Open Access Highly Accessed Research article

Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya

Rishi Aryal1, Xiaozeng Yang2, Qingyi Yu3, Ramanjulu Sunkar4, Lei Li2 and Ray Ming1*

Author Affiliations

1 Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

2 Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA

3 Texas AgriLife Research Center, Department of Plant Pathology and Microbiology, Texas A&M University, Weslaco, TX, 78596, USA

4 Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA

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BMC Genomics 2012, 13:682  doi:10.1186/1471-2164-13-682

Published: 5 December 2012

Additional files

Additional file 1: Figure S1:

Comparison of specific reads in 3 sRNA libraries. Figure S2. qPCR verification of predicted miRNAs. Figure S3. Schematic representation of mapped sRNA reads showing how the single copy reads differ form each other. Figure S4. Percentage of single copy reads in sRNA libraries from 6 plant species. Figure S5. Purine-Pyrimidine distribution on sRNA datasets of 6 plant species obtained from NCBI’s GEO database. Figure S6. Weblogo picture showing frequency of different nucleotides on miRNAs from miRBase. Figure S7. Size distribution of sRNA reads mapped to the PRSV genome. The purple box encloses the total reads from different libraries mapped to the genome. Figure S8. Stem loop structure of all annotated miRNAs from papaya. Table S1. Deep sequencing reads and mapping to the draft genome. Table S2. List of annotated miRNAs in papaya. Table S3. Number of miRNAs reported in miRBase from 9 model plant species. Table S4. List of stem-loop primers and forward primers used to validate the predicted miRNAs.

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