.

[43]   Korsunenko, A.V., Tiutin, A.V. and Semenova, S.K. (2009) Clonal and population RAPD variation of cercariae obtained from Bucephalus polymorphus sporocysts (Trematoda: Bucephalidae). Genetika, 45, 73-80.

 
 
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