Arabidopsis an atlas of morphology and development pdf
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- Arabidopsis: An Atlas of Morphology and Development
- Proteomic and transcriptomic profiling of aerial organ development in Arabidopsis
Metrics details. The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants.
Although several studies have explored gene expression during flower development in the model plant Arabidopsis thaliana on a genome-wide scale, a continuous series of expression data from the earliest floral stages until maturation has been lacking.
Here, we used a floral induction system to close this information gap and to generate a reference dataset for stage-specific gene expression during flower formation. Using a floral induction system, we collected floral buds at 14 different stages from the time of initiation until maturation. Using whole-genome microarray analysis, we identified 7, genes that exhibit rapid expression changes during flower development.
These genes comprise many known floral regulators and we found that the expression profiles for these regulators match their known expression patterns, thus validating the dataset. We analyzed groups of co-expressed genes for over-represented cellular and developmental functions through Gene Ontology analysis and found that they could be assigned specific patterns of activities, which are in agreement with the progression of flower development. Furthermore, by mapping binding sites of floral organ identity factors onto our dataset, we were able to identify gene groups that are likely predominantly under control of these transcriptional regulators.
We further found that the distribution of paralogs among groups of co-expressed genes varies considerably, with genes expressed predominantly at early and intermediate stages of flower development showing the highest proportion of such genes.
Our results highlight and describe the dynamic expression changes undergone by a large number of genes during flower development. They further provide a comprehensive reference dataset for temporal gene expression during flower formation and we demonstrate that it can be used to integrate data from other genomics approaches such as genome-wide localization studies of transcription factor binding sites. The formation of flowers is one of the main models for studying the molecular mechanisms underlying the control of plant development.
Over the past three decades, a large number of regulatory genes, which control a multitude of different processes during flower morphogenesis, have been identified mainly through a combination of forward and reverse genetics approaches [ 1 — 3 ]. Work in Arabidopsis thaliana in particular has led to an understanding of the molecular mechanisms underlying the functions of many of these regulatory genes [ 4 ].
Furthermore, it has yielded detailed insights into the regulatory hierarchies among genes that play roles in the control of floral organ formation [ 5 , 6 ]. With the advent of the genomics era, genetic approaches employed to elucidate the regulation of flower development have been complemented by methods such as global transcript profiling and genome-wide localization studies of transcription factor binding sites.
Unfortunately, this work has been hampered in Arabidopsis by the fact that flowers of this model plant are small and early-stage floral buds are too minute to be dissected reliably through conventional approaches. Also, Arabidopsis flowers are initiated sequentially so that all flowers in an inflorescence are at distinct developmental stages [ 7 ]. As a consequence, the collection of sufficient numbers of flowers at particular stages for analysis by genomic technologies is challenging especially for early flower development.
To circumvent this problem, a number of approaches have been employed: recently, laser capture microdissection has been used to generate transcriptional profiles of early-stage floral buds [ 8 ]. An alternative and largely complementary approach has been the use of floral induction systems, which allow the collection of hundreds of synchronized floral buds from a single plant see below. These systems have been employed to study both temporal and spatial gene expression during the early stages of flower development [ 9 — 14 ].
Other studies have analyzed gene expression in whole inflorescences of wild-type and mutant plants and in some cases relied on the removal of older and relatively large buds that may unduly contribute to RNA preparations from these tissues [ 15 — 19 ]. Moreover, transcript profiling was done with wild-type flowers at individual stages and with distinct floral organ types, but this work has been limited to older flowers, as they can be collected with relative ease [ 17 ].
Obtaining this information could be highly informative as it would provide a comprehensive view of stage-specific gene expression activities over the entire course of development and would constitute an important component of a gene expression map. Furthermore, such a dataset could be used in analyses, in which, for example, data from transcript profiling and genome-wide localization studies are integrated to obtain a better understanding of the gene network that controls flower formation.
