Abstract

Sturgeons are considered as living fossils and have very high evolutionary, economical and conservation values. The multiploidy of sturgeon that has been caused by chromosome duplication may lead to the emergence of new microRNAs (miRNAs) involved in the ploidy and physiological processes. In the present study, we performed the first sturgeon miRNAs analysis by RNA-seq high-throughput sequencing combined with expression assay of microarray and real-time PCR, and aimed to discover the sturgeon-specific miRNAs, confirm the expressed pattern of miRNAs and illustrate the potential role of miRNAs-targets on sturgeon biological processes. A total of 103 miRNAs were identified, including 58 miRNAs with strongly detected signals (signal >500 and P≤0.01), which were detected by microarray. Real-time PCR assay supported the expression pattern obtained by microarray. Moreover, co-expression of 21 miRNAs in all five tissues and tissue-specific expression of 16 miRNAs implied the crucial and particular function of them in sturgeon physiological processes. Target gene prediction, especially the enriched functional gene groups (369 GO terms) and pathways (37 KEGG) regulated by 58 miRNAs (P<0.05), illustrated the interaction of miRNAs and putative mRNAs, and also the potential mechanism involved in these biological processes. Our new findings of sturgeon miRNAs expand the public database of transcriptome information for this species, contribute to our understanding of sturgeon biology, and also provide invaluable data that may be applied in sturgeon breeding.

Highlights

  • Sturgeons, are believed to have separated from other teleosts over 250 MYA, and are referred as living fossils providing a key phylogenetic position for evolutionary studies on vertebrates [1]

  • In-depth study of sturgeon miRNAs would improve the knowledge of sturgeon ploidy, and evolutionary history of sturgeons and vertebrates

  • Our study shows that total 58 of 103 microRNAs were confirmed by both Illumina TruSeq sequencing and microarray in Amur sturgeon Acipenser schrenckii, including 21 miRNAs co-expressed in all five tissues and 16 which have tissue-specific expression

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Summary

Introduction

Sturgeons (order: Acipenseriformes, infraclass: Chondrostei), are believed to have separated from other teleosts over 250 MYA, and are referred as living fossils providing a key phylogenetic position for evolutionary studies on vertebrates [1]. A previous study showed that microRNAs (miRNAs) in Arabidopsis thaliana evolved with a process of genome-wide duplication followed by dispersal and diversification, and the duplicated copies of miRNAs may acquire new functionality during their evolution [6]. A later study proved that almost all of miRNAs of Rainbow trout (Oncorhynchus mykiss) have been retained as duplicated copies [7]. These results indicated that, by chromosome duplication, new miRNAs in sturgeon may be evolved, and reflect new functions. In-depth study of sturgeon miRNAs would improve the knowledge of sturgeon ploidy, and evolutionary history of sturgeons and vertebrates

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