Identification and Expression Analyses of miRNAs from Two Contrasting Flower Color Cultivars of Canna by Deep Sequencing.

miRNAs are endogenous small RNA (sRNA) that play critical roles in plant development processes. Canna is an ornamental plant belonging to family Cannaceae. Here, we report for the first time the identification and differential expression of miRNAs in two contrasting flower color cultivars of Canna, Tropical sunrise and Red president. A total of 313 known miRNAs belonging to 78 miRNA families were identified from both the cultivars. Thirty one miRNAs (17 miRNA families) were specific to Tropical sunrise and 43 miRNAs (10 miRNA families) were specific to Red president. Thirty two and 18 putative new miRNAs were identified from Tropical sunrise and Red president, respectively. One hundred and nine miRNAs were differentially expressed in the two cultivars targeting 1343 genes. Among these, 16 miRNAs families targeting 60 genes were involved in flower development related traits and five miRNA families targeting five genes were involved in phenyl propanoid and pigment metabolic processes. We further validated the expression analysis of a few miRNA and their target genes by qRT-PCR. Transcription factors were the major miRNA targets identified. Target validation of a few randomly selected miRNAs by RLM-RACE was performed but was successful with only miR162. These findings will help in understanding flower development processes, particularly the color development in Canna

Two <i>Canna</i> cultivars having contrasting flower color (A) Tropical sunrise (B) Red president.

<p>Two <i>Canna</i> cultivars having contrasting flower color (A) Tropical sunrise (B) Red president.</p

Gene ontology enrichment analysis of the predicted targets of <i>Canna</i> miRNAs.

<p>Categorization of miRNA-targets genes were performed according to the(A) Biological Processes, (B) Molecular function and (C) Cellular component.</p

Differentially expressed miRNA families between TS and RP.

<p>Differentially expressed miRNA families between TS and RP.</p

Flavonoids, Carotenoids, Xanthophyll and Anthocyanin content of TS and RP.

<p>All the measurements were taken in three biological and five technical replicates. Error bars represent standard deviation of biological and technical replicates.</p

Comparison of the miRNA expression levels determined by deep sequencing and qRT-PCR.

<p>Blue and red colors indicate the fold change obtained by deep sequencing and qRT-PCR, respectively. The error bars indicate the standard deviation obtained from biological and technical replicates.</p

Venn diagrams of conserved and unique miRNAs between TS and RP.

<p>(A) Total conserved and unique miRNAs between TS and RP, (B) Conserved and unique miRNA families between TS and RP, (C) Total conserved and unique miRNA* between TS and RP, (D) Conserved and unique miRNA* families between TS and RP.</p

The homology of identified miRNAs with other plant species.

<p>Values on Y axis indicate the number of homological miRNA families between <i>Canna</i> and other plant species.</p

Detection of cleavage site through RLM-RACE.

<p>5' RLM RACE was used to map the cleavage sites. The partial mRNA sequence from the target genes were aligned with the miRNA. The arrow indicates the cleavage site, and the number above the arrow denotes the frequency of the sequenced clones.</p