The hot pepper (Capsicum annuum) microRNA transcriptome reveals novel and conserved targets: a foundation for understanding MicroRNA functional roles in hot pepper

• Published in: PloS one 2013-05, Vol.8 (5), p.e64238-e64238
• Main Authors: Hwang, Dong-Gyu, Park, June Hyun, Lim, Jae Yun, Kim, Donghyun, Choi, Yourim, Kim, Soyoung, Reeves, Gregory, Yeom, Seon-In, Lee, Jeong-Soo, Park, Minkyu, Kim, Seungill, Choi, Ik-Young, Choi, Doil, Shin, Chanseok
• Format: Article
• Language: English
• Subjects: Agricultural biotechnology; Agriculture; Base Sequence; Bioinformatics; Biology; Capsicum - genetics; Capsicum - growth & development; Capsicum annuum; Cloning; Conserved Sequence; Deoxyribonucleic acid; Developmental stages; DNA; DNA methylation; Environmental management; Epigenetics; Evolution; Flowers & plants; Fruit - genetics; Fruit - growth & development; Gene expression; Gene Expression Profiling; Genomes; Genomics; High-Throughput Nucleotide Sequencing; Life sciences; Methyltransferase; MicroRNAs; MicroRNAs - genetics; miRNA; Molecular Sequence Data; Next-generation sequencing; Peppers; Phase transitions; Plant sciences; Plants (botany); Ribonucleic acid; RNA; RNA polymerase; RNA, Plant - genetics; Sequence Analysis, RNA; Solanaceae
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0064238

MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21 nt in length which play important roles in regulating gene expression in plants. Although many miRNA studies have focused on a few model plants, miRNAs and their target genes remain largely unknown in hot pepper (Capsicum annuum), one of the most important crops cultivated worldwide. Here, we employed high-throughput sequencing technology to identify miRNAs in pepper extensively from 10 different libraries, including leaf, stem, root, flower, and six developmental stage fruits. Based on a bioinformatics pipeline, we successfully identified 29 and 35 families of conserved and novel miRNAs, respectively. Northern blot analysis was used to validate further the expression of representative miRNAs and to analyze their tissue-specific or developmental stage-specific expression patterns. Moreover, we computationally predicted miRNA targets, many of which were experimentally confirmed using 5' rapid amplification of cDNA ends analysis. One of the validated novel targets of miR-396 was a domain rearranged methyltransferase, the major de novo methylation enzyme, involved in RNA-directed DNA methylation in plants. This work provides the first reliable draft of the pepper miRNA transcriptome. It offers an expanded picture of pepper miRNAs in relation to other plants, providing a basis for understanding the functional roles of miRNAs in pepper.