Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

ABSTRACT: 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.

ORGANISM(S): Zea mays

SUBMITTER: Emanuele De Paoli

PROVIDER: E-GEOD-17339 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Detailed analysis of a contiguous 22-Mb region of the maize genome.

Wei Fusheng F Stein Joshua C JC Liang Chengzhi C Zhang Jianwei J Fulton Robert S RS Baucom Regina S RS De Paoli Emanuele E Zhou Shiguo S Yang Lixing L Han Yujun Y Pasternak Shiran S Narechania Apurva A Zhang Lifang L Yeh Cheng-Ting CT Ying Kai K Nagel Dawn H DH Collura Kristi K Kudrna David D Currie Jennifer J Lin Jinke J Kim Hyeran H Angelova Angelina A Scara Gabriel G Wissotski Marina M Golser Wolfgang W Courtney Laura L Kruchowski Scott S Graves Tina A TA Rock Susan M SM Adams Stephanie S Fulton Lucinda A LA Fronick Catrina C Courtney William W Kramer Melissa M Spiegel Lori L Nascimento Lydia L Kalyanaraman Ananth A Chaparro Cristian C Deragon Jean-Marc JM Miguel Phillip San PS Jiang Ning N Wessler Susan R SR Green Pamela J PJ Yu Yeisoo Y Schwartz David C DC Meyers Blake C BC Bennetzen Jeffrey L JL Martienssen Robert A RA McCombie W Richard WR Aluru Srinivas S Clifton Sandra W SW Schnable Patrick S PS Ware Doreen D Wilson Richard K RK Wing Rod A RA

PLoS genetics 20091120 11

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of tra ...[more]

PMID: 19936048

Publication: 1/2

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Dataset Information

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

Publications

Detailed analysis of a contiguous 22-Mb region of the maize genome.

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