RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin
© Secco et al.; licensee BioMed Central Ltd. 2014
Received: 14 January 2014
Accepted: 18 March 2014
Published: 25 March 2014
Highly adapted plant species are able to alter their root architecture to improve nutrient uptake and thrive in environments with limited nutrient supply. Cluster roots (CRs) are specialised structures of dense lateral roots formed by several plant species for the effective mining of nutrient rich soil patches through a combination of increased surface area and exudation of carboxylates. White lupin is becoming a model-species allowing for the discovery of gene networks involved in CR development. A greater understanding of the underlying molecular mechanisms driving these developmental processes is important for the generation of smarter plants for a world with diminishing resources to improve food security.
RNA-seq analyses for three developmental stages of the CR formed under phosphorus-limited conditions and two of non-cluster roots have been performed for white lupin. In total 133,045,174 high-quality paired-end reads were used for a de novo assembly of the root transcriptome and merged with LAGI01 (Lupinus albus gene index) to generate an improved LAGI02 with 65,097 functionally annotated contigs. This was followed by comparative gene expression analysis. We show marked differences in the transcriptional response across the various cluster root stages to adjust to phosphate limitation by increasing uptake capacity and adjusting metabolic pathways. Several transcription factors such as PLT, SCR, PHB, PHV or AUX/IAA with a known role in the control of meristem activity and developmental processes show an increased expression in the tip of the CR. Genes involved in hormonal responses (PIN, LAX, YUC) and cell cycle control (CYCA/B, CDK) are also differentially expressed. In addition, we identify primary transcripts of miRNAs with established function in the root meristem.
Our gene expression analysis shows an intricate network of transcription factors and plant hormones controlling CR initiation and formation. In addition, functional differences between the different CR developmental stages in the acclimation to phosphorus starvation have been identified.
Phosphorus (P) is often one of the most limiting plant nutrients in soils leading to impeded plant growth and development. Although inorganic phosphate (Pi) is often abundant in soils, availability to the plant is limited by slow diffusion and fixation, e.g. as aluminum or iron oxide complexes . Therefore fertilisation with Pi derived from mined rock phosphate is essential in high intensity agriculture to maintain crop productivity. However, Pi is a non-renewable resource and, in conjunction with diminishing energy sources, this will in the future impact on fertiliser costs and food security . It is therefore of high importance to fully understand the mechanisms employed by plants under P deficiency as a knowledge base for the development of smart plants with increased capacity to mine and efficiently use Pi. This will become an increasingly important factor in the necessary sustainable intensification of productivity to feed a growing world population.
Plants have developed adaptive strategies to cope with limiting Pi availability. These physiological and developmental adaptations are collectively referred to as phosphate starvation response (PSR). This includes the transcriptional induction of genes coding for high-affinity phosphate transporters (PHTs) or purple acid phosphatases (PAPs) to increase uptake capacity and mobilisation of Pi . In addition, members of the SPX domain containing protein family (e.g. PHO1, SPX-MFS, NLA) involved in the regulation of Pi homeostasis, and enzymes re-modelling membrane lipid composition to remobilise Pi from phospholipids such as monogalactosyl diacylglycerol synthases (MGDs) and UDP-sulfoquinovose:DAG sulfoquinovosyltransferase (SQD2), are also differentially expressed [4, 5]. A central component of the PSR is the miRNA399/PHO2/PHR1 regulon. In Pi limited conditions the expression of miRNA399 is highly up-regulated by the transcription factor PHR1 leading to the degradation of its target PHO2. This E2 ubiquitin conjugase regulates protein turn-over of target proteins that include PHO1 and Pi transporters [6–9]. Morphological changes in root system architecture such as a decreased primary root growth and increased lateral root formation have been analysed on the molecular level in Arabidopsis . Specialised root structures termed cluster roots formed on lateral roots by dense rootlets of limited growth can be found in a diverse range of plant families such as the Fabaceae and Proteaceae [11, 12].
White lupin (Lupinus albus) has become a model plant for the analysis of cluster root (CR) biology . CR formation is a highly complex process in which developmental changes such as the initiation of lateral roots in addition to metabolic adjustments e.g. increased carboxylate production and secretion, have to be integrated to ensure their functioning. In white lupin foliar application of Pi inhibits cluster root development, providing evidence that systemic signalling is involved in cluster root formation . By contrast, local sensing of Pi-rich soil patches induces cluster root formation to increase root surface area . In addition, the secretion of large amounts of carboxylates such as citrate and malate from mature cluster roots (‘exudative burst’) generates a high and localised concentration able to mobilise Pi from insoluble forms .
