ArticleBMC genomics2020
Predicting and clustering plant CLE genes with a new method developed specifically for short amino acid sequences.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 33 citations in OpenAlex.
- Evolutionary shifts in plant adaptation mediated by phytohormones.Plant communications · 2026Review
- Pan-eukaryotic distribution and deep homology of plant small secreted peptides and their receptors.iScience · 2026Article
- Plant cell wall remodeling and peptide signaling under abiotic and biotic stress.Plant communications · 2026Review
- Tri-arabinosylation facilitates the bioactivity of CLE3 peptide inPlant biotechnology (Tokyo, Japan) · 2025Article
- Research progress of peptides discovery and function in resistance to abiotic stress in plant.Stress biology · 2025Review
- Research Progress of CLE and Its Prospects in Woody Plants.Plants (Basel, Switzerland) · 2025Review
- A plant CLE peptide and its fungal mimic promote arbuscular mycorrhizal symbiosis via CRN-mediated ROS suppression.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The rise of CLAVATA: evidence for CLAVATA3 and WOX signaling in the fern gametophyte.The Plant journal : for cell and molecular biology · 2025Article
- CLAVATA signaling in plant-environment interactions.Plant physiology · 2024Review
- The CLAVATA3/ESR-related peptide family in the biofuel crop pennycress.Frontiers in plant science · 2023Article
- Deeper genomic insights into tomato CLE genes repertoire identify new active peptides.BMC genomics · 2022Article
- Long-distance translocation of CLAVATA3/ESR-related 2 peptide and its positive effect on roots sucrose status.Plant physiology · 2022Article
- Evolution of meristem zonation by CLE gene duplication in land plants.Nature plants · 2022Review
- Receptor-like cytoplasmic kinases PBL34/35/36 are required for CLE peptide-mediated signaling to maintain shoot apical meristem and root apical meristem homeostasis in Arabidopsis.The Plant cell · 2022Article
- Small secreted peptides encoded on the wheat (Frontiers in plant science · 2022Article
- The sequenced genomes of nonflowering land plants reveal the innovative evolutionary history of peptide signaling.The Plant cell · 2021Review
- Possible role of small secreted peptides (SSPs) in immune signaling in bryophytes.Plant molecular biology · 2021Article
- Influence of SwitchgrassFrontiers in plant science · 2021Article
- Correction to: Predicting and clustering plant CLE genes with a new method developed specifically for short amino acid sequences.BMC genomics · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundThe CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity.
resultsWe developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of 12 amino acid residues from the CLE motif in a site-weight dependent manner. In total, 2156 CLE candidates-including 627 novel candidates-were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach taken here provides information on the evolution of the CLE gene family and provides evidence that the CLE and IDA/IDL genes share a common ancestor.
conclusionsOur new approach is applicable to SSPs or other proteins with short conserved domains and hence, provides a useful tool for gene prediction, classification and evolutionary analysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.