Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Characterization of maize B73 transcriptome by hybrid sequencing

ABSTRACT: Zea mays is a leading model for elucidating transcriptional networks in plants, aided by increasingly refined studies of the transcriptome atlas across spatio-temporal, developmental, and environmental dimensions. Limiting this progress are uncertainties about the complete structure mRNA transcripts, particularly with respect to alternatively spliced isoforms. Although second-generation RNA-seq provides a quantitative assay for transcriptional and posttranscriptional events, the accurate reconstruction of full-length mRNA isoforms is challenging with short-read technologies. By producing much longer reads, third generation sequencing offers to solve the assembly problem, but can suffer from lower read accuracy and throughput. Here, we combine these complementary technologies to define and quantify high-confidence transcript isoforms in maize. Six tissues (root, pollen, embryo, endosperm, immature ear, and immature tassel) of the B73 inbred line were used for mRNA sequencing with the Illumina Hiseq2000 PE101 platform to comprehensively quantitate gene/isoform expression. In parallel, intact cDNAs from the same samples were sequenced using the PacBio RS II platform. The latter used six size fractionated libraries (<1kb, 1-2kb, 2-3kb, 3kb-5kb, 4-6kb,>5kb) to generate more than 2 million full length reads. Preliminary findings suggest that mechanisms of alternative splicing are differentially employed between different tissues. In addition, these data show promise to dramatically improve the status of maize genome annotation, with the detection of previously unidentified transcript isoforms, and uncovering previously unrecognized genes. This submission is data of Illumina Hiseq2000 PE101 reads.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Zea mays

SUBMITTER: Bo Wang

PROVIDER: E-MTAB-3826 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.

Wang Bo B Tseng Elizabeth E Regulski Michael M Clark Tyson A TA Hon Ting T Jiao Yinping Y Lu Zhenyuan Z Olson Andrew A Stein Joshua C JC Ware Doreen D

Nature communications 20160624

Zea mays is an important genetic model for elucidating transcriptional networks. Uncertainties about the complete structure of mRNA transcripts limit the progress of research in this system. Here, using single-molecule sequencing technology, we produce 111,151 transcripts from 6 tissues capturing ∼70% of the genes annotated in maize RefGen_v3 genome. A large proportion of transcripts (57%) represent novel, sometimes tissue-specific, isoforms of known genes and 3% correspond to novel gene loci. I ...[more]

PMID: 27339440

Similar Datasets

Project description: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.

Dataset Information

Characterization of maize B73 transcriptome by hybrid sequencing

Publications

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets