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. 2010 Oct;17(4):275-290.
doi: 10.1016/j.sjbs.2010.06.001. Epub 2010 Jun 15.

Molecular systematic study of Cardamine glechomifolia Levl. (Brassicaceae) using internal transcribed spacer sequence of nuclear ribosomal DNA (ITS) and chloroplast trn L and trn L-F sequences

M Ajmal Ali  1 , Dung Luong Van  2 , Soo-Yong Kim  2
Affiliations

Molecular systematic study of Cardamine glechomifolia Levl. (Brassicaceae) using internal transcribed spacer sequence of nuclear ribosomal DNA (ITS) and chloroplast trn L and trn L-F sequences

M Ajmal Ali et al. Saudi J Biol Sci. 2010 Oct.

Abstract

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA, trnL and trnL-F genes of Cardamine glechomifolia Levl. (family Brassicaceae) were sequenced and analyzed with the sequence of related Cardamine species retrieved from NCBI GenBank to detect pattern of evolutionary differentiation. All trees resulting from combined sequence analyses data of ITS, trnL and trnL-F gene resolve that C. glechomifolia - an endemic species to South Korea clade with Cardamine microzyga (100% bootstrap support). The evolutionary history was inferred using the Maximum Parsimony method. The consistency index is (0.588235), the retention index is (0.687500), and the composite index is 0.519622 (0.404412) for all sites and parsimony-informative sites (in parentheses). The result of the analysis using Maximum Parsimony was found congruence with Maximum Likelihood method and in Baseyan analysis.

Keywords: Cardamine glechomifolia; ITS; Molecular systematic; trnL; trnL-F.

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Figures

Figure 1
Figure 1
50% Majority rule tree inferred from combined sequence data analysis of internal transcribed spacer region of nuclear ribosomal DNA, trnL and trnL-F from Cardamine. The tree constructed in MEGA4 after multiple alignment in ClustalX.
Figure 2
Figure 2
A Neighbor-Joining tree inferred from combined sequence data analysis of internal transcribed spacer region of nuclear ribosomal DNA, trnL and trnL-F from Cardamine. The tree constructed in SeaView after multiple alignment in MUSCLE. The scale bar indicates relative length of the branch.
Figure 3
Figure 3
Bayesian phylogeny (consensus tree) based on combined sequence data analysis of internal transcribed spacer region of nuclear ribosomal DNA, trnL and trnL-F from Cardamine.
Figure 4
Figure 4
Bootstrap strict consensus tree based on combined sequence data analysis of internal transcribed spacer region of nuclear ribosomal DNA, trnL and trnL-F from Cardamine. The tree constructed using Maximum Parsimony method in SeaView after multiple alignment in MUSCLE. Bootstrap values greater than 50% in 1000 replicates are shown.
Figure 5
Figure 5
Bootstrap strict consensus tree based on combined sequence data analysis of internal transcribed spacer region of nuclear ribosomal DNA, trnL and trnL-F from Cardamine. The tree constructed using Maximum Likelihood method in SeaView after multiple alignment in MUSCLE. Bootstrap values greater than 50% in 1000 replicates are shown above lines.
Figure 6
Figure 6
A Neighbor-Joining tree based on combined sequence data analysis of internal transcribed spacer region of nuclear ribosomal DNA, trnL and trnL-F from Cardamine. The tree constructed using SeaView after multiple alignment in MUSCLE.
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