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Open Access Highly Accessed Research article

RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks

Jun Kitano12*, Kohta Yoshida1 and Yutaka Suzuki3

Author Affiliations

1 Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan

2 PRESTO, Japan Science and Technology Agency, Honcho Kawaguchi, Saitama 332-0012, Japan

3 Department of Medical Genome Sciences, the University of Tokyo, 5-1-5 Kashiwanoha Kashiwa, Chiba 277-8562, Japan

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BMC Genomics 2013, 14:214  doi:10.1186/1471-2164-14-214

Published: 2 April 2013



Non-coding small RNAs, ranging from 20 to 30 nucleotides in length, mediate the regulation of gene expression and play important roles in many biological processes. One class of small RNAs, microRNAs (miRNAs), are highly conserved across taxa and mediate the regulation of the chromatin state and the post-transcriptional regulation of messenger RNA (mRNA). Another class of small RNAs is the Piwi-interacting RNAs, which play important roles in the silencing of transposons and other functional genes. Although the biological functions of the different small RNAs have been elucidated in several laboratory animals, little is known regarding naturally occurring variation in small RNA transcriptomes among closely related species.


We employed next-generation sequencing technology to compare the expression profiles of brain small RNAs between sympatric species of the Japanese threespine stickleback (Gasterosteus aculeatus). We identified several small RNAs that were differentially expressed between sympatric Pacific Ocean and Japan Sea sticklebacks. Potential targets of several small RNAs were identified as repetitive sequences. Female-biased miRNA expression from the old X chromosome was also observed, and it was attributed to the degeneration of the Y chromosome.


Our results suggest that expression patterns of small RNA can differ between incipient species and may be a potential mechanism underlying differential mRNA expression and transposon activity.

Stickleback; Speciation; Variation; miRNA; piRNA; Ecology; Variation