title: A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.
abstract: RNA-sequencing (RNA-seq) enables in-depth exploration of transcriptomes, but typical sequencing depth often limits its comprehensiveness. In this study, we generated nearly 3 billion RNA-Seq reads, totaling 341 Gb of sequence, from a Zea mays seedling sample. At this depth, a near complete snapshot of the transcriptome was observed consisting of over 90% of the annotated transcripts, including lowly expressed transcription factors. A novel hybrid strategy combining de novo and reference-based assemblies yielded a transcriptome consisting of 126,708 transcripts with 88% of expressed known genes assembled to full-length. We improved current annotations by adding 4,842 previously unannotated transcript variants and many new features, including 212 maize transcripts, 201 genes, 10 genes with undocumented potential roles in seedlings as well as maize lineage specific gene fusion events. We demonstrated the power of deep sequencing for large transcriptome studies by generating a high quality transcriptome, which provides a rich resource for the research community.
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Martin
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Nicole V
authors.initials: NV
authors.lastname: Johnson
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Gross
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
authors.forename: James
authors.initials: J
authors.lastname: Schnable
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Xiandong
authors.initials: X
authors.lastname: Meng
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Mei
authors.initials: M
authors.lastname: Wang
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Devin
authors.initials: D
authors.lastname: Coleman-Derr
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Erika
authors.initials: E
authors.lastname: Lindquist
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.affiliation: Department of Agronomy and Great Lakes Bioenergy Research Center, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA.
authors.forename: Shawn
authors.initials: S
authors.lastname: Kaeppler
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
authors.affiliation: 1] Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA [2] Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Wang
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D036226:Seedlings / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D003313:Zea mays / Q000235:genetics*
chemical_list: D014157:Transcription Factors