GreenPhylDB v2.0: comparative and functional genomics in plants

Rouard, Mathieu; Guignon, Valentin; Aluome, Christelle; Laporte, Marie‐Angélique; Droc, Gaëtan; Walde, C.; Zmasek, Christian M.; Périn, Christophe; Conte, Matthieu

doi:10.1093/nar/gkq811

Cited by 101 publications

(90 citation statements)

References 51 publications

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“…In the present study, we have analyzed more systematically the occurrence of integrated decoy domains in NLRs from 31 plant species: 30 higher plants and one moss species. For our systemic analysis, we used the publicly available data of the GreenPhyl database where a huge number of sequenced genomes have been analyzed with a common set of criteria for establishing protein family clusters (Rouard et al ., 2011). Comparison of this NLR data set with the published, expert‐curated NLR repertoires of A. thaliana and rice showed for both species a good representativeness of the GreenPhyl database and suggested good coverage for the other species.…”

Section: Discussionmentioning

confidence: 99%

Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread

et al. 2016

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Summary Plant immune receptors of the class of nucleotide‐binding and leucine‐rich repeat domain (NLR) proteins can contain additional domains besides canonical NB‐ARC (nucleotide‐binding adaptor shared by APAF‐1, R proteins, and CED‐4 (NB‐ARC)) and leucine‐rich repeat (LRR) domains. Recent research suggests that these additional domains act as integrated decoys recognizing effectors from pathogens. Proteins homologous to integrated decoys are suspected to be effector targets and involved in disease or resistance.Here, we scrutinized 31 entire plant genomes to identify putative integrated decoy domains in NLR proteins using the Interpro search. The involvement of the Zinc Finger–BED type (ZBED) protein containing a putative decoy domain, called BED, in rice (Oryza sativa) resistance was investigated by evaluating susceptibility to the blast fungus Magnaporthe oryzae in rice over‐expression and knock‐out mutants.This analysis showed that all plants tested had integrated various atypical protein domains into their NLR proteins (on average 3.5% of all NLR proteins). We also demonstrated that modifying the expression of the ZBED gene modified disease susceptibility.This study suggests that integration of decoy domains in NLR immune receptors is widespread and frequent in plants. The integrated decoy model is therefore a powerful concept to identify new proteins involved in disease resistance. Further in‐depth examination of additional domains in NLR proteins promises to unravel many new proteins of the plant immune system.

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Section: Discussionmentioning

confidence: 99%

Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread

et al. 2016

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“…We defined the transcriptomes of S. moellendorffii roots (produced from rhizophores via bulbils) from the MZ and the combined EZ + DZ (EDZ) (necessary due to the superimposition of EZ and DZ characters in the S. moellendorffii root; Figure 1A) for three biological replicates each (Figures 5A and 5B;Supplemental Data Set 8). Among the 5465 gene families containing at least one gene from S. moellendorffii and each of the six angiosperms (defined by GreenPhyl; Rouard et al, 2011), we discovered a significant association by family for root-expressed genes in S. moellendorffii and root-expressed genes in angiosperms (P < 0.001; Fisher's exact test; Supplemental Data Sets 2 and 3). Specifically, 81.6% of families that contained a root-expressed gene from each of the six angiosperms also contained a root-expressed S. moellendorffii gene.…”

Section: Selaginella Moellendorffiimentioning

confidence: 90%

“…Among the 6613 gene families that possess at least one gene from each of these six angiosperms (Rouard et al, 2011), we discovered a nonrandom distribution of root-expressed genes (P < 0.001; x 2 test), with root-expressed genes from different species tending to associate in families (Supplemental Data Sets 2 and 3). This suggests that gene families devoted to root functions have been conserved during angiosperm evolution.…”

Section: Root Gene Expression Is Conserved Across Angiospermsmentioning

confidence: 99%

“…Using previously defined Arabidopsis gene family assignments (GreenPhyl v4; Rouard et al, 2011), we discovered that the rootexpressed Arabidopsis genes are not randomly distributed, but tend to cluster among families (P < 0.001, x 2 test; Supplemental Data Sets 2 and 3). Similarly, we observed a nonrandom (clustering) distribution among families for those genes exhibiting preferential root zone expression ($2.0 fold change [FC]; false discovery rate [FDR] # 0.05) in the MZ, the EZ, or the DZ (P < 0.001 for each gene set, x 2 test; Supplemental Data Sets 3 and 4).…”

Section: Gene Expression In Root Development Zones Of Arabidopsismentioning

confidence: 99%

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Conserved Gene Expression Programs in Developing Roots from Diverse Plants

Huang

Schiefelbein

2015

The Plant Cell

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The molecular basis for the origin and diversification of morphological adaptations is a central issue in evolutionary developmental biology. Here, we defined temporal transcript accumulation in developing roots from seven vascular plants, permitting a genome-wide comparative analysis of the molecular programs used by a single organ across diverse species. The resulting gene expression maps uncover significant similarity in the genes employed in roots and their developmental expression profiles. The detailed analysis of a subset of 133 genes known to be associated with root development in Arabidopsis thaliana indicates that most of these are used in all plant species. Strikingly, this was also true for root development in a lycophyte (Selaginella moellendorffii), which forms morphologically different roots and is thought to have evolved roots independently. Thus, despite vast differences in size and anatomy of roots from diverse plants, the basic molecular mechanisms employed during root formation appear to be conserved. This suggests that roots evolved in the two major vascular plant lineages either by parallel recruitment of largely the same developmental program or by elaboration of an existing root program in the common ancestor of vascular plants.

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“…Analysis of species-specific sets was made with a Fisher's exact test (P , 0.0001) on InterPro (version 28) domains. For analyses of specific gene families, the 36,542 Musa protein sequences were inserted in the plant proteome clustering of the GreenPhyl database 57 . Transcription factor families were mostly retrieved based on InterPro domains, using the IPR2genomes tool in GreenphylDB 57 (Supplementary Text).…”

Section: Methodsmentioning

confidence: 99%