Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response

Picart-Picolo, Ariadna; Grob, Stefan; Picault, Nathalie; Franek, Michal; Llauro, Christel; Halter, Thierry; Maier, Tom; Jobet, Edouard; Descombin, Julie; Zhang, Panpan; Vijayapalani, Paramasivan; Baum, Thomas J.; Navarro, Lionel; Dvořáčková, Martina; Mirouze, Marie; Pontvianne, Frédéric

doi:10.1101/gr.261586.120

Cited by 41 publications

(33 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A large number of orthologous genes indicated the evolution of these genes could be possibly by whole genome segmental duplication events. The large numbers of gene duplications could be possibly facilitated by gene expression, gene organization and plant-pathogen response [59,60]. Moreover, the CmDIR, CsDIR and ClDIR, exhibited several orthologous genes, implying these genes had undergone nonfunctionalization, subfunctionalization, or neofunctionalization [61,62].…”

Section: Wide Distribution Of Dir On Different Chromosomes and The Romentioning

confidence: 99%

Comparative Analysis, Characterization and Evolutionary Study of Dirigent Gene Family in Cucurbitaceae and Expression of Novel Dirigent Peptide against Powdery Mildew Stress

Yadav

Wang

Yang

et al. 2021

Genes

View full text Add to dashboard Cite

Dirigent (DIR) proteins are induced under various stress conditions and involved in sterio- and regio-selective coupling of monolignol. A striking lack of information about dirigent genes in cucurbitaceae plants underscores the importance of functional characterization. In this study, 112 DIR genes were identified in six species, and 61 genes from major cultivated species were analyzed. DIRs were analyzed using various bioinformatics tools and complemented by expression profiling. Phylogenetic analysis segregated the putative DIRs into six distinctively known subgroups. Chromosomal mapping revealed uneven distribution of genes, whereas synteny analysis exhibited that duplication events occurred during gene evolution. Gene structure analysis suggested the gain of introns during gene diversification. Gene ontology (GO) enrichment analysis indicates the participation of proteins in lignification and pathogen resistance activities. We also determined their organ-specific expression levels in three species revealing preferential expression in root and leaves. Furthermore, the number of CmDIR (CmDIR1, 6, 7 and 12) and ClDIR (ClDIR2, 5, 8, 9 and 17) genes exhibited higher expression in resistant cultivars after powdery mildew (PM) inoculation. In summary, based on the expression and in-silico analysis, we propose a role of DIRs in disease resistance mechanisms.

show abstract

Section: Wide Distribution Of Dir On Different Chromosomes and The Romentioning

confidence: 99%

Comparative Analysis, Characterization and Evolutionary Study of Dirigent Gene Family in Cucurbitaceae and Expression of Novel Dirigent Peptide against Powdery Mildew Stress

Yadav

Wang

Yang

et al. 2021

Genes

View full text Add to dashboard Cite

show abstract

“…Investigations of the phenotypic consequences from rDNA copy number variation have uncovered a broad range of cellular processes in diverse species. While ribosome deficiencies do result when rDNA copy number drops below a threshold (Delany et al, 1994;French et al, 2003;Ritossa and Atwood, 1966;Sanchez et al, 2017), several other phenotypes have been associated recently with more physiologically relevant rDNA copy number variants that are sufficient for ribosome biogenesis (Gibbons et al, 2014;Ide et al, 2010;Lu et al, 2018;Michel et al, 2005;Paredes et al, 2011;Picart-Picolo et al, 2020;Wang and Lemos, 2017;Xu et al, 2017). Additionally, the plastic nature of the rDNA locus allows copy number fluctuations in the face of stressors such as nutrient availability (Aldrich and Maggert, 2015) or replication defects (Ide et al, 2007;Lynch et al, 2019;Salim et al, 2017;Sanchez et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Coordination of genome replication and anaphase entry by rDNA copy number inS. cerevisiae

