Abstract
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are short (19–25 nucleotides) non-coding RNA molecules that have large-scale regulatory effects on development and stress responses in plants. Verticillium wilt is a vascular disease in plants caused by the fungal pathogen Verticillium dahliae. The objective of this study is to investigate the transcriptional profile of miRNAs and other small non-coding RNAs in Verticillium–inoculated cotton roots. Four small RNA libraries were constructed from mocked and infected roots of two cotton cultured species which are with different Verticillium wilt tolerance (‘Hai-7124’, Gossypium barbadense L., a Verticillium-tolerant cultivar, and ‘Yi-11’, Gossypium hirsutum L. a Verticillium-sensitive cultivar). The length distribution of obtained small RNAs was significantly different between libraries. There were a total of 215 miRNA families identified in the two cotton species. Of them 14 were novel miRNAs. There were >65 families with different expression between libraries. We also identified two trans-acting siRNAs and thousands of endogenous siRNA candidates, and hundred of them exhibited altered expression after inoculation of Verticillium. Interesting, many siRNAs were found with a perfect match with retrotransposon sequences, suggested that retrotransposons maybe one of sources for the generation of plant endogenous siRNAs. The profiling of these miRNAs and other small non-coding RNAs lay the foundation for further understanding of small RNAs function in the regulation of Verticillium defence responses in cotton roots.
Highlights
MicroRNAs are small, non-coding RNAs known for their roles in regulating gene expression by cleaving or inhibiting the translation of target gene transcripts [1,2]
A global survey of small RNAs in Verticillium–infected organisms will facilitate our understanding of the function and regulatory mechanisms of small RNAs in Verticillium–defence response
High-throughput sequencing was performed to identify small RNAs that expressed in Verticillium–inoculated cotton roots
Summary
MicroRNAs (miRNAs) are small, non-coding RNAs known for their roles in regulating gene expression by cleaving or inhibiting the translation of target gene transcripts [1,2]. They can be encoded in their own genes, which are transcribed by RNA polymerase II or exist in introns of protein-coding genes. Recent advances in high-throughput sequencing methods have revolutionized the identification of low-abundance non-conserved miRNAs. several other classes of small regulatory RNAs, distinguished by their origin and biological function, have been identified in recent years. Other endogenous siRNAs are processed from long double-stranded RNAs and often require RNA-dependent RNA polymerases (RDRPs or RDRs) and plant-specific nuclear RNA polymerase (Pol) IV or V [4,5,6]
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