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)


Beyond Bioinformatics

Title

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)

Authors

Pramod Kumar Prasad¹, Veena Tandon¹, Devendra Kumar Biswal², Lalit Mohan Goswami¹ and Anupam Chatterjee³

Affiliation

¹Department of Zoology, North Eastern Hill University, Shillong, Meghalaya, 793022, India

²Bioinformatics Centre, North Eastern Hill University, Shillong, Meghalaya, 793022, India;
³Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, 793033, India.

pramod812@gmail.com; * Corresponding authors

Phone

(+91) 0364 2722312

Fax

(+91) 0364 2722301

Article Type

Hypothesis

Date

received October 10, 2008; revised January 16, 2009; accepted February 07, 2009; published February 28, 2009

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 aBayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNAmolecular 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 (≤ 50 bp in size) can be considered promising tool for trematode species identification. 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.

Keywords

Fasciola hepatica; Fasciola gigantica; secondary structure; internal transcribed spacer; bar coding; motifs

Citation

Prasad et al., Bioinformation 3(7): 314-320 (2009)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics Publishing Group

Copyright

Publisher

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License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.