Analysis of the TCP genes expressed in the inflorescence of the orchid Orchis italica

Sofia De Paolo,Serena Aceto,Luciano Gaudio

doi:10.1038/srep16265

Abstract

TCP proteins are plant-specific transcription factors involved in many different processes. Because of their involvement in a large number of developmental pathways, their roles have been investigated in various plant species. However, there are almost no studies of this transcription factor family in orchids. Based on the available transcriptome of the inflorescence of the orchid Orchis italica, in the present study we identified 12 transcripts encoding TCP proteins. The phylogenetic analysis showed that they belong to different TCP classes (I and II) and groups (PCF, CIN and CYC/TB1), and that they display a number of conserved motifs when compared with the TCPs of Arabidopsis and Oryza. The presence of a specific cleavage site for the microRNA miRNA319, an important post-transcriptional regulator of several TCP genes in other species, was demonstrated for one transcript of O. italica, and the analysis of the expression pattern of the TCP transcripts in different inflorescence organs and in leaf tissue suggests that some TCP transcripts of O. italica exert their role only in specific tissues, while others may play multiple roles in different tissues. In addition, the evolutionary analysis showed a general purifying selection acting on the coding region of these transcripts.

Highlights

Based on the sequence differences in the TCP domain, the members of the TCP family can be classified into two subfamilies, class I and class II[1,3,7]
A first phylogenetic analysis of these virtually translated sequences of O. italica and the TCP proteins of Arabidopsis thaliana and Oryza sativa revealed that none of the TCP transcripts present in the inflorescence transcriptome of O. italica belong to the class II CYC/TEOSINTE BRANCHED1 (TB1)-like group, whose members are involved in the establishment of bilateral symmetry in numerous plant species[26,28,48,49,50,51]
The absence of an assembled transcript in the inflorescence transcriptome of O. italica corresponding to OitaTB1 suggests that this gene is not expressed or it is expressed at very low levels and/or only in specific tissues of the inflorescence of O. italica at the stage of development examined

Summary

Introduction

Based on the sequence differences in the TCP domain, the members of the TCP family can be classified into two subfamilies, class I (or PCF or TCP-P) and class II (or TCP-C)[1,3,7]. The members of the class II subfamily are quite heterogeneous and can be further classified into two sub-clades: the CYC/TB1-like group, known as the ECE group based on the presence of a glutamic acid-cysteine-glutamic acid stretch[9], and the CIN-like group[3]. The role of TCP proteins has been demonstrated in plant immunity responses, through the interaction with pathogenic effectors[17], and in mitochondrial metabolism, through the binding to the cis-acting regulatory element TGGGGCY18 Another relevant role of the TCP genes, in particular the members of the CYC/TB1-like clade, is the establishment of the floral monosymmetry through their interactions with MYB transcription factors and cell cycle proteins[19,20,21]. We examined the expression patterns of the identified TCP transcripts and of the microRNA miR319 in different tissues and performed a comparative analysis to identify conserved motifs among the TCP proteins of O. italica, other orchid species and the model species, Arabidopsis thaliana and Oryza sativa

Methods

Results

Conclusion