In this study, we employed a floral induction system to close this knowledge gap and to monitor temporal gene expression during flower development from the time of initiation to maturation. We validated the resulting dataset and used it to obtain novel insights into the processes underlying the formation of flowers on a global scale through computational approaches. To identify patterns of gene expression during flower development from the time of initiation to maturation stage 13; stages according to [ 7 ] , we employed a previously described floral induction system, which allows the collection of hundreds of floral buds from a single plant [ 9 , 13 , 24 , 25 ].
Ap1 cal plants accumulate inflorescence-like meristems at their shoot apices [ 26 , 27 ], and activation of the AP1-GR fusion protein in this background through treatment of the plants with the steroid hormone dexamethasone results in the transformation of these meristems into floral primordia, which subsequently develop in a largely synchronized manner.
However, at intermediate stages, this synchronization is gradually lost likely due to space constraints [ 9 ]. Despite this overall loss of synchronization, we noticed that flowers at the very tip of the inflorescence heads remained fairly synchronized throughout flower development perhaps due to a larger degree of curvature in his area, which may allow floral buds to develop without coming into contact with neighboring flowers.
For the gene expression profiling experiments, we therefore collected older floral buds days 9 to 13 after dexamethasone treatment, corresponding to stages to 13, respectively from this region alone, while younger flowers were harvested more liberally from the inflorescences of AP1 pro :AP1-GR ap1 cal plants Fig.
To obtain expression data for a large number of distinct floral stages, we collected floral buds at 14 different time-points either immediately before referred to as 0 d time-point or from 1 to 13 d after the induction of flower development through treatment with dexamethasone Fig.
Because early flower development is characterized by dramatic changes in morphology [ 7 ] and involves a large number of transcriptional regulators that control important processes such as floral patterning and floral organ specification [ 4 ], we collected most samples at those stages with intervals in-between time-points ranging from 0.
At later stages of development, the intervals for sample collection were extended to 2 d Fig. Analysis of temporal gene expression during flower development. The development of flowers on a given inflorescence was largely synchronous until day 7. For later time-points h-j , flowers were harvested from the tip of the inflorescences arrowheads after phenotypic assessment. Floral buds from the time of initiation until anthesis corresponding to stage 13 were sampled.
For microarray analysis of the tissue samples, we employed a common reference design e. We then assessed the resulting data for reproducibility and found that the replicates for the individual time-points correlated well Figure S1 in Additional file 1 ; see also Fig.
In order to determine significant expression changes, we applied an F-statistic and searched across the entire dataset for genes with differential expression.
Because many of these transcriptional changes may be caused by the dramatic alterations in floral size and morphology during the course of development and not by specific gene regulatory events, we next sought to identify genes whose expression changed relatively rapidly. To this end, we compared gene expression between consecutive as well as near-by within a 2-d time interval time-points to minimize the effects of morphological alterations and identified 7, genes as differentially expressed Additional file 2.
Many of these differentially expressed genes DEGs were detected at intermediate between 5 and 9 d after dexamethasone treatment and late between 9 and 13 d stages of flower development, and overall, a preponderance of gene activation over repression was observed Table S1 in Additional file 1. Expression profiles of known floral regulators.
Red, green and blue lines represent data from three biologically independent sets of samples, black lines the mean values of the replicate experiments. Note the high reproducibility of the expression data across all time-points. To validate the results of the microarray experiments, we assessed the expression profiles of genes with known roles in different processes during flower development Fig.
This difference might stem from initially low mRNA levels, which might hamper a reliable detection in in situ hybridization or reporter gene essays. We also compared our dataset to those from several previous studies in which temporal [ 8 — 10 , 14 ] and spatial [ 11 , 16 ] gene expression during flower development had been analyzed either in early or in late-stage flowers using different floral induction systems, laser capture microdissection of wild-type flowers, or through a comparison of the gene expression profiles of inflorescences of floral mutants and of the wild type, respectively.
