Identification of microRNAs involved in betalain metabolism in the green and red sectors of amaranth leaves based on Illumina sequencing data

Amaranth plants are rich in betalains. Additionally, the molecular structure and metabolic pathway of betalains are different in amaranth than in beet. To date, only a few studies have examined the regulatory roles of microRNAs (miRNAs) in betalain biosynthesis in plants. Thus, we constructed small RNA libraries for the red and green sectors of amaranth leaves to identify miRNAs associated with betalain biosynthesis. We identified 239 miRNAs including 198 known and 41 novel miRNAs. 493 target genes for the 239 miRNAs were detected in an amaranth transcriptome database. The validation of the expression of 20 miRNAs and nine target genes in a quantitative real-time polymerase chain reaction assay revealed the miRNAs and target genes that were differentially expressed in the two leaf sectors. The miRNAs involved in betalain metabolism in amaranth plants were identified by Illumina sequencing platform. The data presented herein may provide insights into the regulation molecular mechanisms for betalain biosynthesis in amaranth and other plant species.