Giardia lamblia transcriptome analysis using TSS-Seq and RNA-Seq.

Mohammed E M Tolba,Seiki Kobayashi,Yutaka Suzuki,Mihoko Imada,Sumio Sugano

doi:10.1371/journal.pone.0076184

Mohammed E M Tolba, Seiki Kobayashi + Show 3 more

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https://doi.org/10.1371/journal.pone.0076184

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Journal: PloS one	Publication Date: Oct 7, 2013
Citations: 19	License type: CC BY 4.0

Affiliation: Assiut University, The University of Tokyo, Keio University

Abstract

Giardia lamblia is a protozoan parasite that is found worldwide and has both medical and veterinary importance. We applied the transcription start sequence (TSS-seq) and RNA sequence (RNA-seq) techniques to study the transcriptome of the assemblage A WB strain trophozoite. We identified 8000 transcription regions (TR) with significant transcription. Of these regions, 1881 TRs were more than 500 nucleotides upstream of an annotated ORF. Combining both techniques helped us to identify 24 ORFs that should be re-annotated and 60 new ORFs. From the 8000 TRs, we were able to identify an AT-rich consensus that includes the transcription initiation site. It is possible that transcription that was previously thought to be bidirectional is actually unidirectional.

Highlights

Giardia lamblia, a member of the family Hexamitidae, is a diplomonad parasitic protozoan that infects humans and that was discovered by Leeuwenhoek (1681)
We aimed to study the relationship between transcription start sites and annotated genes, to confirm known data about Giardia, to identify possible new open reading frames (ORF) and to determine whether bidirectional transcription is due to conserved motifs
We have applied the transcription start sequence (TSS-seq) technique to analyse the TSSs of trophozoites of the assemblage A strain of Giardia lamblia, WB clone, ATCC50803

Summary

Introduction

Giardia lamblia ( called Giardia intestinalis), a member of the family Hexamitidae, is a diplomonad parasitic protozoan that infects humans and that was discovered by Leeuwenhoek (1681). Giardia has a worldwide distribution and infects a wide range of animals in addition to humans. It is a common cause of diarrhea in both developed and developing countries. Giardia is the most commonly detected human intestinal parasite in the United States [1,2,3]. The life cycle of Giardia is simple, containing only the trophozoite and cyst stages. The exact stimulus for encystation remains unknown, trophozoites begin to encyst in the lower part of the small intestine, and cysts passed in stools are already mature and infective [6,7]

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