ArticleScientific reports2014
A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.
Article in Scientific reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 29 citations in OpenAlex.
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- Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes.Nature genetics · 2018Article
- Barley stripe mosaic virus (BSMV) as a virus-induced gene silencing vector in maize seedlings.Virus genes · 2018Article
- Transcript profile analysis reveals important roles of jasmonic acid signalling pathway in the response of sweet potato to salt stress.Scientific reports · 2017Article
- The dynamic landscape of fission yeast meiosis alternative-splice isoforms.Genome research · 2017Article
- A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize.Frontiers in plant science · 2017Article
- Stress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis.Scientific reports · 2016Article
- A survey of the sorghum transcriptome using single-molecule long reads.Nature communications · 2016Article
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- MaizeGDB update: new tools, data and interface for the maize model organism database.Nucleic acids research · 2016Article
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- Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research.BMC genomics · 2015Article
- Article
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12 authors at 3 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
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.
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