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A Molecular Systematics Research Of Oribatida On The Basis Of The RNA Gene Of Ribosome

Posted on:2008-01-06Degree:MasterType:Thesis
Country:ChinaCandidate:D Y WangFull Text:PDF
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This research chose one representative species from six families of Oribatida, adopted the method of PCR to extend and determined the partial sequences of 18S rDNA and the sequences of 28S rDNA D3 area, used the Ischyropsalis luteipes (the number of Genbank is U91497) as a outgroup. Contrasted and analysed the results with MP,ML and NJ to construct the molecular system tree. Compared with the traditional taxonomy of anagenesis, we studied molecular system of Oribatida.The result of the research showed that: used the ethanol of 70% (about 20mg) to conserve the fresh samples, adopted five methods (CTAB, NaCl, SDS, KAC and reagent box) to distill the genome DNA of Oribatida. Through these five methods, all could acquire the whole genome DNA, but the quantities of them were small. As the templet of PCR, they all could extend the aim bands, although it can be seen that the purity of the distilled genome DNA was low.Through designed the primers, PCR, gel purified, determined the six partial sequences of 18S rDNA (about 540bp), the sequences of 28S rDNA D3 area (about 350bp). Search the result of the sequences on the NCBI for the similarity of BLAST, confirm the obtainer were the goal sequences.Analyzed the total 7 sequences (including the outgroup sequence): the length of partial sequences of 18S rDNA varies from 547 bp to 550 bp, only 4 bp different; the difference of the content of base was not obvious; the percent difference in nucleotide sequence between every two sequences of Oribatida were 1.1%-6.0%. The length of sequence of 28S rDNA D3 area varies from 346 bp to 357 bp, and the most difference of length was 11bp; the difference of the content of base was not obvious; the percent difference between every two sequences of Oribatida were 2.0%-11.8%. Thus it can be seen, the variation degree of the two sections are definite among Oribatida.There are 31 parsimony informative sites in the 18S rDNA sequence, about 5.6% of the total numbers of base. There are 36 parsimony informative sites in the 28S rDNA D3 area, 10.1% of the total number of base, and we can see the number is large. The average rate of transition / transversion were 1.6 and 1.9 respectively. Thereinto, the times of transition between two sequences were more than the times of trans- version. The degree of the bases displace was not saturated and fit for the system analyses. The results of PTP test were all significant (P=0.001), also proved that the data were according with parsimony hypothesis, all the original data have strong growth information. Used the two sections to discuss system phylogenesis, partial results of the former conflicted with the traditional, but all those of the latter were consistent with the traditional. Therefore, the significance of the partial sequences of 18S rDNA is limited to study system phylogenesis of oribatida advanced steps, but that of the 28S rDNA D3 area was very big.According to morphological characters, Euphthiracaridae and Phthiracaridae are both belonging to ptychoid oribatid mites. All the phylogenesis trees are consistent with Euphthiracaridae and Phthiracaridae being clustered together. Pterogasterine oribatid mites include Scheloribatidae and Parakalumnidae, which was proved by phylogenesis trees on the basis of the 28S and 18S+28S data. In tradional evolvemental views, ptychoid oribatid mites were the original, which was consilient with molecular systems research, because Euphthiracaridae and Phthiracaridae clustered separately on the MP and ML trees. But the results on the NJ tree did not agree with that.In this research, we can see that the results of MP synthesis are not very stable; on the basic branch, it is always similar on the MP and ML tree; the structure of NJ tree was consistent with system taxonomy, and its bootstrap confidence level was higher than that of MP and ML tree. So the results of NJ tree were probably more reliable.Used 28S rDNA D3 area sequences to discuss ptychoid oribatid mites'phylogeny status. Adopted MP, ML and NJ three methods to deal with the data from 11 relative sequences of Arachnida available in the GenBank. The results of MP and NJ analysis showed that ptychoid oribatid mites first clustered with other families of oribatida, then with Prostigmata. But on the ML tree ptychoid oribatid mites clustered with Prostigmata firstly, then with other families of oribatida. So ptychoid oribatid mites must belong to Acariformes, and should probably belong to oribatida, which accorded with traditional views.
Keywords/Search Tags:Oribatida, D3 fragment of 28S rDNA, Systemic taxonomy
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