The plant hormones auxin and cytokinin are important players in the regulation of cluster root development which is not surprising given their central function in the control of root development identified in non-cluster root forming model species such as Arabidopsis . In this species auxin is involved in the root architectural changes under Pi deficiency leading to reduced primary root growth and increased lateral root formation [18–20]. Cytokinin has an antagonistic role to auxin by promoting cell differentiation, inhibition of lateral root formation and preventing their formation in close proximity to each other [21–23]. In white lupin there is also increasing evidence for an involvement of auxin in the control of cluster root formation. The exogenous application of auxin promotes cluster root formation while auxin transport inhibitors have an impeding effect. Also, several genes involved in auxin signalling have been identified as expressed in developing cluster roots [24–26]. Similarly to observations on lateral root initiation in Arabidopsis, cytokinin also inhibits the formation of cluster roots in white lupin under Pi deficiency [26, 27].
Here we analyse cluster root formation in white lupin under phosphate limitation by RNA-seq. This is the first study that analyses different developmental stages of a forming cluster root on a transcriptomic scale. Our next-generation sequencing data contribute to the available information on the white lupin transcriptome as a further step in developing this species into a model plant for cluster root biology. We identify a complex network of hormone pathways and transcription factors involved in the regulation of early cluster root formation. In addition, functional differences between the various parts of the cluster root in the acclimation to phosphate deficiency are discovered.
Assembly of RNA-seq data and integration into LAGI01
Characteristics of white lupin de novo assemblies
No. of reads
No. of contigs
Average contig length
P-deficiency induces genes of the classical phosphate starvation response in cluster root tissues
Transcriptional control of metabolic acclimation to P deficiency
Thus far, no genome-wide transcriptomic study investigating the response of different developmental stages of a cluster root has been published. We therefore analysed our dataset for differences in the response of the three tissues under phosphate starvation. When analysing expression of classical PSI genes in the same tissues of plants grown under –P and + P conditions, i.e. MCR vs. MR and TCR vs. TR, genes belonging e.g. to the PHT1, SPX and PAP family showed a very similar response in the two tissue comparisons (Additional file 9). This indicates that the primary transcriptional response of genes directly involved in phosphate acquisition and homeostasis are regulated to a similar degree across the different stages of cluster root development.
In addition, several genes coding for membrane transporters were differentially expressed between MCR and TCR (Additional file 10). Interestingly, there was also a differential response of nitrate, ammonium and sulfate transporters. While a nitrate transporter homologous to NRT1.5 involved in root to shoot transport of NO3− in Arabidopsis was more highly expressed in the MCR, several others (e.g. NRT1.7, NRT2.4) showed higher expression in the TCR. Similarly, lupin homologs of sulfate transporters belonging to the SULTR3 family (SULTR3;1, SULTR3;5) were more abundant in the MCR and high-affinity transporters such as SULTR1;1 and SULTR1;3 showing higher expression in the TCR (Additional file 10).
Taken together, these results show that with the exception of genes directly involved in uptake and homeostasis of phosphate the cluster root tip was not involved in the metabolic acclimation of the cluster root to phosphate deficiency. Only genes directly involved in the uptake or recycling of phosphate were transcriptionally responding in this tissue. By contrast, the mature part of the cluster root was solely responsible to sustain the exudative burst and necessary anaplerotic reactions, thus also supporting Pi uptake of the root tip by making insoluble Pi available through exudation of carboxylates.
Regulation of cluster root formation by hormones and transcription factors
For Clusters 2 and 3 we identified only a limited number of GO terms enriched (Figure 5B and Additional file 11) with associated genes relating to oxidative stress (PRX, FBA, GAP-DH, ANNEXIN) and iron homeostasis (FER, VIT) (Figure 6A). These genes have lower expression in the younger stages of the cluster roots, e.g. homologs of the iron uptake regulator FER and peroxidase show a 30-fold and 15-fold lower expression in the TCR than the MCR (Figure 6A). This is in agreement with results identifying oxidative stress through reactive oxygen (ROS) production as a confounding effect of phosphate starvation [30, 31]. Our results provide evidence that this is more so in the mature part of the cluster root, likely as a consequence of the higher metabolic activity. However, the peroxidase homologs were more highly expressed in the root tip than in the mature part of P-sufficient plants.
