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RNA. 2015 Feb;21(2):230-42. doi: 10.1261/rna.045799.114. Epub 2014 Dec 18.

Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp).

Author information

1
Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan.
2
Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.
3
Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan University Affiliated Research Center, NASA Ames Research Center, Moffett Field, California 94043, USA.
4
Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0882, Japan.
5
Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0882, Japan akio@sfc.keio.ac.jp.

Abstract

MicroRNAs have been identified and analyzed in various model species, but an investigation of miRNAs in nonmodel species is required for a more complete understanding of miRNA evolution. In this study, we investigated the miRNAs of the nonmodel species Triops cancriformis (tadpole shrimp), a "living fossil," whose morphological form has not changed in almost 200 million years. Dramatic ontogenetic changes occur during its development. To clarify the evolution of miRNAs, we comparatively analyzed its miRNAs and the components of its RNAi machinery. We used deep sequencing to analyze small RNA libraries from the six different developmental stages of T. cancriformis (egg, first-fourth instars, and adult), and also analyzed its genomic DNA with deep sequencing. We identified 180 miRNAs (87 conserved miRNAs and 93 novel candidate miRNAs), and deduced the components of its RNAi machinery: the DICER1, AGO1-3, PIWI, and AUB proteins. A comparative miRNA analysis of T. cancriformis and Drosophila melanogaster showed inconsistencies in the expression patterns of four conserved miRNAs. This suggests that although the miRNA sequences of the two species are very similar, their roles differ across the species. An miRNA conservation analysis revealed that most of the conserved T. cancriformis miRNAs share sequence similarities with those of arthropods, although T. cancriformis is called a "living fossil." However, we found that let-7 and DICER1 of T. cancriformis are more similar to those of the vertebrates than to those of the arthropods. These results suggest that miRNA systems of T. cancriformis have evolved in a unique fashion.

KEYWORDS:

T. cancriformis; deep sequencing; development; evolution; microRNA

PMID:
25525151
PMCID:
PMC4338350
DOI:
10.1261/rna.045799.114
[Indexed for MEDLINE]
Free PMC Article

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