RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacksReport as inadecuate

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BMC Genomics

, 14:214

Non-human and non-rodent vertebrate genomics


BackgroundNon-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.

ResultsWe 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.

ConclusionsOur 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.

KeywordsStickleback Speciation Variation miRNA piRNA Ecology Variation AbbreviationsmiRNAmicroRNA

mRNAmessenger RNA

piRNAPiwi-interacting RNA

LGlinkage group

RPMreads per million

PCAprincipal component analysis

ANOVAanalysis of variance

tRNAtransfer RNA

rRNAribosomal RNA.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-214 contains supplementary material, which is available to authorized users.

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Author: Jun Kitano - Kohta Yoshida - Yutaka Suzuki

Source: https://link.springer.com/

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