Genome-Wide Analysis of MicroRNAs in Sacred Lotus, Nelumbo nucifera (Gaertn) Yun Zheng & Guru Jagadeeswaran & Kanchana Gowdu & Nian Wang & Shaohua Li & Ray Ming & Ramanjulu Sunkar Received: 29 April 2013 / Accepted: 3 July 2013 # Springer Science+Business Media New York 2013 Abstract MicroRNAs (miRNAs) are small non-coding reg- ulatory RNAs that degrade or repress protein synthesis of their messenger RNA targets. This mode of posttranscrip- tional gene regulation is critical for plant growth and devel- opment as well as adaptation to stress conditions. Sacred lotus (Nelumbo nucifera) is a land plant but adapted to the aquatic environment. It is a basal eudicot in the order Proteales, with significant taxonomic importance. Thus iden- tification of miRNAs in sacred lotus could provide informa- tion about miRNA evolution, particularly the conservation as well as divergence of miRNAs in dicots. To identify conserved and novel miRNAs in sacred lotus, small RNA libraries from leaves and flowers were sequenced as well as computational strategy was employed. These approaches resulted in identification of 81 miRNAs that can be grouped into 41 conserved/known miRNA families and 52 novel miRNAs forming 49 novel miRNA families. Using 3 mis- matches between miRNAs and their mRNA targets as cutoff, we have predicted 137 genes as targets for the conserved and known miRNAs. Overall, this analysis provided a glimpse of miRNA-dependent posttranscriptional gene regulations in sacred lotus. Keywords MicroRNAs . MicroRNA targets . Post- transcriptional gene regulation . Sacred lotus . Small RNAs Abbreviations AGO Argonaute ARF Auxin response factor AP2-like Apetala 2-like transcription factor CSD Cu/Zn superoxide dismutase DCL1 Dicer like-1 GRFs Growth regulating factors HD-Zip factors Homeodomain leucine zipper family of transcription factors HEN1 Hua Enhancer 1 HYL1 Hyponastic leaves 1 miRNAs MicroRNAs NAC factors NAM, ATAF1/2 and CUC2 domain containing transcription factors NBS-LRR genes Nucleoside-binding site leucine rich repeat genes RISC RNA-induced silencing complex RPTM Reads per ten million SE Serrate 1 SPL Squamosa promoter binding protein-like tasiRNAs Trans-acting small interfering RNAs TCP factors Teosinte branched 1, Cycloidea, PCF (TCP)-domain protein family TIR1 Transport inhibitor response 1 Communicated by: Luiz Vieira Electronic supplementary material The online version of this article (doi:10.1007/s12042-013-9127-z) contains supplementary material, which is available to authorized users. Y. Zheng : G. Jagadeeswaran : K. Gowdu : R. Sunkar Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74074, USA Y. Zheng Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai 200433, China N. Wang : S. Li Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China R. Ming Department of Plant Biology, University of Illinois, UIUC, Urbana Champaign, IL, USA R. Sunkar (*) Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA e-mail: ramanjulu.sunkar@okstate.edu Tropical Plant Biol. DOI 10.1007/s12042-013-9127-z