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)

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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.
Email		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
License		This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.