Kwan

Alvino

Lynch

et al. 2021

Preprint

View full text Add to dashboard Cite

Ribosomal DNA (rDNA) copy number varies widely among individuals in many species, but the phenotypic consequences of such copy number fluctuations remain largely unexplored. In the yeast Saccharomyces cerevisiae, each rDNA repeat contains an origin of replication. Previous studies have demonstrated that the yeast rDNA locus can be a significant competitor for replication resources, suggesting that rDNA copy number variation may affect timely completion of genome-wide replication. We hypothesized that reduction in rDNA copy number and thus rDNA replication origins would reduce competition from the rDNA locus and thereby improve non-rDNA genome replication. To test this hypothesis, we engineered yeast strains with short rDNA arrays of 35 copies, a minimal copy number that still maintains wild type level ribosome function. Contrary to our hypothesis, the minimal rDNA strain displayed classic replication defects: decreased plasmid maintenance, delayed completion of chromosomal replication, and increased sensitivity to replication stress agonists. Although a normal rDNA array replicates late in S phase, the minimal rDNA array initiated replication in early S phase, resulting in delayed replication across the non-rDNA portions of the genome. Moreover, we discovered that absence of the rDNA fork barrier protein Fob1p increased DNA damage sensitivity in strains with early replicating rDNA. We present evidence that this increased sensitivity may be due to compromised regulation of cyclin phosphatase Cdc14p and premature entry into anaphase. Our results indicate that precocious rDNA replication, rather than total number of rDNA origins, compromises replication of the genome. Taken together, we suggest that the rDNA's large, late-replicating state is evolutionarily conserved to promote genome stability through timely genome replication and coordination of S phase completion with anaphase entry.

show abstract

“…Additionally, the epigenetic landscape can be even more dynamic when genetic material is reshuffled (SVs and TEs) as a consequence of the applied stress. It is well known that structural variants in several plant species can generate wide phenotypic diversity (for example, The 1001 Genomes Consortium, 2016 ; Zhou et al, 2019 ; Alonge et al, 2020 ) and some of which can enable improved stress tolerance, recently demonstrated by studies such as Kalladan et al (2017) , Catacchio et al (2019) , Picart-Picolo et al (2020) . Yet, genetic mutations in methyltransferase enzymes for tuning epigenetic stability ( Shen et al, 2014 ; Sasaki et al, 2019 ), or heritable genome rearrangements catalyzed by TE insertions can contain the necessary stress-response DMRs that may function to either deteriorate fitness or for adding a newly acquired stress tolerance that allows future generations to adapt to the altered environmental condition ( Quadrana and Colot, 2016 ).…”

Section: Can Stress-response Physiology Hedge Transgenerational Methymentioning

confidence: 99%

How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity

Srikant

Drost

2021

Front. Plant Sci.

View full text Add to dashboard Cite

Climate adaptation through phenotypic innovation will become the main challenge for plants during global warming. Plants exhibit a plethora of mechanisms to achieve environmental and developmental plasticity by inducing dynamic alterations of gene regulation and by maximizing natural variation through large population sizes. While successful over long evolutionary time scales, most of these mechanisms lack the short-term adaptive responsiveness that global warming will require. Here, we review our current understanding of the epigenetic regulation of plant genomes, with a focus on stress-response mechanisms and transgenerational inheritance. Field and laboratory-scale experiments on plants exposed to stress have revealed a multitude of temporally controlled, mechanistic strategies integrating both genetic and epigenetic changes on the genome level. We analyze inter- and intra-species population diversity to discuss how methylome differences and transposon activation can be harnessed for short-term adaptive efforts to shape co-evolving traits in response to qualitatively new climate conditions and environmental stress.

show abstract

Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response

Abstract: Service Email Alerting click here. top right corner of the article or Receive free email alerts when new articles cite this article-sign up in the box at the http://genome.cshlp.org/subscriptions

Cited by 41 publications

References 70 publications

Comparative Analysis, Characterization and Evolutionary Study of Dirigent Gene Family in Cucurbitaceae and Expression of Novel Dirigent Peptide against Powdery Mildew Stress

Comparative Analysis, Characterization and Evolutionary Study of Dirigent Gene Family in Cucurbitaceae and Expression of Novel Dirigent Peptide against Powdery Mildew Stress

Coordination of genome replication and anaphase entry by rDNA copy number inS. cerevisiae

How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity

Contact Info

Product

Resources

About