Abstract
BackgroundThe CLE (CLAVATA3/Endosperm Surrounding Region-related) gene family encodes small signaling peptides that are primarily involved in coordinating stem cell fate in different types of plant meristems. Their roles in vascular cambium have highlighted their potential function in wood formation. Apart from recent advances on identification and characterization of CLE genes, little is known about this gene family in a tree species.ResultsFifty PtCLE genes were identified from the Populus trichocarpa genome and were classified into four major groups based on sequence similarity. Analysis of the genomic organization of PtCLE genes indicates that genome duplication, as well as the diversity in the CLE motif, have contributed to the expansion of CLE gene family in poplar. A comparison with functionally characterized Arabidopsis CLE protein sequences showed that many PtCLE proteins are closely related to their predicted Arabidopsis counterparts. Particularly, PtCLE3, PtCLE12, PtCLE14 and PtCLE38 comprised an identical CLE motif to AtCLE41/TDIF, which is known as a regulator of vascular cambium homeostasis, strongly supporting the idea that similar signaling pathways exist in both species to regulate wood formation and secondary growth. Transcriptome profiling revealed that PtCLE genes generally were differentially expressed while some PtCLE genes exhibited tissue-specific expression patterns. Moreover, compared to their Arabidopsis counterparts, PtCLE genes showed either similar or distinct expression patterns, implying functional conservation in some cases and functional divergence in others.ConclusionsOur study provides a genome-wide analysis of the CLE gene family in poplar, and highlights the potential roles of key PtCLE genes in the regulation of secondary growth and wood formation. The comparative analysis revealed that functional conservation may exist between PtCLEs and their AtCLE orthologues, which was further supported by transcriptomic analysis. Transcriptional profiling provided further insights into possible functional divergence, evidenced by differential expression patterns of various PtCLE genes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2504-x) contains supplementary material, which is available to authorized users.
Highlights
The CLE (CLAVATA3/Endosperm Surrounding Region-related) gene family encodes small signaling peptides that are primarily involved in coordinating stem cell fate in different types of plant meristems
AtCLE1, AtCLE3, AtCLE4, and AtCLE7, for example, were predominantly expressed in the Arabidopsis root pericycle, and their expressions were induced under nitrogen-deficient conditions [28]
Further studies have shown that multiple receptors, including CLV1, RPK2, CRN/SOL2 and CLV2, are required for the successful nematode infection of Arabidopsis roots [31, 32]
Summary
The CLE (CLAVATA3/Endosperm Surrounding Region-related) gene family encodes small signaling peptides that are primarily involved in coordinating stem cell fate in different types of plant meristems. Their roles in vascular cambium have highlighted their potential function in wood formation. The CLE genes have been found in many plant species and some plant parasitic nematodes, while the functions of Other than their roles in stem cell homoeostasis, CLE genes have been found to participate in a range of biological processes [2,3,4,5,6]. Further studies have shown that multiple receptors, including CLV1, RPK2, CRN/SOL2 and CLV2, are required for the successful nematode infection of Arabidopsis roots [31, 32]
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