title: Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.).
abstract: BACKGROUND
  Cotton fiber development undergoes rapid and dynamic changes in a single cell type, from fiber initiation, elongation, primary and secondary wall biosynthesis, to fiber maturation. Previous studies showed that cotton genes encoding putative MYB transcription factors and phytohormone responsive factors were induced during early stages of ovule and fiber development. Many of these factors are targets of microRNAs (miRNAs) that mediate target gene regulation by mRNA degradation or translational repression.
  
  
  RESULTS
  Here we sequenced and analyzed over 4 million small RNAs derived from fiber and non-fiber tissues in cotton. The 24-nucleotide small interfering RNAs (siRNAs) were more abundant and highly enriched in ovules and fiber-bearing ovules relative to leaves. A total of 31 miRNA families, including 27 conserved, 4 novel miRNA families and a candidate-novel miRNA, were identified in at least one of the cotton tissues examined. Among 32 miRNA precursors representing 19 unique miRNA families identified, 7 were previously reported, and 25 new miRNA precursors were found in this study. Sequencing, miRNA microarray, and small RNA blot analyses showed a trend of repression of miRNAs, including novel miRNAs, during ovule and fiber development, which correlated with upregulation of several target genes tested. Moreover, 223 targets of cotton miRNAs were predicted from the expressed sequence tags derived from cotton tissues, including ovules and fibers. The cotton miRNAs examined triggered cleavage in the predicted sites of the putative cotton targets in ovules and fibers.
  
  
  CONCLUSIONS
  Enrichment of siRNAs in ovules and fibers suggests active small RNA metabolism and chromatin modifications during fiber development, whereas general repression of miRNAs in fibers correlates with upregulation of a dozen validated miRNA targets encoding transcription and phytohormone response factors, including the genes found to be highly expressed in cotton fibers. Rapid and dynamic changes in siRNAs and miRNAs may contribute to ovule and fiber development in allotetraploid cotton.
authors.affiliation: Section of Molecular Cell and Developmental Biology, The University of Texas at Austin, One University Station, A-4800, Austin, TX 78712, USA. davidpang@mail.utexas.edu
authors.forename: Mingxiong
authors.initials: M
authors.lastname: Pang
authors.forename: Andrew W
authors.initials: AW
authors.lastname: Woodward
authors.forename: Vikram
authors.initials: V
authors.lastname: Agarwal
authors.forename: Xueying
authors.initials: X
authors.lastname: Guan
authors.forename: Misook
authors.initials: M
authors.lastname: Ha
authors.forename: Vanitharani
authors.initials: V
authors.lastname: Ramachandran
authors.forename: Xuemei
authors.initials: X
authors.lastname: Chen
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Triplett
authors.forename: David M
authors.initials: DM
authors.lastname: Stelly
authors.forename: Z Jeffrey
authors.initials: ZJ
authors.lastname: Chen
mesh_terms: D001483:Base Sequence; D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D055106:Genome-Wide Association Study; D003368:Gossypium / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000235:genetics; D012333:RNA, Messenger / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D018744:DNA, Plant; D035683:MicroRNAs; D009711:Nucleotides; D012333:RNA, Messenger; D034741:RNA, Small Interfering