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Genome wide identification and functional prediction of long non-coding RNAs in Brassica rapa

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Abstract

Long non-coding RNAs (LncRNAs) are a large, diverse class of RNA molecules that has garnered attention for their potential to regulate gene expression and been identified in various organisms. Here we report the first prediction of lncRNAs in Brassica rapa (B. rapa) genome using computational method. We subjected the publicly available full length cDNA sequences and identified 2237 candidate lncRNAs, characterized their functions based on insilico methods. Housekeeping and small regulatory non-coding RNAs (ncRNAs) were removed from the pool. Although 14–15 % of the total sequences were predicted to be non-coding initially, on filtering only 4.6 % of the total sequences were predicted as lncRNAs carrying a large number of simple repeats. The lncRNAs had an average length of 497 bp and were mapped on each chromosome of B. rapa. They were classified to 4 groups based on their origin. Thirty six motifs involving transcription related activities, signaling mechanism and stress response were identified in the lncRNAs. Repeat elements and neighboring genes of the lncRNAs were analyzed since they were associated in function and regulating the expression of these long non-coding RNAs. We believe that this study would be an initial and reference for any further studies regarding long non-coding RNAs in B. rapa and other Brassica crops.

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Acknowledgments

This work was supported by Golden Seed Project (No.213002-04-4-SB110), Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development Administration (RDA) and Korea Forest Service (KFS). We would also like to thank Dr. Sathishkumar Natarajan, from Sunchon National University for his valuable support.

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  1. Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 305-764, Korea

    Parameswari Paul, Vignesh Dhandapani, Su Ryun Choi & Yong Pyo Lim

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  1. Parameswari Paul
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  2. Vignesh Dhandapani
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  3. Su Ryun Choi
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Correspondence to Yong Pyo Lim.

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Paul, P., Dhandapani, V., Choi, S.R. et al. Genome wide identification and functional prediction of long non-coding RNAs in Brassica rapa . Genes Genom 38, 547–555 (2016). https://doi.org/10.1007/s13258-016-0405-7

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