Genomic Approach to Study Floral Development Genes in Rosa sp.

Dubois, Annick; Remay, Arnaud; Raymond, Olivier; Balzergue, Sandrine; Chauvet, Aurélie; Maene, Marion; Pécrix, Yann; Yang, Shuhua; Jeauffre, Julien; Thouroude, Tatiana; Boltz, Véronique; Martin‐Magniette, Marie‐Laure; Janczarski, Stéphane; Legeai, Fabrice; Renou, Jean-Pierre; Vergne, Philippe; Bris, Manuel Le; Foucher, Fabrice; Bendahmane, Mohammed

doi:10.1371/journal.pone.0028455

Cited by 47 publications

(32 citation statements)

References 54 publications

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“…rosaceae.org/). Based on these data, expression profiles of 4,765 transcripts were detected in rose from floral transition to flower senescence using a newly developed Affymetrix microarray (Dubois et al, 2011). Moreover, application of next-generation sequencing technologies greatly promoted the study on rose genomics.…”

Section: Discussion Floral Transcriptome and Ethylene-responsive Profmentioning

confidence: 99%

“…In addition, microarray analysis showed that expression of two AUX/IAA genes, one ARF gene, and one Brassinosteroid-regulated protein (Brassinosteroid Upregulated Protein1) gene were significantly altered during flower opening of Rosa spp. (Dubois et al, 2011). The integration of these hormonal signals into a model of petal growth requires further investigation.…”

Section: Discussion Floral Transcriptome and Ethylene-responsive Profmentioning

confidence: 99%

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An NAC Transcription Factor Controls Ethylene-Regulated Cell Expansion in Flower Petals

et al. 2013

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Cell expansion is crucial for plant growth. It is well known that the phytohormone ethylene functions in plant development as a key modulator of cell expansion. However, the role of ethylene in the regulation of this process remains unclear. In this study, 2,189 ethylene-responsive transcripts were identified in rose (Rosa hybrida) petals using transcriptome sequencing and microarray analysis. Among these transcripts, an NAC (for no apical meristem [NAM], Arabidopsis transcription activation factor [ATAF], and cup-shaped cotyledon [CUC])-domain transcription factor gene, RhNAC100, was rapidly and dramatically induced by ethylene in the petals. Interestingly, accumulation of the RhNAC100 transcript was modulated by ethylene via microRNA164-dependent posttranscriptional regulation. Overexpression of RhNAC100 in Arabidopsis (Arabidopsis thaliana) substantially reduced the petal size by repressing petal cell expansion. By contrast, silencing of RhNAC100 in rose petals using virus-induced gene silencing significantly increased petal size and promoted cell expansion in the petal abaxial subepidermis (P , 0.05). Expression analysis showed that 22 out of the 29 cell expansion-related genes tested exhibited changes in expression in RhNAC100-silenced rose petals. Moreover, of those genes, one cellulose synthase and two aquaporin genes (Rosa hybrida Cellulose Synthase2 and R. hybrida Plasma Membrane Intrinsic Protein1;1/2;1) were identified as targets of RhNAC100. Our results suggest that ethylene regulates cell expansion by fine-tuning the microRNA164/RhNAC100 module and also provide new insights into the function of NAC transcription factors.

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Section: Discussion Floral Transcriptome and Ethylene-responsive Profmentioning

confidence: 99%

Section: Discussion Floral Transcriptome and Ethylene-responsive Profmentioning

confidence: 99%

An NAC Transcription Factor Controls Ethylene-Regulated Cell Expansion in Flower Petals

et al. 2013

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“…We identified over 100 transcripts likely involved in flower developmental processes (Additional file 10). These transcripts in Achimenes largely show similar expression patterns seen in other flowering plants [22, 25, 74]. The orthologs of many well-known MADS-box genes (e.g., AP1, AP3, PI, and AG ) are crucial for orchestrating floral organ identify [75, 76].…”

