Search

SUMMARY: The genomic integrity of every organism is endangered by various intrinsic and extrinsic stresses. To maintain genomic integrity, a sophisticated DNA damage response (DDR) network is activated rapidly after DNA damage. Notably, the fundamental DDR mechanisms are conserved in eukaryotes. However, knowledge about many regulatory aspects of the plant DDR is still limited. Important, yet little understood, regulatory factors of the DDR are the long non‐coding RNAs (lncRNAs). In humans, 13 lncRNAs functioning in DDR have been characterized to date, whereas no such lncRNAs have been characterized in plants yet. By meta‐analysis, we identified the putative long intergenic non‐coding RNA induced by DNA damage (LINDA) that responds strongly to various DNA double‐strand break‐inducing treatments, but not to replication stress induced by mitomycin C. After DNA damage, LINDA is rapidly induced in an ATM‐ and SOG1‐dependent manner. Intriguingly, the transcriptional response of LINDA to DNA damage is similar to that of its flanking hypothetical protein‐encoding gene. Phylogenetic analysis of putative Brassicales and Malvales LINDA homologs indicates that LINDA lncRNAs originate from duplication of a flanking small protein‐encoding gene followed by pseudogenization. We demonstrate that LINDA is not only needed for the regulation of this flanking gene but also fine‐tuning of the DDR after the occurrence of DNA double‐strand breaks. Moreover, Δlinda mutant root stem cells are unable to recover from DNA damage, most likely due to hyper‐induced cell death. Significant Statement: We unraveled the functional relevance of the first putative lncRNA within the DNA damage response network of Arabidopsis thaliana. This putative lncRNA, termed LINDA, is an important part of the DNA damage response network, as it is needed for accurate regulation of cell death and cell cycle progression. [ABSTRACT FROM AUTHOR]

Summary Because seed yield is the major factor determining the commercial success of grain crop cultivars, there is a large interest to obtain more understanding of the genetic factors underlying this trait. Despite many studies, mainly in the model plant Arabidopsis thaliana, have reported transgenes and mutants with effects on seed number and/or seed size, knowledge about seed yield parameters remains fragmented. This study investigated the effect of 46 genes, either in gain- and/or loss-of-function situations, with a total of 64 Arabidopsis lines being examined for seed phenotypes such as seed size, seed number per silique, number of inflorescences, number of branches on the main inflorescence and number of siliques. Sixteen of the 46 genes, examined in 14 Arabidopsis lines, were reported earlier to directly affect in seed size and/or seed number or to indirectly affect seed yield by their involvement in biomass production. Other genes involved in vegetative growth, flower or inflorescence development or cell division were hypothesized to potentially affect the final seed size and seed number. Analysis of this comprehensive data set shows that of the 14 lines previously described to be affected in seed size or seed number, only nine showed a comparable effect. Overall, this study provides the community with a useful resource for identifying genes with effects on seed yield and candidate genes underlying seed QTL. In addition, this study highlights the need for more thorough analysis of genes affecting seed yield. [ABSTRACT FROM AUTHOR]

Large-scale comparison of sequence polymorphism and divergence at numerous genomic loci within and between closely related species can reveal signatures of natural selection. Here, we present a population genomics study based on direct sequencing of 61 mitotic cell cycle genes from 30 Arabidopsis thaliana accessions and comparison of the resulting data to the close relative Arabidopsis lyrata. We found that the Arabidopsis core cell cycle (CCC) machinery is not highly constrained but is subject to different modes of selection. We found patterns of purifying selection for the cyclin-dependent kinase (CDK), CDK subunit, retinoblastoma, and WEE1 gene families. Other CCC gene families often showed a mix of one or two constrained genes and relaxed purifying selection on the other genes. We found several large effect mutations in CDKB1;2 that segregate in the species. We found a strong signature of adaptive protein evolution in the Kip-related protein KRP6 and departures from equilibrium at CDKD;1 and CYCA3;3 consistent with the operation of selection in these gene regions. Our data suggest that within Arabidopsis, the genetic robustness of cell cycle-related processes is more due to functional redundancy than high selective constraint. [ABSTRACT FROM AUTHOR]

Somatic polyploidy caused by endoreplication is observed in arthropods, molluscs, and vertebrates but is especially prominent in higher plants, where it has been postulated to be essential for cell growth and fate maintenance. However, a comprehensive understanding of the physiological significance of plant endopolyploidy has remained elusive. Here, we modeled and experimentally verified a high-resolution DNA endoploidy map of the developing Arabidopsis thaliana root, revealing a remarkable spatiotemporal control of DNA endoploidy levels across tissues. Fitting of a simplified model to publicly available data sets profiling root gene expression under various environmental stress conditions suggested that this root endoploidy patterning may be stress-responsive. Furthermore, cellular and transcriptomic analyses revealed that inhibition of endoreplication onset alters the nuclear-to-cellular volume ratio and the expression of cell wall-modifying genes, in correlation with the appearance of cell structural changes. Our data indicate that endopolyploidy might serve to coordinate cell expansion with structural stability and that spatiotemporal endoreplication pattern changes may buffer for stress conditions, which may explain the widespread occurrence of the endocycle in plant species growing in extreme or variable environments. [ABSTRACT FROM AUTHOR]