PHYLOGENETIC ANALYSIS of Sphaerirostris Picae (ACANTHOCEPHALA: CENTRORHYNCHIDAE) BASED on LARGE and SMALL SUBUNIT RIBOSOMAL DNA GENE
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International Journal of Parasitology Research ISSN: 0975-3702 & E-ISSN: 0975-9182, Volume 4, Issue 2, 2012, pp.-106-110. Available online at http://www.bioinfo.in/contents.php?id=28. PHYLOGENETIC ANALYSIS OF Sphaerirostris picae (ACANTHOCEPHALA: CENTRORHYNCHIDAE) BASED ON LARGE AND SMALL SUBUNIT RIBOSOMAL DNA GENE RADWAN N.A. Department of Zoology, Faculty of Science, University of Tanta, Tanta, Egypt. *Corresponding Author: Email- [email protected] Received: December 10, 2012; Accepted: December 18, 2012 Abstract- The purpose of the present study was to add new 18S and 28S DNA gene sequences data to Sphaerirostris picae (Rudolphi, 1819) Golvan, 1960 and analyze the generated sequences to define the taxonomic placement of genus Sphaerirostris and providing a better resolution inside the Palaeacanthocephala. Two regions: 18S and 28S of nuclear ribosomal DNA of S. picae were amplified using polymerase chain reaction and sequenced following the instructions of GATC German company facility. Mealign module in the DNAStar Lasergene V7 was used to design a forward and reverse primer of 28S DNA gene. 18S and 28S DNA gene sequences of S. picae were aligned with sequences for both genes of Palacanthocephalans retrieved from GenBank. Results were analyzed using distance matrix methods UPGMA. The resulting phylogenetic trees suggest a paraphyletic arrangement of the two Palaeacanthocephala orders; Echi- norhynchida and Polymorphida depending on the placement of the three echinorhynchids, Transvena, Rhadinorhynchus and Gorgorhyn- choides in the polymorphid clade. The present study is the first to generate gene sequences of genus Sphaerirostris and discuss its rela- tionships within Palaeacanthocephala. Further comprehensive studies should be done for other species of genus Sphaerirostris and fami- ly Centrorhynchidae as all based on molecular phylogenetic analysis to solve their taxonomic overlapping. Keywords- Sphaerirostris picae, Acanthocephala, Ribosomal DNA, Degenerate primer, Phylogenetic analysis Citation: Radwan N.A. (2012) Phylogenetic Analysis of Sphaerirostris picae (Acanthocephala: Centrorhynchidae) Based on Large and Small Subunit Ribosomal DNA Gene. International Journal of Parasitology Research, ISSN: 0975-3702 & E-ISSN: 0975-9182, Volume 4, Issue 2, pp.-106-110. Copyright: Copyright©2012 Radwan N.A. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited. Introduction classification based on the structure of the proboscis and shape and number of its hooks is not consistent with phylogenetic rela- Acanthocephalans have been related to Rotifera, Nematoda, tionships [3]. Nematomorpha and Gastrotricha [1]. Most phylogenetic analyses of phylum Acanthocephala, based on structural and molecular Amin, et al. [7] reported that, since the erection of Sphaerirostris data, have focused on its relationships to other invertebrate phyla, (family Centrorhynchidae) as a subgenus of Centrorhynchus Lűhe, however studies deal with the inter-relations between different 1911 [8], its taxonomy has been in a state of confusion and largely Acanthocephala families and species with uncertain taxonomy are dependent on the use of proboscis armature, especially the num- still out of focus. ber of proboscis hooks rows. This character has proven to be ex- tremely variable through the genus, so a good number of synony- Verweyen, et al. [2] reported that the first molecular phylogenetic mies were made. The authors accelerated that this genus is in analyses of Acanthocephala made by Garey, et al. [3] confirmed need to a serious taxonomic revision that will be enhanced by dif- the major taxonomic grouping of the traditional classifications. In ferent types of analyses based on the molecular criteria. this grouping, Palaeacanthocephala is placed close to the Eoacan- thocephala, with the Archiacanthocephala being the most basal The purpose of the present study was to add new 18S and 28S taxon. According to Herlyn, et al. [4], the monophyly of the Pal- DNA gene sequences data to S. picae as a member of the family aeacanthocephala is still a matter of debate. Consequently, the Centrorhynchidae (Paleacanthocephala). Such data may help in assumed phylogeny of taxa within the Acanthocephala varies, plac- understanding and defining the taxonomic placement of genus ing either archiacanthocephalans [1,5] or palaeacanthocephalans Sphaerirostris and providing a better resolution inside the Pal- [6] at the base of the taxon. aeacanthocephala. The phylogenetic relationships of S. picae were examined with 21 acanthocephalan species belonging to 9 related Molecular data using 18S and/or 28S DNA gene sequences of families that all are belongings to the class Palaeacanthocephala, family Centrorhynchidae are very limited and has indicated that the International Journal of Parasitology Research ISSN: 0975-3702 & E-ISSN: 0975-9182, Volume 4, Issue 2, 2012 || Bioinfo Publications || 106 Phylogenetic Analysis of Sphaerirostris picae (Acanthocephala: Centrorhynchidae) Based on Large and Small Subunit Ribosomal DNA Gene. as inferred from partial 18S and 28S DNA sequences. The study forward.5´ GGGCCGTAGACGACCAAGTGTT -3´ and used an algorithm ClustalW2 for designing degenerate primers reverse. 