The study investigates the Glutamate-Like Receptors (GLRs) gene in Asparagus officinalis and Arabidopsis thaliana through comparative phylogenomics and structural modeling approaches. Sequence alignment and phylogenetic analysis revealed evolutionary conservation and functional divergence among GLR homologs. Structural modeling indicated similar 3D conformations and ligand-binding domains, suggesting a conserved mechanism of signal perception. Differences in specific amino acid residues hinted at species-specific adaptations in receptor function. Expression profiling supported the gene’s involvement in growth regulation and stress responses. Molecular docking predicted potential interactions with key signaling molecules. These findings enhance understanding of GLR evolution and its physiological significance in plants, offering insights for future crop improvement and stress tolerance research.

Keywords: GLR Gene, Glutamate-Like Receptors (GLRs), Asparagus officinalis, Arabidopsis thaliana, Comparative Phylogenomics, Structural Modelling, Protein Structure Prediction, Gene Evolution, Plant Signaling, Calcium Signaling, Ligand-Gated Ion Channels, Molecular Docking, Sequence Alignment, Phylogenetic Analysis, Functional Genomics.

TAIR (The Arabidopsis Information Resource) (n.d.). Arabidopsis genome and gene resources. TAIR. https:// www.arabidopsis.org/.

Rice Genome Annotation Project (IRGSP) (n.d.). Rice genome annotation and resources. IRGSP. https://rice.uga. edu/.

Tomato Genome (n.d.). Tomato genome database. TED. http://ted.bti.cornell.edu/.

National Center for Biotechnology Information (n.d.). Sorghum bicolor protein sequences. NCBI. https://www. ncbi.nlm.nih.gov/.

MaizeGDB (n.d.). Maize genetics and genomics database. MaizeGDB. https://www.maizegdb.org/.

CottonGen (n.d.). Cotton research and breeding database. CottonGen. https://www.cottongen.org/.

Olatunji, O., et al. (2024). In silico analysis of glutamate receptors in Capsicum chinense: Structure, evolution, and molecular interactions. Plants, 13(6): 812. https://doi.org/10.3390/plants13060812.

The Spruce (n.d.). How to plant, grow, and harvest asparagus. The Spruce. https://www.thespruce.com/how- to-plant-and-grow-asparagus-1402814.

Arias, A.M., & Pujol, M. (2020). Green and white asparagus (Asparagus officinalis): A source of developmental, chemical and urinary intrigue. Metabolites, 10(1): 17. https://doi.org/10.3390/metabo10010017.

Turano, F.J., et al. (2023). Merging signaling with structure: Functions and mechanisms of plant glutamate receptor ion channels. Annual Review of Plant Biology, 74(1): 415–452. https://doi.org/10.1146/annurev-arplant-070522- 033255.

Singh, M., Zhao, C., & Wang, Q. (2022). Roles of glutamate receptor-like channels (GLRs) in plant growth and response to environmental stimuli. Plants, 11(24): 3450. https://doi.org/10.3390/plants11243450.

Meinke, D. (2018). Biology in bloom: A primer on the Arabidopsis thaliana model system. Genetics, 208(4): 1337–1349. https://doi.org/10.1534/genetics.118.300755.

MEGA Software (n.d.). Phylogenetic analysis and molecular evolution. MEGA. https://www.megasoftware.net/.

Département de Biologie et Chimie des Protéines (CNRS/UCBL) (n.d.). NPS@: GOR4 secondary structure prediction. NPSA. https://npsaprabi.ibcp.fr/cgibin/npsa_automat.pl?page=/npsa/npsa_gor4.html.

AlphaFold Server (n.d.). Protein structure prediction. AlphaFold. https://alphafoldserver.com/.

ChimeraX Development Team (n.d.). UCSF ChimeraX home page. UCSF. https://www.cgl.ucsf.edu/chimerax/.

GalaxyWEB (n.d.). Protein structure refinement server. GalaxyWEB. https://galaxy.seoklab.org/cgi-bin/submit. cgi?type=refine2.

MolProbity (n.d.). Protein structure validation. MolProbity. http://molprobity.biochem.duke.edu/.

SAVES v6.1 (n.d.). Structure validation server. UCLA. https://saves.mbi.ucla.edu/.

Expasy (n.d.). Swiss bioinformatics resource portal. SIB. https://www.expasy.org/.

ClusPro 2.0 (n.d.). Protein–protein docking server. ClusPro. https://cluspro.bu.edu/login.php.

PyMOL (n.d.). Molecular visualization. PyMOL. https://www.pymol.org/.

Source of Funding:

This study received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.

Competing Interests Statement:

The authors declare that they have no competing interests related to this work.

Consent for publication:

The authors declare that they consented to the publication of this study.

Authors' contributions:

Conceptualization, U.B.; methodology, U.B.; formal analysis, A.B.; investigation, M.B.; writing—original draft preparation, U.B; writing—review and editing, U.B.; supervision, U.B. All authors have read and agreed to the published version of the manuscript.

Availability of data and materials:

Supplementary information is available from the authors upon reasonable request.

Institutional Review Board Statement:

The study was approved by the Institutional Review Board of Bahauddin Zakariya University, Multan.

Informed Consent:

Not applicable for this study.