Identification and characterization of the Populus trichocarpa CLE family.
Identification and characterization of the Populus trichocarpa CLE family.
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DOI：
10.1186/s12864-016-2504-x
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发表时间：
2016-03-02
期刊：
影响因子：
4.4
通讯作者：
Wang G
中科院分区：
文献类型：
--
作者：
Han H;Zhang G;Wu M;Wang G
CLE （CLAVATA3/胚乳周围区域相关）基因家族编码小信号肽，主要参与协调不同类型植物分生组织的干细胞命运。它们在维管形成层中的作用突出了它们在木材形成中的潜在功能。除了最近在CLE基因的鉴定和表征方面取得的进展外，对该基因家族在树种中的了解甚少。从毛杨基因组中鉴定出50个PtCLE基因，并根据序列相似性将其分为4大类群。对PtCLE基因的基因组组织分析表明，基因组的重复和CLE基序的多样性促进了白杨CLE基因家族的扩展。与功能性鉴定的拟南芥CLE蛋白序列的比较表明，许多PtCLE蛋白与其预测的拟南芥对应物密切相关。特别是，PtCLE3、PtCLE12、PtCLE14和PtCLE38与AtCLE41/TDIF具有相同的CLE基序，而AtCLE41/TDIF被认为是维管形成层稳态的调节因子，这有力地支持了两种物种中存在相似的信号通路来调节木材形成和次生生长的观点。转录组分析显示，PtCLE基因普遍存在差异表达，而一些PtCLE基因表现出组织特异性表达模式。此外，与拟南芥相比，PtCLE基因表现出相似或不同的表达模式，这意味着某些情况下功能保守，而另一些情况下功能分化。本研究对杨树CLE基因家族进行了全基因组分析，并强调了关键PtCLE基因在调控杨树次生生长和木材形成中的潜在作用。比较分析显示PtCLEs与其AtCLE同源物之间可能存在功能守恒，转录组学分析进一步支持了这一观点。转录谱分析提供了进一步了解可能的功能差异，各种PtCLE基因的差异表达模式证明了这一点。本文的在线版本（doi:10.1186/s12864-016-2504-x）包含补充材料，可供授权用户使用。
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. 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. 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. The online version of this article (doi:10.1186/s12864-016-2504-x) contains supplementary material, which is available to authorized users.