5´GGAAAGCGCTCGCCAAGTTATT 3´ [2]. which are of particular value in amplifying homologous genes from The second is 28S DNA gene using degenerate designed primers: different organisms. forward 5´GTAA\G CGGCGAGTGAACTGGGAAG\TA -3´ and Materials and Methods reserve 5´TA\CACACTCGGACTAGAA A\C C A\C CA 3´. Specimen and DNA Isolation PCR mixture (50µl) contained 25µl Maxima Hot Start PCR Master S. picae was collected from the small intestine of the Hooded crow Mix (Fermentas), 1μl final concentration of each primer, 17μl nucle- Corvus corone cornix, Linnaeus 1758, which is a common resident ase-free and 6μl of template DNA solution. PCR cycling parameter inhibiting cultivated land and wooded terrain in Nile Delta and val- for 18S DNA gene included initial denaturation period at 95°C for ley in Egypt. For identification, worms were preserved in 70% etha- 10 min, annealing at 58°C for 1 min and extension at 72°C for 45 nol, stained with Mayer’s carmine, mounted in Canada balsam [9] seconds followed by another 35 cycles at the same denaturation, and identified according to Dimitrova, et al. [10,11]. Specimens annealing and extension temperatures and finished with a 10 min were stored at -20°C until nucleic acid was extracted. DNA extrac- final extension at 72°C (after the modification of Garey, et al. [2]). A tion followed Chloroform-Isoamyl alcohol method [12]. Three repli- negative control (no template) was also performed for every PCR ca each of one worm were homogenized on ice in TE buffer (10 run to determine any potential contamination of the PCR products. mM Tris–HCl, pH 7.5, 10 mM NaCl, 1 mM EDTA) and digested by PCR products were evaluated by electrophoresis of 4µl PCR mix- adding 400µl of TE buffer, 40µl 10% sodium dodecyl sulphate ture through 1% agarose gel against I Kb ladder (Fementas), and (SDS) and 10µl of 20mg/ml protienase K, then incubated in 55°C cleaned up using Gene JET™ PCR purification Kit (fermentas) and overnight. The supernatant was extracted twice with buffered phe- the purified DNA was stored at -20°C. 2µl of PCR product was nol (pH 8.0) and once with chloroform/isoamyl alcohol (24:1). The sequenced using an ABI big dye terminator kit following the instruc- aqueous layer (~ 400µl) was collected and 16µl of 5 M NaCl and tions of GATC German company facility and an ABI 3730xl DNA 420µl ice cold isopropanaol were added. The sample was cooled sequencer . in the refrigerator at -20°C for 10 min and centrifuged for 5 min at 15,000 rpm. The supernatant was poured off and after complete Phylogenetic Analysis drying of the pellet, 50µ of the TE buffer was added and left for 30 In addition to the 18S and 28S DNA gene sequences generated in min to complete dissolving. The sample was stored at -20°C till this study, additional 21 sequences for 18S DNA and 16 for 28S use. DNA genes of other Paleacanthocephalans and one out group Designing the Degenerate Primers of 28S DNA Gene were obtained from the GenBank [Table-1]. The ClustalW2 algo- rithm was used to visualize the consensus sequences and the The DNA sequences of 28S DNA gene of 23 species accession dendogram. The dendograms were built depending on the molecu- numbers from AB500157.1 to AB500179.1 were retrieved from the lar based evolution set by Pearson and Lipman [15]. The matrix sequence database of NCBI. FASTA file format of the previous methods UPGMA (Unweighted-Pair-Group Methods with Arithmetic sequences was used in the algorithm type of the Blast (Basic local Mean) was used to present the dendrograms and the relation be- alignment search tool). Expected values (E-values) was calculated tween homologous sequences based on the produced multiple to infer homology and distance of similarity between the sequences sequence alignment [16]. [13]. Results The mealign module implentend in the DNAStar Lasergene V7 used the Clustal W2 algorithm for alignment collected sequences DNA Sequencing and Data Set and produced the conserved blocks, which were used to design the degeneracy primers. All primer characteristics were adjusted. Pri- The sequence obtained for 18S DNA is a 385 nucleotides long mer Blast tool [14] was used to detect the homology