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Genome Biology and Evolution Advance Access originally published online on July 6, 2009
Genome Biology and Evolution (2009) Vol. 2009:165; doi:10.1093/gbe/evp017 published on July 24, 2009
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© 2009 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

High Throughput Genome-Wide Survey of Small RNAs from the Parasitic Protists Giardia intestinalis and Trichomonas vaginalis

Xiaowei (Sylvia) Chen*, Lesley J. Collins*,{dagger}, Patrick J. Biggs* and David Penny*,{dagger}

* Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
{dagger} Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand

E-mail: sylvia.x.chen{at}gmail.com.


  Abstract

RNA interference (RNAi) is a set of mechanisms which regulate gene expression in eukaryotes. Key elements of RNAi are small sense and antisense RNAs from 19 to 26 nt generated from double-stranded RNAs. MicroRNAs (miRNAs) are a major type of RNAi-associated small RNAs and are found in most eukaryotes studied to date. To investigate whether small RNAs associated with RNAi appear to be present in all eukaryotic lineages, and therefore present in the ancestral eukaryote, we studied two deep-branching protozoan parasites, Giardia intestinalis and Trichomonas vaginalis. Little is known about endogenous small RNAs involved in RNAi of these organisms. Using Illumina Solexa sequencing and genome-wide analysis of small RNAs from these distantly related deep-branching eukaryotes, we identified 10 strong miRNA candidates from Giardia and 11 from Trichomonas. We also found evidence of Giardia short-interfering RNAs potentially involved in the expression of variant-specific surface proteins. In addition, eight new small nucleolar RNAs from Trichomonas are identified. Our results indicate that miRNAs are likely to be general in ancestral eukaryotes and therefore are likely to be a universal feature of eukaryotes.

Keywords: ancestral eukaryotes, miRNA, protists, RNA evolution

Accepted June 30, 2009

James Lake, Associate Editor


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