For each pair-wise comparison, we found a significant overlap between the datasets and the one described in this study Table S2 in Additional file 1 and Additional file 3 , further validating the results of our time-course experiment. Because functionally related genes are often co-expressed during development, we used a k -means algorithm to group the DEGs into 15 clusters with distinct gene expression profiles Fig.
Notable exceptions include genes in clusters 5, 11 and 15, which are up-regulated during early flower development and are repressed at intermediate to late stages.
Also, clusters 6 and 7 contain genes that are expressed at the earliest floral stages and are subsequently down-regulated. Genes assigned to clusters 4 and 12 are activated during early flower development when organ primordia are initiated and remain expressed until flowers have reached maturity, suggesting that many of them might play roles during the course of floral organ morphogenesis.
Genes showing differential expression during flower development. Groups of co-expressed genes were identified among 7, differentially expressed genes detected in the time-course experiment. For a different representation of the individual clusters, see Figure S3.
To obtain insights into the functions of the genes assigned to each of the clusters and to further validate the microarray data, we mapped the groups of co-expressed genes onto an Arabidopsis gene expression atlas we had generated previously [ 13 ] based on published data Fig. We then determined the percentage of genes with maximum Fig. For some of the clusters, this analysis allowed predictions of the predominant location of gene expression.
For example, a high percentage of genes with maximum expression in pollen was identified in clusters 2, 3, , and Genes assigned to these clusters were predominantly expressed from or after the 9-d time-point and thus at stages when pollen formation occurs [ 46 ].
Clusters 6, 7, and 13 contained the highest proportion of genes with maximum expression in meristems, in agreement with the observation that genes in these clusters are strongly expressed during the earliest floral stages, but are repressed towards more intermediate stages when meristematic activity in flowers ceases.
The highest percentage of genes with maximum expression in ovules was found in cluster 15, which contains relatively few genes that are strongly expressed around the 7 and 9-day time-points corresponding to floral stages ; Fig. Mapping groups of co-expressed genes onto an Arabidopsis gene expression atlas. Results for cluster 3 are shown as an example. Individual tissue and organ samples of the gene expression atlas shown in full in Additional file 4 were grouped together as indicated.
Note a preponderance of expression in stamen and pollen samples. GO terms directly associated with flower formation e. As described above, these clusters contain genes that are repressed at early to mid-stages clusters 6 and 7 or are activated during early flower development clusters 11 and 12 and remain expressed at least until the end of the intermediate phase of flower development.
Genes involved in cell differentiation were enriched in clusters 8 and 10, which contain genes with predominant expression at late stages of flower development stages Many of these genes exhibit maximum expression in pollen Fig.
Genes involved in the response to different phytohormones such as jasmonic acid, auxin, and abscisic acid were detected as enriched predominantly in cluster 8, in agreement with the known roles of these hormones in various processes during late-stage flower development, which include stamen and pollen formation as well as the maturation of petals [ 48 ].
In contrast, genes involved in the response to gibberellin were over-represented in cluster 4, which contains genes that are induced at the end of the early phase of flower development and remain active until floral maturity has been reached. In agreement with this observation, it has been shown that gibberellins are required for proper floral organ growth and elongation [ 49 ].
In sum, the results of these analyses allowed us to attribute specific functions to the individual clusters that together account for many of the processes known to occur during flower development. Gene Ontology terms enriched in the dataset. Adjusted p- values for selected GO terms related to a developmental functions and b cellular and regulatory processes are indicated for each cluster through color-coding see bars at the top right for colors used.
For a full list of GO terms enriched in the dataset, see Additional file 5. Floral organ identity factors are necessary and sufficient for the specification and development of the different types of floral organs [ 5 , 6 ]. They act in a combinatorial manner as predicted by the well-supported A BCE model of floral organ identity specification [ 50 — 52 ].
Insights into the functions of these master regulators, which with the exception of APETALA2 all belong to the family of MADS-domain proteins and are components of higher-order regulatory protein complexes [ 53 ], have been obtained in recent years through a combination of genome-wide localization studies and gene perturbation experiments [ 5 , 6 ]. This work has resulted in the identification of some of their direct target genes and of the cellular and developmental processes they control.
