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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.


Sample of sequence motif in PROSITE format (from 5' to 3' ends) and Pattern matching of ITS motifs of differentgeographical isolates of fasciolid species
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Related In: Results  -  Collection


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Figure 3: Sample of sequence motif in PROSITE format (from 5' to 3' ends) and Pattern matching of ITS motifs of differentgeographical isolates of fasciolid species

Mentions: A total of 15 ITS2 PROSITE motifs were tested by BLAST analysis against the generalized GenBank database at NCBI (Figure 3). The Fasciola motifs exhibited exact or perfect matches with Fasciola from different geographical isolates with significant E‐value scores. Eight (pattern 1‐8) out of 15 Fasciola motifs exactly matched the sequences of Fasciola isolates from GenBank (best hits = more than 100; 100% of identity; E-values = 2e-16 to 1e-17). Five (pattern 11‐15) showed (best hits = more than 100; 95% identity and significant E‐value ranging from 5e-14 to 1e-14). The remaining two motifs (pattern 9‐10) exhibited more than 100 best hits with 92% identity and an E‐value score ranging from 4e-11 to 1e-11 (Tables 2 & 3 in supplementary material).


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)

Sample of sequence motif in PROSITE format (from 5' to 3' ends) and Pattern matching of ITS motifs of differentgeographical isolates of fasciolid species
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Sample of sequence motif in PROSITE format (from 5' to 3' ends) and Pattern matching of ITS motifs of differentgeographical isolates of fasciolid species
Mentions: A total of 15 ITS2 PROSITE motifs were tested by BLAST analysis against the generalized GenBank database at NCBI (Figure 3). The Fasciola motifs exhibited exact or perfect matches with Fasciola from different geographical isolates with significant E‐value scores. Eight (pattern 1‐8) out of 15 Fasciola motifs exactly matched the sequences of Fasciola isolates from GenBank (best hits = more than 100; 100% of identity; E-values = 2e-16 to 1e-17). Five (pattern 11‐15) showed (best hits = more than 100; 95% identity and significant E‐value ranging from 5e-14 to 1e-14). The remaining two motifs (pattern 9‐10) exhibited more than 100 best hits with 92% identity and an E‐value score ranging from 4e-11 to 1e-11 (Tables 2 & 3 in supplementary material).

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.