Given the extensive differences observed in the transcriptomes of the three cluster root stages and the complex developmental changes involved it is not surprising we also observed differences in gene expression levels for several transcription factors (TFs) across the three cluster root samples other than the already described AUX/IAA and FER. For several contigs with homology to the AP2/ERF class TFs of the PLETHORA family (PLT2/3/7) expression was about 30- and 10-fold higher in the cluster root tip than in the immature and mature cluster root tissues, respectively, while it was not changed in the P-sufficient MR and TR (Figure 6B). Similarly, homologs of the homeodomain-leucin zipper transcription factor ATHB2 were most highly expressed in the TCR. Several other TFs (SCR, MGP, WOX5, PHB, PHV) of the regulatory network controlling the activity and cell fate within the root meristem also show higher expression in the TCR (Figure 6B). For these there is an at least 8-fold higher expression in the TCR than in the MCR and little difference between TR and MR. Interestingly, the expression of a homolog of the bHLH transcription factor UPB1 (UPBEAT1), a repressor of peroxidase expression and central regulator of ROS balance controlling the transition from proliferation to differentiation in the root , was contrasting with peroxidase expression in the cluster roots but not the non-cluster root (Figure 6A and B).
Cytokinin (CK) is also an important regulator of cell differentiation within the root and also repressed the expression of PHB and miRNA165. Therefore CK is also a component of the regulatory network governing root development . Correspondingly, several LAGI02 contigs with sequence homology to the Arabidopsis cytokinin oxidases (CKX) involved in CK degradation, are down-regulated by about 5-fold in the TCR when compared to the MCR (Figure 6A). At the same time a lupin homolog of the Arabidopsis cytokinin receptor CRE1 was about 5-fold more highly expressed in the TCR than in the MCR. These gene expression patterns suggest an increase in local cytokinin concentration and CK sensitivity towards the root tip to remove inhibition of lateral root development and observed responsiveness of PSR genes [33, 34].
Thus, our data identified a complex regulatory circuit of transcription factors and of the plant hormones auxin and cytokinin involved in the initiation of cluster roots in white lupin. These prime lateral root formation, promote their initiation and elongation under P-limited conditions.
Identification of pri-miRNAs expressed in the cluster root
Metabolic acclimation to P-limitation
Cluster root formation is an important adaptive trait to cope with limiting P-availability in several plant species. Analysis of the molecular mechanisms underpinning this complex developmental process will give a better understanding of the ways plants cope with limited P supply. Advances in next-generation sequencing technology permit probing for transcriptome-wide changes in gene expression in non-model species such as white lupin. Incorporation of our RNA-seq data into the existing data set , thus generating an improved sequence resource, in conjunction with functional gene annotation, will allow white lupin to become a molecular model species for the analysis of cluster root development. We have started to exploit this resource by analysis of transcriptomic differences in several stages of cluster root formation. Phosphate starvation-induced changes in gene expression were very similar when comparing root tip and mature parts of P-sufficient with P-deficient plants, respectively. This included mainly well characterised genes involved in the uptake, re-distribution and homeostasis of phosphate, i.e. phosphate transporters, SPX-domain genes or genes involved in lipid remodelling. Very similar sets of genes have been identified in studies of the root transcriptome in species such as white lupin , Arabidopsis [37–39] and rice [40–42]. By contrast, tissue-specific differences identify functional specialisation of the different cluster root stages of P-starved plants. In the MCR changes in gene expression are geared to support the metabolic reactions involved in the synthesis and secretion of large amounts of organic acids, i.e. up-regulation of genes belonging to the TCA cycle or glycolysis. This confirms earlier results in a spatially higher resolution and on a transcriptome-wide scale [26, 43]. Our results indicate that the root tip is not producing or exporting organic acids and depend for this on the mature part of the cluster root. However, the root tip increases Pi uptake and acquisition capacity to profit from the exudative burst and subsequently liberated phosphate from insoluble complexes.
