The CLAVATA3/ESR-related peptide family in the biofuel crop pennycress

Authors: HAGELTHORN, LYNNE - University Of California Berkeley; Fletcher, Jennifer

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/18/2023
Publication Date: 8/4/2023
Citation: Hagelthorn, L., Fletcher, J.C. 2023. The CLAVATA3/ESR-related peptide family in the biofuel crop pennycress. Frontiers in Plant Science. 14. Article 1240342. https://doi.org/10.3389/fpls.2023.1240342.
DOI: https://doi.org/10.3389/fpls.2023.1240342

Interpretive Summary: The CLAVATA3/ESR-related (CLE) family of small signaling proteins is responsible for controlling key aspects of plant development. Pennycress is a relative of broccoli, cauliflower and canola that is being grown across the US Midwest during an otherwise fallow period of the typical corn/soybean rotation to improve soil quality and to harvest the seeds for biofuels. Understanding the CLE family offers a major avenue for future domestication efforts of pennycress as development is inextricably tied with yield. Here we report the identification and analysis of the 27 members of the CLE family in pennycress. We uncover their gene structure, evolutionary relationships, and expression in various plant tissues including seed-specific expression. Specifically, we combine our own dataset and previously published datasets to uncover the expression during plant growth of 25 of the 27 CLE family members. This gene family shows a striking conservation with the model species Arabidopsis thaliana, suggesting that established research may be successfully translated to this novel crop. These results provide critical value in the domestication effort for pennycress by characterizing potential key developmental regulatory genes.

Technical Abstract: CLAVATA3/ESR-related (CLE) peptides perform a variety of important functions in plant development and historically have been targeted during domestication of existing crops. Pennycress (Thlaspi arvense) is an emerging biofuel crop currently undergoing domestication that offers novel monetary incentives as a winter cover crop during an otherwise fallow period of the corn/soybean farming rotation. Here we report the characterization of the CLE gene family in pennycress through homology comparison of the CLE motif with other dicot species by conducting a Hidden Markov Model and maximum likelihood phylogenetic analysis supplemented with manual annotation. Twenty-seven pennycress CLE genes were identified, and their expression analyzed through transcriptome profiling and RT-qPCR. Our study provides a genome-wide analysis of the CLE gene family in pennycress and carries significant value for accelerating the domestication of this crop through identification of potential key developmental regulatory genes.