The 3D chromatin organization plays a major role in the control of gene expression. However, our comprehension of the governing principles behind nuclear organization remains incomplete. Particularly, the spatial segregation of loci with similar repressive transcriptional states in plants poses a significant yet poorly understood puzzle. In this study, employing a combination of genetics and advanced 3D genomics approaches, we demonstrated that a redistribution of facultative heterochromatin marks in regions usually occupied by constitutive heterochromatin marks disrupts the 3D genome compartmentalisation. This disturbance, in turn, triggers novel chromatin interactions between genic and transposable element (TE) regions. Interestingly, our results imply that epigenetic features, constrained by genetic factors, intricately mold the landscape of 3D genome organisation. This study sheds light on the profound genetic-epigenetic interplay that underlies the regulation of gene expression within the intricate framework of the 3D genome. Our findings highlight the complexity of the relationships between genetic determinants and epigenetic features in shaping the dynamic configuration of the 3D genome.

In recent years, the exploration of genome three-dimensional (3D) conformation has yielded profound insights into the regulation of gene expression and cellular functions in both animals and plants. While animals exhibit a characteristic genome topology defined by topologically associating domains (TADs), plants display similar features with a more diverse conformation across species. Employing advanced high-throughput sequencing and microscopy techniques, we investigated the landscape of 26 histone modifications and RNA polymerase II distribution in tomato ( Solanum lycopersicum ). Our study unveiled a rich and nuanced epigenetic landscape, shedding light on distinct chromatin states associated with heterochromatin formation and gene silencing. Moreover, we elucidated the intricate interplay between these chromatin states and the overall topology of the genome. Employing a genetic approach, we delved into the role of the histone modification H3K9ac in genome topology. Notably, our investigation revealed that the ectopic deposition of this chromatin mark triggered a reorganization of the 3D chromatin structure, defining different TAD-like borders. Our work emphasizes the critical role of H3K9ac in shaping the topology of the tomato genome, providing valuable insights into the epigenetic landscape of this agriculturally significant crop species.

Tomato is one of the most important crops for human consumption. Its production is affected by the actinomycete Clavibacter michiganensis subsp. michiganensis (Cmm), one of the most devastating bacterial pathogens of this crop. Several wild tomato species represent a source of natural resistance to Cmm. Here, we contrasted the transcriptomes of the resistant wild tomato species Solanum arcanum LA2157 and the susceptible species Solanum lycopersicum cv. Ailsa Craig, during the first 24 h of challenge with Cmm. We used three analyses approaches which demonstrated to be complementary: mapping to S. lycopersicum reference genome SL3.0; semi de novo transcriptome assembly; and de novo transcriptome assembly. In a global context, transcriptional changes seem to be similar between both species, although there are some specific genes only upregulated in S. arcanum during Cmm interaction, suggesting that the resistance regulatory mechanism probably diverged during the domestication process. Although S. lycopersicum showed enriched functional groups related to defense, S. arcanum displayed a higher number of induced genes related to bacterial, oomycete, and fungal defense at the first few hours of interaction. This study revealed genes that may contribute to the resistance phenotype in the wild tomato species, such as those that encode for a polyphenol oxidase E, diacyl glycerol kinase, TOM1-like protein 6, and an ankyrin repeat-containing protein, among others. This work will contribute to a better understanding of the defense mechanism against Cmm, and the development of new control methods.

Background: Plant developmental plasticity, particularly in root system architecture, is fundamental to understanding adaptability and agricultural sustainability. Existing automated phenotyping solutions face limitations, including binary segmentation approaches, restricted structural analysis capabilities, and text-based interfaces that limit accessibility, with most focusing solely on root structures while overlooking valuable information from simultaneous analysis of multiple plant organs. Findings: ChronoRoot 2.0 builds upon established low-cost hardware while significantly enhancing software capabilities and usability. The system employs nnUNet architecture for multi-class segmentation, demonstrating significant accuracy improvements while simultaneously tracking 6 distinct plant structures encompassing root, shoot, and seed components: main root, lateral roots, seed, hypocotyl, leaves, and petiole. This architecture enables easy retraining and incorporation of additional training data without requiring machine learning expertise. The platform introduces dual specialized graphical interfaces: a Standard Interface for detailed architectural analysis with novel gravitropic response parameters and a Screening Interface enabling high-throughput analysis of multiple plants through automated tracking. Functional principal component analysis integration enables discovery of novel phenotypic parameters through temporal pattern comparison. We demonstrate multi-species analysis, with Arabidopsis thaliana and Solanum lycopersicum, both morphologically distinct plant species. Three use cases in Arabidopsis thaliana and validation with tomato seedlings demonstrate enhanced capabilities: circadian growth pattern characterization, gravitropic response analysis in transgenic plants, and high-throughput etiolation screening across multiple genotypes. Conclusions: ChronoRoot 2.0 maintains the low-cost, modular hardware advantages of its predecessor while dramatically improving accessibility through intuitive graphical interfaces and expanded analytical capabilities. The open-source platform makes sophisticated temporal plant phenotyping more accessible to researchers without computational expertise. Software availability: https://chronoroot.github.io