Section: Discussionmentioning

confidence: 89%

“…Linking protein evolution to the convergent evolution of these different pollination syndromes may provide evidence for shared or different genetic routes to these forms. Previous studies have suggested the pathways involved in pigment production, particularly anthocyanins, are involved in pollination syndrome transitions [45, 74, 75]. …”

Section: Discussionmentioning

confidence: 99%

Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

Roberts

Roalson

2017

BMC Genomics

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BackgroundFlowers have an amazingly diverse display of colors and shapes, and these characteristics often vary significantly among closely related species. The evolution of diverse floral form can be thought of as an adaptive response to pollination and reproduction, but it can also be seen through the lens of morphological and developmental constraints. To explore these interactions, we use RNA-seq across species and development to investigate gene expression and sequence evolution as they relate to the evolution of the diverse flowers in a group of Neotropical plants native to Mexico—magic flowers (Achimenes, Gesneriaceae).ResultsThe assembled transcriptomes contain between 29,000 and 42,000 genes expressed during development. We combine sequence orthology and coexpression clustering with analyses of protein evolution to identify candidate genes for roles in floral form evolution. Over 25% of transcripts captured were distinctive to Achimenes and overrepresented by genes involved in transcription factor activity. Using a model-based clustering approach we find dynamic, temporal patterns of gene expression among species. Selection tests provide evidence of positive selection in several genes with roles in pigment production, flowering time, and morphology. Combining these approaches to explore genes related to flower color and flower shape, we find distinct patterns that correspond to transitions of floral form among Achimenes species.ConclusionsThe floral transcriptomes developed from four species of Achimenes provide insight into the mechanisms involved in the evolution of diverse floral form among closely related species with different pollinators. We identified several candidate genes that will serve as an important and useful resource for future research. High conservation of sequence structure, patterns of gene coexpression, and detection of positive selection acting on few genes suggests that large phenotypic differences in floral form may be caused by genetic differences in a small set of genes. Our characterized floral transcriptomes provided here should facilitate further analyses into the genomics of flower development and the mechanisms underlying the evolution of diverse flowers in Achimenes and other Neotropical Gesneriaceae.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3623-8) contains supplementary material, which is available to authorized users.

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“…However, these rose ESTs remained limited to genes expressed during floral development and to date sequence information for only about 5000 genes exists in the databases [4]. Despite their relatively limited number, the available ESTs for the rose have been valuable for the identification of several novel genes associated with flower characters such as the scent related germacrene D synthase, O-methyltransferases and alcohol acetyltransferase genes [3,5-10].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome database resource and gene expression atlas for the rose

et al. 2012

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BackgroundFor centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce.ResultsHere, we used a combination of Illumina and 454 sequencing technologies to generate information on Rosa sp. transcripts using RNA from various tissues and in response to biotic and abiotic stresses. A total of 80714 transcript clusters were identified and 76611 peptides have been predicted among which 20997 have been clustered into 13900 protein families. BLASTp hits in closely related Rosaceae species revealed that about half of the predicted peptides in the strawberry and peach genomes have orthologs in Rosa dataset. Digital expression was obtained using RNA samples from organs at different development stages and under different stress conditions. qPCR validated the digital expression data for a selection of 23 genes with high or low expression levels. Comparative gene expression analyses between the different tissues and organs allowed the identification of clusters that are highly enriched in given tissues or under particular conditions, demonstrating the usefulness of the digital gene expression analysis. A web interface ROSAseq was created that allows data interrogation by BLAST, subsequent analysis of DNA clusters and access to thorough transcript annotation including best BLAST matches on Fragaria vesca, Prunus persica and Arabidopsis. The rose peptides dataset was used to create the ROSAcyc resource pathway database that allows access to the putative genes and enzymatic pathways.ConclusionsThe study provides useful information on Rosa expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy.

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Genomic Approach to Study Floral Development Genes in Rosa sp.

Cited by 47 publications

References 54 publications

An NAC Transcription Factor Controls Ethylene-Regulated Cell Expansion in Flower Petals

An NAC Transcription Factor Controls Ethylene-Regulated Cell Expansion in Flower Petals

Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

Transcriptome database resource and gene expression atlas for the rose

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