High-throughput sequencing of small RNAs in Zea mays (maize)

  • Emanuele De Paoli (Contributor)
  • Fusheng Wei (Contributor)
  • Chengzhi Liang (Contributor)
  • Jianwei Zhang (Contributor)
  • Shiguo Zhou (Contributor)
  • Lixing Yang (Contributor)
  • Yujun Han (Contributor)
  • Shiran Pasternak (Contributor)
  • Apurva Narechania (Contributor)
  • Lifang Zhang (Contributor)
  • Kai Ying (Contributor)
  • Kristi Collura (Contributor)
  • David Kudrna (Contributor)
  • Jennifer Currie (Contributor)
  • Jinke Lin (Contributor)
  • Hye Ran Kim (Contributor)
  • Angelina Angelova (Contributor)
  • Gabriel Scara (Contributor)
  • Marina Wissotski (Contributor)
  • Wolfgang Golser (Contributor)
  • Laura Courtney (Contributor)
  • Scott Kruchowski (Contributor)
  • Stephanie Adams (Contributor)
  • Catrina Fronick (Contributor)
  • William Courtney (Contributor)
  • Melissa Kramer (Contributor)
  • Lori Spiegel (Contributor)
  • Lidia Nascimento (Contributor)
  • Ananth Kalyanaraman (Contributor)
  • Cristian Chaparro (Contributor)
  • Ning Jiang (Contributor)
  • Yeisoo Yu (Contributor)
  • Srinivas Aluru (Contributor)
  • Doreen Ware (Contributor)



Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different maize tissues (including leaves, ears and tassels) collected from wild-type plants of the B73 variety. The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, ears and tassels of maize variety B73 (wild-type). Plants were grown in a flood irrigated plot at the University of Arizona (Tucson, AZ, USA) in 2007 and organs were pooled from several plants for each library. Young leaves were collected from 6-weeks-old seedlings. Post-meiotic immature ears were harvested from 10- and 11-week old plants while pre-meiotic tassels were collected from 8-week old plants. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen) and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Lyudmila Sidorenko and Vicki Chandler for providing the plant material and Kan Nobuta for assistance with the computational methods.
Date made available2009

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