Genome-Wide Profiling of miRNAs and Other Small Non-Coding RNAs in the <em>Verticillium dahliae</em>–Inoculated Cotton Roots

<div><p>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 <em>Verticillium dahliae</em>. 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’, <em>Gossypium barbadense</em> L., a Verticillium-tolerant cultivar, and ‘Yi-11’, <em>Gossypium hirsutum</em> 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.</p> </div

Abundance of two trans-acting siRNA genes (<i>TAS3</i>).

<p>Abundance of two trans-acting siRNA genes (<i>TAS3</i>).</p

The small RNAs with a perfect match to U75227.1|GBU75227 <i>G. barbadense</i> strain Giza 75 <i>copia</i> retrotransposon.

<p>The color represents abundance of the sequences.</p

Distribution of miRNA counts over different tag abundance categories from the four libraries.

<p>Distribution of miRNA counts over different tag abundance categories from the four libraries.</p

Summary statistics of small RNAs sequenced from roots.

<p>Summary statistics of small RNAs sequenced from roots.</p

The length distribution of small RNAs in <i>G. hirsutum</i> roots (A) and <i>G. barbadense</i> roots (B).

<p>Gh-mock: mock-infected <i>G. hirsutum</i> roots; Gh-inft: Verticillium-infected <i>G. hirsutum</i> roots; Gb-mock: mock-infected <i>G. barbadense</i> roots; Gb-inft: Verticillium-infected <i>G. barbadense</i> roots.</p

Differentially expressed miRNAs between libraries.

<p>Gh-mock: mock-infected <i>G. hirsutum</i> roots; Gh-inft: Verticillium-infected <i>G. hirsutum</i> roots; Gb-mock: mock-infected <i>G. barbadense</i> roots; Gb-inft: Verticillium-infected <i>G. barbadense</i> roots.</p

The possible relation of ROS, DNA methylation, SNPv and SNPr.

<p>The possible relation of ROS, DNA methylation, SNPv and SNPr.</p

Salt tolerance index and numbers of SNPv in different varieties.

<p>Salt tolerance index and numbers of SNPv in different varieties.</p

Distribution on the chromosomes of SNPv of eight varieties and chip SNP.

<p>1~4: the salt sensitive varieties: Hengmian3, GK50, Xinyan96-48, ZhongS9612; 5~8: the salt tolerant varieties: CRI35, Zhong9807, CRI 44, Kanghuangwei164; 9: Illumina Cotton SNP 70K Chip.</p