Identification and characterization of the Populus trichocarpa CLE family

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.

The CLE gene family in Populus trichocarpa

“…1,8,9 The CLE genes have been found in many plant species, whereas the roles of most identified CLE genes remained to be elucidated. 2,[10][11][12][13][14][15] As the 2 most known members of CLE peptide family, AtCLV3 and AtCLE40 are key regulators in coordinating stem cell homeostasis in the SAM (Shoot Apical Meristem) and RAM (Root Apical Meristem), respectively. 1 Other than their functions in stem cell fate, it has been also revealed that the CLE peptides are important players in modulating various plant growth and developmental processes such as nodulation, [16][17][18] protoxylem formation, 19 embryogenesis and endosperm development, 20 phloem formation, 21 pollen growth, 22 and lateral root expansion.…”

“…To this end, we undertook a genome-wide analysis in Populus trichocarpa to identify CLE genes and gain additional insights into their potential roles in various aspects of poplar growth and development, focusing on CLE genes exhibiting expression in vascular tissues which might be important for wood formation. 11 A total of 50 PtCLE proteins were identified from Populus trichocarpa and classified into 4 major groups. In-depth sequence analysis enabled us to identify PtCLE homologous copies in poplar and PtCLE orthologous copies between poplar and Arabidopsis.…”

“…Transcriptomic analysis revealed that PtCLE genes generally were differentially expressed while some PtCLE genes exhibited tissue-specific expression patterns. 11 The presence of multiple PtCLEs in a single tissue type, exhibiting overlapping expression patterns, implies that the widespread redundancies among PtCLE genes. In comparison to their Arabidopsis counterparts, PtCLE genes exhibited either similar or different expression patterns, implying functional conservation in some cases and functional divergence in others.…”

“…In comparison to their Arabidopsis counterparts, PtCLE genes exhibited either similar or different expression patterns, implying functional conservation in some cases and functional divergence in others. 11 Intriguingly, a group of 4 PtCLE proteins (PtCLE3/PtCLE12/PtCLE14/PtCLE38) shares an identical CLE motif as that of AtCLE41/TDIF. The expression patterns of PtCLE3 and PtCLE12 are similar to that of AtCLE41/TDIF.…”

“…Altogether, these results imply that the existence of multiple CLE-RLK signaling pathways to modulate the secondary growth and wood formation in poplar. 11 In silico gene expression study also revealed that a number of PtCLE genes are predominantly expressed in various vascular tissues other than cambium, e.g. secondary phloem, developing xylem and mature xylem tissues, 11 suggesting diverse roles of PtCLE genes and a highly complicated regulatory network for the poplar vascular development.…”