Previously, a close link between the regulation of sulfate and nitrate homeostasis under phosphate deficiency has been shown [44–46]. We identify an extra level of complexity by which the uptake and translocation of these anions between the various tissues of the developing cluster root is regulated. In addition, sustained uptake of iron under phosphate starvation can lead to iron toxicity and therefore reduced iron uptake is a mechanism to protect meristem activity . The down-regulation of a homolog of the transcriptional regulator of iron responses FER/FIT and a vacuolar iron transporter VIT in the TCR confirms this interconnection of iron and phosphate homeostasis and its importance for the root tip [40, 48, 49].
Hormonal control of cluster root development
Cluster root formation provides insight into how plants use general regulatory components to form specialised structures to adapt to their environment. We show that white lupin uses the same set of plant hormones (i.e. auxin and cytokinin) and transcription factors identified in model plant species with a less complex root architecture, such as Arabidopsis and rice [50, 51], to initiate and regulate cluster root formation. The increased expression of CYC and CDK genes towards the cluster root tip reflects the cell proliferation and divisions occurring in the meristematic zone of the tip and the initiation of laterals from pericycle cells in the differentiation zone . Several genes of the auxin-mediated signalling cascade are differentially expressed in the analysed cluster root stages with higher transcript abundance in the root tip. The auxin efflux carriers of the PIN family are essential to generate the auxin gradient within the root by polar transport towards the tip following the ‘fountain model’, leading to the primed state of lateral root founder cells and thus controlling lateral root initiation [52, 53]. Members of the LAX auxin-influx carrier family are involved in the auxin accumulation close to the lateral root primordium promoting lateral root emergence , while the Aux/IAA protein family in conjunction with auxin response factor (ARFs) regulate the expression of downstream genes . The high expression of YUC2 and IAMT1 towards the cluster root tip points to the importance of local auxin synthesis in cluster root formation. YUC2 is directly involved in the synthesis of auxin and has been shown to be expressed in the root meristem in Arabidopsis [56, 57]. This flavin-monooxygenase is part of the main auxin biosynthetic pathway and catalyses the conversion of the precursor indole-3-pyruvic acid into the active auxin IAA . Recently, a role for root-derived auxin in cluster root formation has also been shown in white lupin  and here we identify YUC2 as a likely biosynthetic enzyme involved. IAMT1 encodes an IAA carboxyl methyltransferases converting IAA to methyl-IAA ester and involved in the regulation of auxin homeostasis . The two genes NPH3 and WAT1 regulate growth by modification of the subcellular targeting of the auxin efflux carrier PIN2 and secondary cell wall formation by altering root auxin concentration, respectively [59, 60]. Recently, CK has also been identified as an important signalling component in the Pi-deficiency induced changes in lupin root architecture . In addition, studies in Arabidopsis have shown that CK prevents the initiation of lateral roots in close proximity. The observed lower expression of the CK degrading enzyme CKX and the up-regulation of the CK receptor CRE1 towards the cluster root tip provides evidence that the formation of cluster roots depends on a localised accumulation and increased ability to perceive CK in this part of the root to allow for the dense formation of lateral roots .
Differentially expressed transcription factors
Several transcription factors (TFs) known to regulate root meristem function and lateral root initiation in Arabidopsis are also differentially regulated in the three cluster root stages of white lupin. Members of the PLETHORA (PLT) family of TFs regulate cell proliferation, elongation and differentiation via an auxin-induced expression gradient along the root . In Arabidopsis the GRAS TF family member SCARECROW (SCR), the zinc finger TF MAGPIE (MGP) and the HD-Zip TF WOX5 are major regulators in maintaining the stem cell niche in the quiescent centre of the root meristem. SCR is also involved in the differentiation process leading to the specific root tissue types . Additionally, SCR forms a regulatory network together with the transcription factors PHABULOSA and PHAVOLUTA (PHB/PHV), two TFs also differentially expressed in the TCR and MCR, and microRNA165/6 to consolidate cell identities in the developing root . Interestingly, PHB has recently been shown to regulate cytokinin (CK) signalling by activating the CK biosynthesis gene IPT7 . Root hairs are an important site of nutrient uptake as they increase root surface area and in white lupin their formation is induced already two days after lateral root emergence . In agreement with this is the expression of homologs of the central regulator of root hair formation RSL1 in the ICR and RSL2 towards the mature part of the cluster root. These bHLH-type transcription factors are essential for root hair development and consequently mutants of the corresponding genes in Arabidopsis, Lotus and Physcomitrella are deficient of root hairs [63–65].