Furthermore, it has been shown that the floral organ identity factors bind to many of the same sites in the Arabidopsis genome [ 13 ] and that their global binding patterns undergo changes as flower development progresses, at least in part as a consequence of stage-specific alterations in chromatin accessibility [ 14 ]. Also, the majority of genes bound by these transcription factors at early floral stages do not respond transcriptionally when the activities of the floral homeotic genes are perturbed [ 12 , 13 ].
While the molecular mechanisms underlying these observations are currently not well understood, it is clear that from binding data alone it is difficult to identify their bona fide target genes.
Largely independent of the transcription factor under study, we found the highest degree of binding site enrichment in clusters 6, 7, 11, and 12 Fig. Cluster 5 also showed a significant enrichment for genes with binding sites, but only for SEP3 and AP1, and not at the earliest stage 2 time-point.
The genes assigned to these different clusters have in common that their transcription changes at the time or shortly after the expression of the floral organ identity genes commences around stage 3.
Furthermore, they contain many genes associated with the specification of floral organ identity, as well as the regulation of floral organ development and meristem determinacy Fig.
Hence, genes in these clusters containing binding sites for the MADS-domain proteins are good candidates for target genes. In fact, they do contain many of the genes known to act directly downstream of these floral regulators Additional file 6.
However, one caveat of this analysis is that the floral organ identity factors appear to have largely distinct sets of target genes despite their overlapping binding patterns [ 5 ]. Therefore, while genes that are differentially expressed during early flower development and that contain binding sites for MADS-domain proteins are likely under control of floral organ identity factors, the exact regulatory complex that might be active in the regulation of a given gene cannot be readily deduced without additional data from floral organ identity gene-specific perturbation experiments.
Distribution of genes with binding sites for floral organ identity factors.
Skip to search form Skip to main content You are currently offline. Some features of the site may not work correctly. DOI: Bowman Published Biology. This is the first atlas to document the morphology and development of Arabidopsis thaliana, the small flowering plant which emerged during the 's as the primary model for research in the surging field of plant biology. Arabidopsis is the plant of choice for many studies in genetics, biochemistry, development, and radiation biology. This atlas consists of contributions from many of the world's leading Arabidopsis laboratories and is a "must have" volume for plant biologists.
A fundamental question in biology is how morphogenesis integrates the multitude of processes that act at different scales, ranging from the molecular control of gene expression to cellular coordination in a tissue. Using machine-learning-based digital image analysis, we generated a three-dimensional atlas of ovule development in Arabidopsis thaliana , enabling the quantitative spatio-temporal analysis of cellular and gene expression patterns with cell and tissue resolution. We discovered novel morphological manifestations of ovule polarity, a new mode of cell layer formation, and previously unrecognized subepidermal cell populations that initiate ovule curvature. Our work demonstrates the analytical power of a three-dimensional digital representation when studying the morphogenesis of an organ of complex architecture that eventually consists of cells. How organs attain their species-specific size and shape in a reproducible manner is an important question in biology.
Arabidopsis: An Atlas of Morphology and Development
Metrics details. The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thaliana on a genome-wide scale, a continuous series of expression data from the earliest floral stages until maturation has been lacking. Here, we used a floral induction system to close this information gap and to generate a reference dataset for stage-specific gene expression during flower formation. Using a floral induction system, we collected floral buds at 14 different stages from the time of initiation until maturation.
Proteomic and transcriptomic profiling of aerial organ development in Arabidopsis
This atlas documents the morphology and development of Arabidopsis thaliana, a small flowering plant which emerged during the s as a primary model for research in the field of plant biology. It covers embryogenesis, vegetative and root growth, reproduction and host-pathogen interaction. Read more Please choose whether or not you want other users to be able to see on your profile that this library is a favorite of yours. Finding libraries that hold this item
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