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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.


Predicted ITS2 RNA secondary structures and their structure formation enthalpies according to MFOLD
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Related In: Results  -  Collection


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Figure 4: Predicted ITS2 RNA secondary structures and their structure formation enthalpies according to MFOLD

Mentions: Six predicted RNA secondary structures werereconstructed from the unique sequences with highestnegative free energy of F. gigantica to provide the basicinformation for phylogenetic analysis (Figure 4). The ITS2 plus flanking regions of nuclear region ranged from 606bpin F. gigantica India to a minimum length of 361bp in F. gigantica China. The secondary structural features of ITS2 regions as shown in the figure were analysed based on conserved stems and loops. F. sp. Japan, F. gigantica Indonesia, F. gigantica Zambia and F. hepatica Uruguay exhibited same type of secondary structures. F. gigantica isolates from India and China show overall similarity in the ITS2 rRNA folding and have identical secondary structure. Secondary structures of the remaining species are weakly variable. The observed similarities at the secondary structural level are further reflected at the energy level. The only difference in their topology is due to differences in nucleotide sequences. These secondary structure predictions indicate that the domains basepair to form a core region central to several stem features implying that conservedness is more important for the proper rRNA folding pattern. Moreover the observed phylogenetic trend was identified with respect to the target accessibility sites for the seven different isolates. The orders of preference were interior loop, bulge loop, multiple branch loop, hairpin loop and exterior loop in all the isolates. The topology based only on the predicted RNA secondary structure of the ITS2 region resolved most relationships among the species studied. Bayesian analysis of the alignment retained the same topology and supported the same branches as the primary sequences (Figure 4). ITS2 sequence of the Indian isolate revealed closest similarity with the Chinese isolate (Fasciola gigantica) with significant bootstrap value.


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)

Predicted ITS2 RNA secondary structures and their structure formation enthalpies according to MFOLD
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Predicted ITS2 RNA secondary structures and their structure formation enthalpies according to MFOLD
Mentions: Six predicted RNA secondary structures werereconstructed from the unique sequences with highestnegative free energy of F. gigantica to provide the basicinformation for phylogenetic analysis (Figure 4). The ITS2 plus flanking regions of nuclear region ranged from 606bpin F. gigantica India to a minimum length of 361bp in F. gigantica China. The secondary structural features of ITS2 regions as shown in the figure were analysed based on conserved stems and loops. F. sp. Japan, F. gigantica Indonesia, F. gigantica Zambia and F. hepatica Uruguay exhibited same type of secondary structures. F. gigantica isolates from India and China show overall similarity in the ITS2 rRNA folding and have identical secondary structure. Secondary structures of the remaining species are weakly variable. The observed similarities at the secondary structural level are further reflected at the energy level. The only difference in their topology is due to differences in nucleotide sequences. These secondary structure predictions indicate that the domains basepair to form a core region central to several stem features implying that conservedness is more important for the proper rRNA folding pattern. Moreover the observed phylogenetic trend was identified with respect to the target accessibility sites for the seven different isolates. The orders of preference were interior loop, bulge loop, multiple branch loop, hairpin loop and exterior loop in all the isolates. The topology based only on the predicted RNA secondary structure of the ITS2 region resolved most relationships among the species studied. Bayesian analysis of the alignment retained the same topology and supported the same branches as the primary sequences (Figure 4). ITS2 sequence of the Indian isolate revealed closest similarity with the Chinese isolate (Fasciola gigantica) with significant bootstrap value.

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.