• The study reveals more than one hundred small peptides potentially involved in flower formation in the model plant Arabidopsis.
• Many of these peptides are also present in other plant species, suggesting important and conserved functions across the plant kingdom.
• The use of peptides is becoming increasingly relevant in the context of sustainable agriculture, and these findings may inspire new biotechnological tools.

Twenty‑five years after the sequencing of the human genome (February 2001) and the genome of the model plant Arabidopsis thaliana (December 2000), the scientific community continues to uncover entire chapters of information that remained hidden in that first “book of life”. While genome sequencing provided the alphabet and basic punctuation of genomes, large gaps persisted in understanding how gene expression is regulated and which elements still remained unidentified.

One such gap stems from the original genome annotations, which considered only proteins longer than 100 amino acids, since large‑scale bioinformatic identification of shorter proteins was not feasible with the technologies available at the time. However, the rise of new experimental approaches such as ribosome profiling (Ribo‑seq) has revealed thousands of small open reading frames (sORFs) capable of encoding functional peptides, known as SEPs (sORF‑encoded peptides). This “non‑conventional peptidome” is emerging as a fundamental component of eukaryotic cell physiology.

In organisms as diverse as bacteria and mammals, peptides with key biological roles are already known—from antimicrobials such as the seven‑amino‑acid microcin of E. coli to powerful cellular regulators. In plants, although conventional peptides are well characterised in stress responses and developmental processes, the specific study of SEPs is still in its early stages.

Now, in a recently published study in Plant Physiology, a team at CRAG led by ICREA Research Professor José Luis Riechmann presents the first comprehensive characterization of the sORF‑derived peptidome during flower development in Arabidopsis thaliana.

An atlas of peptides in floral development

Using a bioinformatic analysis of the Arabidopsis genome, the researchers generated a database of putative peptides and used it in experiments on inflorescences at different developmental stages employing mass spectrometry (LC‑MS/MS), an extremely precise technique capable of detecting and quantifying endogenous peptides even at very low concentrations.

To identify peptides specific to different floral organs, the team compared the peptidome of mutant lines affecting the development of sepals, petals, stamens, and carpels. This strategy enabled the identification of 132 peptides, 60 of which were specifically associated with floral organs. Among these, most were linked to stamens (46), followed by petals (13) and carpels (1).

Conserved and potentially functional peptides

Comparative analyses showed that 103 of the 132 identified peptides have homologs in at least one other plant species, including agriculturally important crops such as rice (Oryza sativa), maize (Zea mays), melon (Cucumis melo), and tomato (Solanum lycopersicum). This evolutionary conservation suggests that many of these SEPs may play essential roles in plant development and physiology.

The CRAG team also confirmed the expression of 20 of these peptides in flowers using reporter constructs (GFP-GUS), providing further experimental evidence for their potential biological relevance.

Finally, through computational prediction of subcellular localization, they determined that approximately 30% of these SEPs could localize to mitochondria, and around 13% to the extracellular secretion system, pointing to important functions in metabolic and signalling processes—similar to what is seen in animals.

“This work reveals a part of the genome that, from a functional point of view, had remained unnoticed for years; these small peptides may be key pieces in understanding how flowers develop”, highlights José Luis Riechmann, leading author of the study.

Towards a new understanding of floral development

The results of this study suggest that SEPs may play important roles in the formation, differentiation, and functioning of floral organs. The work provides an initial —exploratory but essential— map to understand how these small molecules may act as key regulators of development.

These findings open the door to future research aimed at determining the precise function of these peptides, potentially leading to new lines of inquiry in basic biology as well as plant biotechnology in other flowering species.

Potential applications in agriculture

In the context of a transition toward more sustainable agriculture with reduced chemical inputs, peptides used as biostimulants are emerging as precision treatments capable of modulating plant physiological responses. Their use represents an emerging technology with currently high operational costs, mainly due to demands in synthesis, formulation and stability. However, these bioactive molecules can be highly profitable in high‑value crops such as centuries‑old olive groves or fruit trees, where the per‑plant investment is fully justified.

Reference Article

Raquel Álvarez-Urdiola, José Tomás Matus, Víctor M. González-Miguel, Martí Bernardo-Faura, José Luis Riechmann. The non-conventional peptidome of Arabidopsis flower development. Plant Physiology (2026), https://doi.org/10.1093/plphys/kiag047

About the authors and funding of the study

This work was supported by grants BFU2014-58289-P and PID2022- 139578NB-I00 (funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”) and 2017SGR718 and 2021SGR00792 (from the Agencia de Gestió d’Ajuts Universitaris i de Recerca) to J.L.R.; and by institutional grants SEV-2015-0533 and CEX2019-000902-S (funded by MCIN/AEI/10.13039/501100011033) and by the CERCA Programme/Generalitat de Catalunya. R.A.-U. was supported by fellowship PRE2018-084278 funded by MCIN/AEI/ 10.13039/501100011033 and by “ESF Investing in your future.”