The detected down-regulation of the lupin TF homolog of ERF6, a regulator of the response to oxidative stress , is in agreement with the ROS-related stress induction under phosphate limitation. The accumulation of H2O2 in the root cortex has been observed for P-deprived Arabidopsis plants . Interestingly, we also found a contrasting expression of the TF UBP1 and peroxidases in the cluster root. In Arabidopsis UBP1 regulates the expression of peroxidases within the root tip, thereby modulating the distribution of ROS species and controlling the transition from proliferation to differentiation . Together, these results may indicate that reactive oxygen species are signalling molecules, but also products of oxidative stress, that require a complex regulation of local concentrations in the developing white lupin cluster root.
White lupin pri-miRNAs
In addition to plant hormones and transcription factors, miRNAs are also important components in the regulation of root development . We have been able to identify several primary transcripts of miRNAs (pri-miRNAs) expressed in the white lupin cluster root. We could not identify a homolog of pri-miRNA399, a highly induced miRNA under P-deficiency, in our cluster root assembly. This is not surprising as the mature miRNA in white lupin has been found exclusively in leaves, showing an up-regulation under P-limited growth conditions , likely to serve as a phloem-mobile signal [69, 70]. miRNA156 was more abundant in cluster roots than in the P-supplied roots. Although the function of this miRNA in the regulation of P homeostasis is not known, it is up-regulated under phosphate starvation in the roots of white lupin and Arabidopsis [35, 36]. In Arabidopsis targets of miRNA166 are the TFs PHB and PHV, for which white lupin homologs show variation in transcript abundance across the cluster root tissues, and these form a regulatory circuit to control cell fate in the root meristem . The targets of miRNA393 are several F-Box proteins of the TIR1 subfamily (TIR1, AFB1/2/3) of auxin receptors and a TF of the bHLH family (bHLH77). In agreement with this it has been shown that the modulation of auxin sensitivity under phosphate deficiency, responsible for the alteration in lateral root patterning, is dependent on TIR1 . With auxin being the major signalling molecule controlling root development it is therefore likely that miRNA393 and TIR1 play a role in the auxin-mediated regulation of cluster root formation. For the other identified miRNAs transcript abundance was similar across the analysed root tissues. This is in agreement with findings that only a few pri-miRNA show an altered expression under abiotic stresses although the abundance of the corresponding mature miRNA changes. This discrepancy has been attributed to differential turn-over of the mature miRNA and the processing efficiency of the pri-miRNAs [71, 72].
In conclusion, cluster root formation is a complex process that integrates spatiotemporally developmental events from the sensing of nutrient limitation, especially phosphorus, to the formation of a morphologically highly organised structure. We have identified an intricate network of signalling components and accompanying changes in gene expression controlling the formation of cluster roots. This also allows the plant to acclimate to Pi limitation in the different developmental stages of the cluster root. A better understanding of such adaptive mechanisms will help in improving plants by increasing their phosphate acquisition efficiency.
Plants were grown and tissue harvested identical to Florez-Sarasa et al.. Briefly, seeds of white lupin (Lupinus albus L. cv. Kiev mutant) were sown and germinated in pots filled with washed sand. Seedlings were carefully removed and the roots gently washed free of sand. Seven-day-old seedlings of uniform size were then transferred to a solution culture system each holding 20 L of continuously aerated nutrient solution (pH5.5) with the following composition: 5 mM KNO3, 1.5 mM Ca(NO3)2, 1 mM MgSO4, 23.1 μM H3BO3, 0.38 μM ZnSO4, 0.29 μM Na2MoO4, 0.16 μM CuSO4, 4.85 μM MnSO4, 19.14 μM Fe-EDDHA and for P sufficient plants supplemented with 1 mM NH4H2PO4 for the + P treatment. The entire nutrient solution was fully changed twice a week and pH was checked daily and readjusted back to around pH5.5. The plants were grown in a temperature-controlled glasshouse, with tubs half-immersed in a basin maintained at 19–22°C. The tubs were randomized and rotated weekly. Roots at the 6 to 8-trifoliolate stage were excised as root tips (TR, 1.5 cm of the root apex) and mature root (MR, 1.5 cm from the root base) for P sufficient plants and root tip (TCR, 1.5 cm of the root apex, free of visible laterals), immature cluster root (ICR, 1 cm following the TCR with developing laterals) and mature cluster root (MCR, 1 cm with only mature laterals) for P-deficient plants identical to Florez-Sarasa et al.. The experiment was performed in three independent biological replicates.
