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Use of sequence motifs as barcodes and secondary structures of internal transcribed spacer 2 (ITS2, rDNA) for identification of the Indian liver fluke, Fasciola (Trematoda: Fasciolidae).

Prasad PK, Tandon V, Biswal DK, Goswami LM, Chatterjee A - Bioinformation (2009)

Bottom Line: However, RNA secondary structures are particularly useful in systematics because they include characteristics that give "morphological" information which is not found in the primary sequence.The latter approach allowed us to include both primary sequence and RNA molecular morphometrics and revealed a close relationship with isolates of F. gigantica from China, Indonesia and Japan, the isolate from China with significant bootstrap values being the closest.Using the novel approach of molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships of the various isolates of fasciolid species have been discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Zoology, North Eastern Hill University, Shillong, Meghalaya, 793022, India.

ABSTRACT
Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics that give "morphological" information which is not found in the primary sequence. Also DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat are useful for identification of trematodes. The species of liver flukes of the genus Fasciola (Platyhelminthes: Digenea: Fasciolidae) are obligate parasitic trematodes residing in the large biliary ducts of herbivorous mammals. While Fasciola hepatica has a cosmopolitan distribution, the other major species, i.e., F. gigantica is reportedly prevalent in the tropical and subtropical regions of Africa and Asia. To determine the Fasciola sp. of Assam (India) origin based on rDNA molecular data, ribosomal ITS2 region was sequenced (EF027103) and analysed. NCBI databases were used for sequence homology analysis and the phylogenetic trees were constructed based upon the ITS2 using MEGA and a Bayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNA molecular morphometrics and revealed a close relationship with isolates of F. gigantica from China, Indonesia and Japan, the isolate from China with significant bootstrap values being the closest. ITS2 sequence motifs allowed an accurate in silico distinction of liver flukes. The data indicate that ITS2 motifs (

No MeSH data available.


Phylogenetic trees of ITS2 sequences of fasciolid species showing bootstrap values. (A) Neighbor Joining; (B)Maximum Parsimony; (C) Hypothetical Bayesian analysis
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Related In: Results  -  Collection


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Figure 2: Phylogenetic trees of ITS2 sequences of fasciolid species showing bootstrap values. (A) Neighbor Joining; (B)Maximum Parsimony; (C) Hypothetical Bayesian analysis

Mentions: Phylogenetic trees were obtained by comparing the sequences of F. gigantica and available ITS sequences forother fasciolid species. Phylogenetic analyses using the various distance methods and character method like Maximum Parsimony showed that the topology is similar among the trees obtained with significant bootstrap support for the clades. The values of 70% and above in the bootstrap test of phylogenetic accuracy indicates reliable grouping among different members of fasciolids. The phylogenetic trees constructed in MEGA revealed a close relationship with isolates of F. gigantica from China, Indonesia and Japan (Figure 2).


Use of sequence motifs as barcodes and secondary structures of internal transcribed spacer 2 (ITS2, rDNA) for identification of the Indian liver fluke, Fasciola (Trematoda: Fasciolidae).

Prasad PK, Tandon V, Biswal DK, Goswami LM, Chatterjee A - Bioinformation (2009)

Phylogenetic trees of ITS2 sequences of fasciolid species showing bootstrap values. (A) Neighbor Joining; (B)Maximum Parsimony; (C) Hypothetical Bayesian analysis
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2655052&req=5

Figure 2: Phylogenetic trees of ITS2 sequences of fasciolid species showing bootstrap values. (A) Neighbor Joining; (B)Maximum Parsimony; (C) Hypothetical Bayesian analysis
Mentions: Phylogenetic trees were obtained by comparing the sequences of F. gigantica and available ITS sequences forother fasciolid species. Phylogenetic analyses using the various distance methods and character method like Maximum Parsimony showed that the topology is similar among the trees obtained with significant bootstrap support for the clades. The values of 70% and above in the bootstrap test of phylogenetic accuracy indicates reliable grouping among different members of fasciolids. The phylogenetic trees constructed in MEGA revealed a close relationship with isolates of F. gigantica from China, Indonesia and Japan (Figure 2).

Bottom Line: However, RNA secondary structures are particularly useful in systematics because they include characteristics that give "morphological" information which is not found in the primary sequence.The latter approach allowed us to include both primary sequence and RNA molecular morphometrics and revealed a close relationship with isolates of F. gigantica from China, Indonesia and Japan, the isolate from China with significant bootstrap values being the closest.Using the novel approach of molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships of the various isolates of fasciolid species have been discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Zoology, North Eastern Hill University, Shillong, Meghalaya, 793022, India.

ABSTRACT
Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics that give "morphological" information which is not found in the primary sequence. Also DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat are useful for identification of trematodes. The species of liver flukes of the genus Fasciola (Platyhelminthes: Digenea: Fasciolidae) are obligate parasitic trematodes residing in the large biliary ducts of herbivorous mammals. While Fasciola hepatica has a cosmopolitan distribution, the other major species, i.e., F. gigantica is reportedly prevalent in the tropical and subtropical regions of Africa and Asia. To determine the Fasciola sp. of Assam (India) origin based on rDNA molecular data, ribosomal ITS2 region was sequenced (EF027103) and analysed. NCBI databases were used for sequence homology analysis and the phylogenetic trees were constructed based upon the ITS2 using MEGA and a Bayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNA molecular morphometrics and revealed a close relationship with isolates of F. gigantica from China, Indonesia and Japan, the isolate from China with significant bootstrap values being the closest. ITS2 sequence motifs allowed an accurate in silico distinction of liver flukes. The data indicate that ITS2 motifs (

No MeSH data available.