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Peer-reviewedCC BYNature Plants

A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination

  • Caroline A Martin1,2
  • Kylee R Cogdill2
  • Alesandra L Pusey2
  • Mary A. Gehring3,4,5,6
6 affiliations
  1. 1Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
  2. 2Whitehead Institute for Biomedical Research, Cambridge, MA, USA
  3. 3Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. [email protected]
  4. 4Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. [email protected]
  5. 5Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA, USA. [email protected]
  6. 6Whitehead Institute for Biomedical Research, Cambridge, MA, USA. [email protected]
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Abstract

Successful seed development is essential for flowering plant reproduction and requires the coordination of three genetically distinct tissues: the embryo and endosperm, which are the products of fertilization, and the maternal seed coat. Our understanding of the transcriptional programs underlying tissue-specific functions and inter-tissue coordination in seeds remains incomplete. To address this, we performed single-nucleus RNA sequencing on Arabidopsis thaliana seeds at 3, 5 and 7 days after pollination. Here we characterized all major seed cell or nucleus types, further refined transcriptional states in the endosperm and mapped signatures of selection on cell-type-specific genes. Among other findings, our analyses reveal the compartmentalization of genes involved in brassinosteroid-responsive transcription factor activation, abundant endosperm expression of genes that encode short, secreted peptides, and expression enrichment of rapidly evolving genes in endosperm and seed coat subtypes, illuminating the cell type and species specificity of seed genes.

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Cite

BibTeXRIS
BibTeX
@article{martin2026transcriptional,
  title = {{A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination}},
  author = {Caroline A Martin and Kylee R Cogdill and Alesandra L Pusey and Mary A. Gehring},
  journal = {Nature Plants},
  year = {2026},
  month = may,
  doi = {10.1038/s41477-026-02295-8},
  url = {https://doi.org/10.1038/s41477-026-02295-8},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination
AU  - Caroline A Martin
AU  - Kylee R Cogdill
AU  - Alesandra L Pusey
AU  - Mary A. Gehring
PY  - 2026
DA  - 2026/05/21
JO  - Nature Plants
DO  - 10.1038/s41477-026-02295-8
UR  - https://doi.org/10.1038/s41477-026-02295-8
AB  - Successful seed development is essential for flowering plant reproduction and requires the coordination of three genetically distinct tissues: the embryo and endosperm, which are the products of fertilization, and the maternal seed coat. Our understanding of the transcriptional programs underlying tissue-specific functions and inter-tissue coordination in seeds remains incomplete. To address this, we performed single-nucleus RNA sequencing on Arabidopsis thaliana seeds at 3, 5 and 7 days after pollination. Here we characterized all major seed cell or nucleus types, further refined transcriptional states in the endosperm and mapped signatures of selection on cell-type-specific genes. Among other findings, our analyses reveal the compartmentalization of genes involved in brassinosteroid-responsive transcription factor activation, abundant endosperm expression of genes that encode short, secreted peptides, and expression enrichment of rapidly evolving genes in endosperm and seed coat subtypes, illuminating the cell type and species specificity of seed genes.
SN  - 2055-026X
SN  - 2055-0278
ER  -