RNA extraction and next generation sequencing
The total RNA from the roots tissues was extracted using the Spectrum Plant Total RNA kit (Sigma-Aldrich, Castle Hill, Australia) according to the manufacturer’s instructions. The integrity and quality of the total RNA was checked using NanoDrop 1000 Spectrophotometer and formaldehyde agarose gel electrophoresis. RNA was only used when the Abs260 nm/Abs280 nm ratio was >1.8.
For RNA-seq library synthesis, 1 μg of total RNA was first depleted of rRNA using the Ribo-Zero rRNA Magnetic Kit (Plant Seed/Root kit, Epicentre, Madison, USA). Sequencing libraries were generated using the TruSeq RNA Sample Prep Kit (Illumina, Scoresby, Australia). Sequencing was then performed on a Hiseq 1000 as a 2 × 101 bp paired-end run according to manufacturer’s instructions (Illumina, Scoresby, Australia). RNA-seq read data were deposited to the NCBI Sequence Read Archive (NCBI SRA) under accession number SRA145661.
De novotranscriptome assembly and functional classification
For the assembly of RNA-seq reads into contigs the Velvet/Oases pipeline was applied . In total 133,045,174 paired-end reads of the three replicates from the five tissues samples were obtained. These reads were of high quality with a Phred score of above +30 and a minimal length of 90 bases. For optimisation of Velvet assembly parameters a Perl-based script was used (VelvetOptimiser Version 2.2.5, Victorian Bioinformatics Consortium, Monash University) which identified an optimal k-mer length of 67 for the assembly. To combine the obtained contigs with LAGI01 , the two assemblies were merged using CD-HIT-EST . For annotation, homology searches were performed with Blast2go  against the NCBI database using the blastx algorithm with a cut-off of E < 10−15and targeted searches using the BLAT algorithm  against the soybean (Gmax_189) and Arabidopsis (TAIR10) transcriptome releases. Finally, contigs below 200 bp in length, with no assigned annotation or identified as contamination were removed from the assembly to yield the Lupinus albus Gene Index Version 2 (LAGI02) with a total of 65,097 contigs (sequences supplied in Additional files 2 and 3). Because the highest similarity in homology searches was observed between the soybean and lupin transcriptomes, GO terms for LAGI02 contigs were assigned based on the Gmax_189 genome release.
Gene expression and data analysis
For gene expression analysis RNA-seq reads obtained for the three biological replicates for each tissue were mapped to the LAGI02 transcriptome using the Bowtie tool . For quantification of transcript abundances and identification of significant changes in transcript expression the Cuffdiff tool with a upper quartile normalisation and multi read correction was applied to obtain FPKM values . Hierarchical clustering was performed using the Manhattan distance matrix of the heatmap.2 function in the gplots package of the R environment. Over-representation of GO terms within gene clusters was identified with the BiNGO plugin for Cytoscape using a hypergeometric test after Benjamini and Hochberg FDR correction with a significance level of p < 0.01 . For predication of miRNA hairpin structures the Vienna RNA websuite was used .
Availability of supporting data
All sequences for LAGI02 contigs and their annotation are available as additional files (Additional files 1, 2 and 3). RNA-seq read data has been deposited in the NCBI SRA database under accession SRA145672.
We would like to thank Xing Wang (School of Plant Biology, The University of Western Australia) for technical assistance with plant growth and for tissue collection and Hans Lambers (School of Plant Biology, The University of Western Australia) for critical comments on the manuscript. This work was supported by the Australian Research Council (FS10010002; D.S.), (CEO561495, CE140100008; J.W.), contributions by the Australian Research Council and the Department of Agriculture and Food WA (LP0990355; O.B.), the National Science Foundation of China (31172024, 31201675; H.S.) and the Ministry of Science and Technology of China (2010DFA31080, 2011CB100303; H.S.).
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