title: Catalog of Erycina pusilla miRNA and categorization of reproductive phase-related miRNAs and their target gene families.
abstract: The orchid Erycina pusilla has a short life cycle and relatively low chromosome number, making it a potential model plant for orchid functional genomics. To that end, small RNAs (sRNAs) from different developmental stages of different organs were sequenced. In this miRNA mix, 33 annotated miRNA families and 110 putative miRNA-targeted transcripts were identified in E. pusilla. Fifteen E. pusilla miRNA target genes were found to be similar to those in other species. There were putative novel miRNAs identified by 3 different strategies. The genomic sequences of the four miRNAs that were identified using rice genome as the reference can form the stem loop structure. The t0000354 miRNA, identified using rice genome sequences and a Phalaenopsis study, had a high read count. The target gene of this miRNA is MADS (unigene30603), which belongs to the AP3-PI subfamily. The most abundant miRNA was E. pusilla miR156 (epu-miR156), orthologs of which work to maintain the vegetative phase by repressing the expression of the SQUAMOSA promoter-binding-like (SPL) transcription factors. Fifteen genes in the E. pusilla SPL (EpSPL) family were identified, nine of which contained the putative epu-miR156 target site. Target genes of epu-miR172, also a key regulator of developmental changes in the APETALA2 (EpAP2) family, were identified. Experiments using 5'RLM-RACE demonstrated that the genes EpSPL1, 2, 3, 4, 7, 9, 10, 14 and EpAP2-9, -10, -11 were regulated by epu-miR156 and epu-miR172, respectively.
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan. cslin99@gate.sinica.edu.tw
authors.forename: Choun-Sea
authors.initials: CS
authors.lastname: Lin
authors.forename: Jeremy J W
authors.initials: JJ
authors.lastname: Chen
authors.forename: Yao-Ting
authors.initials: YT
authors.lastname: Huang
authors.forename: Chen-Tran
authors.initials: CT
authors.lastname: Hsu
authors.forename: Hsiang-Chia
authors.initials: HC
authors.lastname: Lu
authors.forename: Ming-Lun
authors.initials: ML
authors.lastname: Chou
authors.forename: Li-Chi
authors.initials: LC
authors.lastname: Chen
authors.forename: Chia-I
authors.initials: CI
authors.lastname: Ou
authors.forename: Der-Chih
authors.initials: DC
authors.lastname: Liao
authors.forename: Ysuan-Yu
authors.initials: YY
authors.lastname: Yeh
authors.forename: Song-Bing
authors.initials: SB
authors.lastname: Chang
authors.forename: Su-Chen
authors.initials: SC
authors.lastname: Shen
authors.forename: Fu-Huei
authors.initials: FH
authors.lastname: Wu
authors.forename: Ming-Che
authors.initials: MC
authors.lastname: Shih
authors.forename: Ming-Tsair
authors.initials: MT
authors.lastname: Chan
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001483:Base Sequence; D053898:Biosynthetic Pathways / Q000235:genetics; D005091:Exons / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D007438:Introns / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism*; D008969:Molecular Sequence Data; D005810:Multigene Family; D029595:Orchidaceae / Q000235:genetics*; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D012098:Reproduction / Q000235:genetics
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant