ArticlePlant physiology2013
RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing.
Article in Plant physiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 130 papers.
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130 citing papers in PubMed, 244 citations in OpenAlex.
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- Weighted gene co-expression network analysis - based selection of hub genes related to phenolic and volatile compounds and seed coat color in sorghum.BMC plant biology · 2025Article
- Global identification and regulatory network analysis reveal the significant roles of lncRNAs during anther and pollen development in Arabidopsis.Plant cell reports · 2025Article
- Fixation of Expression Divergences by Natural Selection inInternational journal of molecular sciences · 2024Article
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- Arabidopsis class A S-acyl transferases modify the pollen receptors LIP1 and PRK1 to regulate pollen tube guidance.The Plant cell · 2024Article
- The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize.The Plant cell · 2024Article
- A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture.G3 (Bethesda, Md.) · 2023Article
- Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis.Plant reproduction · 2023Article
- Exploration into Natural Variation Genes Associated with Determinate and Capitulum-like Inflorescence inInternational journal of molecular sciences · 2023Article
- Transcriptomic Insight into the Pollen Tube Growth ofPlants (Basel, Switzerland) · 2023Article
- A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture.bioRxiv : the preprint server for biology · 2023Article
- Article
- Cell-type-specific alternative splicing in the Arabidopsis germline.Plant physiology · 2023Article
- Thermosensitivity of pollen: a molecular perspective.Plant cell reports · 2023Review
- Transcriptome profiling reveals the roles of pigment formation mechanisms in yellow Paeonia delavayi flowers.Molecular genetics and genomics : MGG · 2023Article
- Building a pipeline to identify and engineer constitutive and repressible promoters.Quantitative plant biology · 2023Article
- Salt Stress Tolerance inPlants (Basel, Switzerland) · 2022Article
70 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Pollen grains of Arabidopsis (Arabidopsis thaliana) contain two haploid sperm cells enclosed in a haploid vegetative cell. Upon germination, the vegetative cell extrudes a pollen tube that carries the sperm to an ovule for fertilization. Knowing the identity, relative abundance, and splicing patterns of pollen transcripts will improve our understanding of pollen and allow investigation of tissue-specific splicing in plants. Most Arabidopsis pollen transcriptome studies have used the ATH1 microarray, which does not assay splice variants and lacks specific probe sets for many genes. To investigate the pollen transcriptome, we performed high-throughput sequencing (RNA-Seq) of Arabidopsis pollen and seedlings for comparison. Gene expression was more diverse in seedling, and genes involved in cell wall biogenesis were highly expressed in pollen. RNA-Seq detected at least 4,172 protein-coding genes expressed in pollen, including 289 assayed only by nonspecific probe sets. Additional exons and previously unannotated 5' and 3' untranslated regions for pollen-expressed genes were revealed. We detected regions in the genome not previously annotated as expressed; 14 were tested and 12 were confirmed by polymerase chain reaction. Gapped read alignments revealed 1,908 high-confidence new splicing events supported by 10 or more spliced read alignments. Alternative splicing patterns in pollen and seedling were highly correlated. For most alternatively spliced genes, the ratio of variants in pollen and seedling was similar, except for some encoding proteins involved in RNA splicing. This study highlights the robustness of splicing patterns in plants and the importance of ongoing annotation and visualization of RNA-Seq data using interactive tools such as Integrated Genome Browser.
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