The PI/GLO-like locus in orchids: Duplication and purifying selection at synonymous sites within Orchidinae (Orchidaceae)

Cantone, Carmela; Gaudio, Luciano; Aceto, Serena

doi:10.1016/j.gene.2011.04.004

Cited by 13 publications

(9 citation statements)

References 46 publications

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“…The MADS-box degenerate primer MADS_F (Table 1) and a poly-T primer were used to amplify 1 µl of first strand cDNA using the LongAmp Taq PCR Kit (New England Biolabs) [19], [32]. The amplification products were cloned into the pGEM-T Easy vector (Promega); more than 50 clones were sequenced using the plasmid primers T7 and SP6 and sequencing reactions were run on an ABI 310 Automated Sequencer (Applied Biosystems).…”

Section: Methodsmentioning

confidence: 99%

The Analysis of the Inflorescence miRNome of the Orchid Orchis italica Reveals a DEF-Like MADS-Box Gene as a New miRNA Target

et al. 2014

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Plant microRNAs (miRNAs) are small, regulatory non-coding RNAs involved in a wide range of biological processes, from organ development to response to stimuli. In recent years, an increasing number of studies on model plant species have highlighted the evolutionary conservation of a high number of miRNA families and the existence of taxon-specific ones. However, few studies have examined miRNAs in non-model species such as orchids, which are characterized by highly diversified floral structures and pollination strategies. Therefore, we analysed a small RNA library of inflorescence tissue of the Mediterranean orchid Orchis italica to increase the knowledge on miRNAs in a non-model plant species. The high-throughput sequencing and analysis of a small RNA library of inflorescence of O. italica revealed 23 conserved and 161 putative novel miRNA families. Among the putative miRNA targets, experimental validation demonstrated that a DEF-like MADS-box transcript is cleaved by the homolog of miR5179 of O. italica. The presence of conserved miRNA families in the inflorescence of O. italica indicates that the basic developmental flower regulatory mechanisms mediated by miRNAs are maintained through evolution. Because, according to the “orchid code” theory, DEF-like genes exert a key function in the diversification of tepals and lip, the cleavage-mediated inhibitory activity of miR5179 on a OitaDEF-like transcript suggests that, in orchids, miRNAs play an important role in the diversification of the perianth organs.

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Section: Methodsmentioning

confidence: 99%

The Analysis of the Inflorescence miRNome of the Orchid Orchis italica Reveals a DEF-Like MADS-Box Gene as a New miRNA Target

et al. 2014

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“…A paralog copy of OrcPI , OrcPI2 , has been recently identified in O. italica and other members of the Orchidoideae subfamily. The two PI/GLO -like genes exhibit different selective pressures, particularly on the synonymous sites, and seem to have experienced subfunctionalization [129]. In O. italica , four AP3/DEF -like genes are also present (Aceto et al ., unpublished data).…”

Section: The Orchid Class B Mads-box Genesmentioning

confidence: 99%

The MADS and the Beauty: Genes Involved in the Development of Orchid Flowers

Aceto

Gaudio

2011

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Since the time of Darwin, biologists have studied the origin and evolution of the Orchidaceae, one of the largest families of flowering plants. In the last two decades, the extreme diversity and specialization of floral morphology and the uncoupled rate of morphological and molecular evolution that have been observed in some orchid species have spurred interest in the study of the genes involved in flower development in this plant family. As part of the complex network of regulatory genes driving the formation of flower organs, the MADS-box represents the most studied gene family, both from functional and evolutionary perspectives. Despite the absence of a published genome for orchids, comparative genetic analyses are clarifying the functional role and the evolutionary pattern of the MADS-box genes in orchids. Various evolutionary forces act on the MADS-box genes in orchids, such as diffuse purifying selection and the relaxation of selective constraints, which sometimes reveals a heterogeneous selective pattern of the coding and non-coding regions. The emerging theory regarding the evolution of floral diversity in orchids proposes that the diversification of the orchid perianth was a consequence of duplication events and changes in the regulatory regions of the MADS-box genes, followed by sub- and neo-functionalization. This specific developmental-genetic code is termed the “orchid code.”

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“…In orchids, the MADS-box genes involved in formation of the perianth are well characterized (Mondragon-Palomino et al 2009; Aceto and Gaudio 2011; Cantone et al 2011; Mondragon-Palomino and Theissen 2011; Pan et al 2011, 2014; Salemme et al 2011, 2013a; Aceto et al 2014; Acri-Nunes-Miranda and Mondragon-Palomino 2014), and recent studies have highlighted the role of the MADS-box gene AGL6 in the formation of the orchid lip (Hsu et al 2015; Huang et al 2016). Conversely, few studies are available on orchid TCP genes (Mondragon-Palomino and Trontin 2011; De Paolo et al 2015; Lin et al 2016), and the MYB genes that are possibly involved in orchid flower symmetry have not been characterized.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome-Wide Identification and Expression Analysis of DIVARICATA- and RADIALIS-Like Genes of the Mediterranean Orchid Orchis italica

Valoroso

Paolo

Iazzetti

et al. 2017

Genome Biology and Evolution

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Bilateral symmetry of flowers is a relevant novelty that has occurred many times throughout the evolution of flowering plants. In Antirrhinum majus, establishment of flower dorso-ventral asymmetry is mainly due to interaction of TCP (CYC and DICH) and MYB (DIV, RAD, and DRIF) transcription factors. In the present study, we characterized 8 DIV-, 4 RAD-, and 2 DRIF-like genes from the transcriptome of Orchis italica, an orchid species with bilaterally symmetric and resupinate flowers. We found a similar number of DIV- and RAD-like genes within the genomes of Phalaenopsis equestris and Dendrobium catenatum orchids. Orchid DIV- and RAD-like proteins share conserved motifs whose distribution reflects their phylogeny and analysis of the genomic organization revealed a single intron containing many traces of transposable elements. Evolutionary analysis has shown that purifying selection acts on the DIV- and RAD-like coding regions in orchids, with relaxation of selective constraints in a branch of the DIV-like genes. Analysis of the expression patterns of DIV- and RAD-like genes in O. italica revealed possible redundant functions for some of them. In the perianth of O. italica, the ortholog of DIV and DRIF of A. majus are expressed in all tissues, whereas RAD is mainly expressed in the outer tepals and lip. These data allow for proposal of an evolutionary conserved model in which the expression of the orthologs of the DIV, RAD, and DRIF genes might be related to establishment of flower bilateral symmetry in the nonmodel orchid species O. italica.

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The PI/GLO-like locus in orchids: Duplication and purifying selection at synonymous sites within Orchidinae (Orchidaceae)

Cited by 13 publications

References 46 publications

The Analysis of the Inflorescence miRNome of the Orchid Orchis italica Reveals a DEF-Like MADS-Box Gene as a New miRNA Target

The Analysis of the Inflorescence miRNome of the Orchid Orchis italica Reveals a DEF-Like MADS-Box Gene as a New miRNA Target

The MADS and the Beauty: Genes Involved in the Development of Orchid Flowers

Transcriptome-Wide Identification and Expression Analysis of DIVARICATA- and RADIALIS-Like Genes of the Mediterranean Orchid Orchis italica

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