title: The hot pepper (Capsicum annuum) microRNA transcriptome reveals novel and conserved targets: a foundation for understanding MicroRNA functional roles in hot pepper.
abstract: 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.
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.
authors.forename: Dong-Gyu
authors.initials: DG
authors.lastname: Hwang
authors.forename: June Hyun
authors.initials: JH
authors.lastname: Park
authors.forename: Jae Yun
authors.initials: JY
authors.lastname: Lim
authors.forename: Donghyun
authors.initials: D
authors.lastname: Kim
authors.forename: Yourim
authors.initials: Y
authors.lastname: Choi
authors.forename: Soyoung
authors.initials: S
authors.lastname: Kim
authors.forename: Gregory
authors.initials: G
authors.lastname: Reeves
authors.forename: Seon-In
authors.initials: SI
authors.lastname: Yeom
authors.forename: Jeong-Soo
authors.initials: JS
authors.lastname: Lee
authors.forename: Minkyu
authors.initials: M
authors.lastname: Park
authors.forename: Seungill
authors.initials: S
authors.lastname: Kim
authors.forename: Ik-Young
authors.initials: IY
authors.lastname: Choi
authors.forename: Doil
authors.initials: D
authors.lastname: Choi
authors.forename: Chanseok
authors.initials: C
authors.lastname: Shin
mesh_terms: D001483:Base Sequence; D002212:Capsicum / Q000235:genetics* / Q000254:growth & development; D017124:Conserved Sequence; D005638:Fruit / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D018749:RNA, Plant / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant