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Related Experiment Video

Updated: Jan 11, 2026

An Efficient Method for Quantitative, Single-cell Analysis of Chromatin Modification and Nuclear Architecture in Whole-mount Ovules in Arabidopsis
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Developmentally regulated genes drive phylogenomic splits in ovule evolution.

Veronica M Sondervan1,2, Gil Eshel1, Kranthi Varala3

  • 1Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.

Nature Communications
|November 13, 2025
PubMed
Summary
This summary is machine-generated.

Gymnosperms, ancient seed plants, hold key genes for seed evolution. This study analyzed their transcriptomes to find genes influencing major plant evolutionary splits, aiding seed gene discovery and crop improvement.

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Area of Science:

  • Plant evolutionary biology
  • Genomics
  • Molecular biology

Background:

  • Seed evolution fundamentally reshaped terrestrial ecosystems and agriculture.
  • Gymnosperms, as the earliest seed-bearing plants, represent a valuable, yet underexplored, genetic resource for understanding seed development.
  • Identifying genes involved in seed evolution can provide insights into plant diversification and crop enhancement.

Purpose of the Study:

  • To explore the genomic potential of gymnosperms for uncovering genes critical to seed evolution.
  • To identify phylogenomic markers supporting key evolutionary divergences in plant history.
  • To discover and validate novel ovule-regulated genes influencing plant evolution.

Main Methods:

  • Deep transcriptome sequencing was performed on 14 gymnosperms, 4 angiosperms, and 2 ferns.
  • Phylogenetically informative ortholog groups were identified.
  • Differential gene expression analysis in ovules and leaves was conducted to find evolutionary support.
  • Candidate genes were validated in gymnosperm ovule structures.

Main Results:

  • 22,429 phylogenetically informative ortholog groups were identified across the studied plant lineages.
  • Differentially expressed genes in ovules and leaves provided significant support for evolutionary splits between seed/non-seed plants, gymnosperms/angiosperms, and within gymnosperms.
  • Unreported candidate ovule-regulated genes in Arabidopsis were identified using gymnosperm data.
  • 4,076 candidate ovule genes influencing evolutionary splits were uncovered, with expression validated in gymnosperm ovules.

Conclusions:

  • Gymnosperm transcriptomes are a rich source for discovering genes involved in seed evolution.
  • Ovule and leaf gene expression patterns are crucial for understanding major plant evolutionary events.
  • This research provides a valuable resource for seed gene discovery, plant conservation efforts, and the improvement of agricultural crops.