ArticleGenome biology2014
Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 82 citations in OpenAlex.
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- Mining of Root-Specific Expression Genes and Their Core Cis-Regulatory Elements in Plants.International journal of molecular sciences · 2025Article
- MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.Nature communications · 2024Article
- Genome-wide investigation of the LARP gene family: focus on functional identification and transcriptome profiling of ZmLARP6c1 in maize pollen.BMC plant biology · 2024Article
- Transcriptome analysis of ovules offers early developmental clues after fertilization in3 Biotech · 2023Article
- The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation.The Plant cell · 2022Article
- DNA demethylation affects imprinted gene expression in maize endosperm.Genome biology · 2022Article
- Consequences of whole genome duplication for 2n pollen performance.Plant reproduction · 2021Review
- ZmCCT regulates photoperiod-dependent flowering and response to stresses in maize.BMC plant biology · 2021Article
- Characterization of novel pollen-expressed transcripts reveals their potential roles in pollen heat stress response in Arabidopsis thaliana.Plant reproduction · 2021Article
- A Maize Male Gametophyte-Specific Gene Encodes ZmLARP6c1, a Potential RNA-Binding Protein Required for Competitive Pollen Tube Growth.Frontiers in plant science · 2021Article
- Evolutionary Genomics of Plant Gametophytic Selection.Plant communications · 2020Review
- Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions.The Plant cell · 2020Article
- High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements.PLoS genetics · 2020Article
- Genome-wide identification, phylogenetic and expression analysis of the maize HECT E3 ubiquitin ligase genes.Genetica · 2019Article
- Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits.Plant biotechnology journal · 2019Article
- Fine-Tuning the Expression of Duplicate Genes by Translational Regulation inFrontiers in plant science · 2019Article
- Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry.Plant physiology · 2018Article
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPlant gametophytes play central roles in sexual reproduction. A hallmark of the plant life cycle is that gene expression is required in the haploid gametophytes. Consequently, many mutant phenotypes are expressed in this phase.
resultsWe perform a quantitative RNA-seq analysis of embryo sacs, comparator ovules with the embryo sacs removed, mature pollen, and seedlings to assist the identification of gametophyte functions in maize. Expression levels were determined for annotated genes in both gametophytes, and novel transcripts were identified from de novo assembly of RNA-seq reads. Transposon-related transcripts are present in high levels in both gametophytes, suggesting a connection between gamete production and transposon expression in maize not previously identified in any female gametophytes. Two classes of small signaling proteins and several transcription factor gene families are enriched in gametophyte transcriptomes. Expression patterns of maize genes with duplicates in subgenome 1 and subgenome 2 indicate that pollen-expressed genes in subgenome 2 are retained at a higher rate than subgenome 2 genes with other expression patterns. Analysis of available insertion mutant collections shows a statistically significant deficit in insertions in gametophyte-expressed genes.
conclusionsThis analysis, the first RNA-seq study to compare both gametophytes in a monocot, identifies maize gametophyte functions, gametophyte expression of transposon-related sequences, and unannotated, novel transcripts. Reduced recovery of mutations in gametophyte-expressed genes is supporting evidence for their function in the gametophytes. Expression patterns of extant, duplicated maize genes reveals that selective pressures based on male gametophytic function have likely had a disproportionate effect on plant genomes.
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