ArticleNature communications2016
Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 304 papers.
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304 citing papers in PubMed.
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- Differences in Peripheral Blood Gene Expression of Xinjiang Brown Cattle with Varying Somatic Cell Counts.Biology · 2026Article
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- Isoform-resolved transcriptomics reveals stage-specific isoform switching and protein domain remodeling inTranscription · 2026Article
- Full-length transcriptome sequencing analysis and characterization of MADS-box genes in Rhododendron fortunei.BMC plant biology · 2026Article
- Full-length transcriptome atlas of porcine skeletal muscle reveals isoform-resolved genetic regulatory mechanisms for muscle growth.BMC genomics · 2026Article
- Long-read sequencing and proteomics reveal blood transcriptome and protein expression profiles in multiple primary lung cancers.BMC cancer · 2026Article
- Combined SMRT and Illumina RNA Sequencing Reveals the Alternative Splicing-Mediated Regulation of Anthocyanin Accumulation in Potato (Plants (Basel, Switzerland) · 2026Article
- Full-Length transcriptome assembly and SSR marker development for Spinibarbus hollandi using PacBio SMRT sequencing.Scientific reports · 2026Article
- Transcript isoforms and alternative splicing in polyploid Brassica napus under heat and cold stress.Annals of botany · 2026Article
- Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research.Nucleic acids research · 2026Article
- Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.Bioinformatics advances · 2026Article
- Genome-wide identification and analysis of the FLA gene family in maize (Zea mays L.) and its expression in response to abiotic stresses.BMC plant biology · 2025Article
- Identification of maize genes that condition early systemic infection of sugarcane mosaic virus through single-cell transcriptomics.Plant communications · 2025Article
- Integrating Arabidopsis and crop species gene discovery for crop improvement.The Plant cell · 2025Review
244 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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. In other cases, the identified transcripts have improved existing gene models. Averaging across all six tissues, 90% of the splice junctions are supported by short reads from matched tissues. In addition, we identified a large number of novel long non-coding RNAs and fusion transcripts and found that DNA methylation plays an important role in generating various isoforms. Our results show that characterization of the maize B73 transcriptome is far from complete, and that maize gene expression is more complex than previously thought.
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