title: Identification and characterization of the Populus trichocarpa CLE family.
abstract: BACKGROUND
  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. Apart from recent advances on identification and characterization of CLE genes, little is known about this gene family in a tree species.
  
  
  RESULTS
  Fifty 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.
  
  
  CONCLUSIONS
  Our 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.
authors.affiliation: Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry; National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China; College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, Shaanxi, China. superhhb@126.com.
authors.forename: Huibin
authors.initials: H
authors.lastname: Han
authors.affiliation: Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry; National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China; College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, Shaanxi, China. hua_897957227@163.com.
authors.forename: Guohua
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry; National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China; College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, Shaanxi, China. wumengyao712@163.com.
authors.forename: Mengyao
authors.initials: M
authors.lastname: Wu
authors.affiliation: Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry; National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China; College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, Shaanxi, China. guodong_wang@snnu.edu.cn.
authors.forename: Guodong
authors.initials: G
authors.lastname: Wang
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis; D058506:Cambium / Q000254:growth & development; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018519:Meristem / Q000254:growth & development; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D018547:Plant Stems / Q000254:growth & development; D032107:Populus / Q000235:genetics* / Q000254:growth & development; D016415:Sequence Alignment; D014934:Wood / Q000254:growth & development