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Volume 5, Issue 4, Pages 889-900 (July 2012) A Comparative miRNAome Analysis Reveals Seven Fiber Initiation-Related and 36 Novel miRNAs in Developing Cotton Ovules Zheng-Ming Wang, Wei Xue, Chun-Juan Dong, Long-Guo Jin, Shao-Min Bian, Chuan Wang, Xiu-Yun Wu, Jin-Yuan Liu Molecular Plant Volume 5, Issue 4, Pages 889-900 (July 2012) DOI: 10.1093/mp/ssr094 Copyright © 2012 The Authors. All rights reserved. Terms and Conditions

Figure 1. Length Distribution of Small RNAs in Developing Cotton Ovules (–3 to +3 dpa). Molecular Plant 2012 5, 889-900DOI: (10.1093/mp/ssr094) Copyright © 2012 The Authors. All rights reserved. Terms and Conditions

Figure 2. Northern Blot Analysis of the Conserved miRNA Families and the Newly Identified miRNAs in Cotton Ovules at –3, –1, 0, +1, and +3 dpa from Wild-Type Upland Cotton and the fl Mutant, Respectively. The numbers under the blots indicate the relative abundance of miRNAs, which was calculated using U6 as a loading control. Molecular Plant 2012 5, 889-900DOI: (10.1093/mp/ssr094) Copyright © 2012 The Authors. All rights reserved. Terms and Conditions

Figure 3 Net Increase or Decrease of Normalized Sequence Reads of the Conserved miRNA Families and the Newly Identified miRNA Families in the Wild-Type Library, Relative to the Fiberless Mutant Libraries. Those with a relative change greater than 30% are highlighted in boldface. Molecular Plant 2012 5, 889-900DOI: (10.1093/mp/ssr094) Copyright © 2012 The Authors. All rights reserved. Terms and Conditions

Figure 4 Validation and Expression Analysis of Target Genes. (A) Mapping of target mRNA cleavage sites by RLM-RACE. The arrows indicate the cleavage sites and the numbers show the frequency of clones sequenced. (B) Quantitative real-time PCR analysis of the target mRNAs of miRNAs. The data represent the mean values ± SD of three replicates. Molecular Plant 2012 5, 889-900DOI: (10.1093/mp/ssr094) Copyright © 2012 The Authors. All rights reserved. Terms and Conditions

Figure 5 A Possible Functional Network of Fiber Initiation-Related miRNAs in Cotton Ovules. The arrows indicate positive regulation and the nail shapes represent negative regulation. SCL, Scarecrow-like family transcription factor; ARF3, auxin response factor 3; GASA, GASA family protein; LIM, LIM domain protein; SPL9, Squamosa promoter-binding protein-like 9; PSF, pre-mRNA splicing factor. Molecular Plant 2012 5, 889-900DOI: (10.1093/mp/ssr094) Copyright © 2012 The Authors. All rights reserved. Terms and Conditions