PlantChatter

Rhynchospora tenuis undergoes obligate, genome-wide achiasmy in both male and female meiosis.

To cause rice blast disease, the filamentous fungus Magnaporthe oryzae develops a specialised infection cell called an appressorium, which generates enormous turgor to breach the rice leaf cuticle. Although key regulators of appressorium development have been identified, it is not known how they drive the extensive transcriptional reprogramming required for infection-related morphogenesis. Here, we show that the Pmk1 MAP kinase orchestrates plant infection by regulating a transcriptional network controlled by the Mst12 and Bip1 transcription factors. Bip1 is regulated both by Pmk1-dependent phosphorylation and at the transcriptional level, while Mst12 binds to a cis-acting element upstream of BIP1 essential for pathogenesis. Bip1 and Mst12 are both necessary for regulating a set of Pmk1-dependent appressorium-specific genes, including transcriptional regulators, cell wall-degrading enzymes, and effector proteins. In addition, Mst12 specifically regulates functions required for appressorium-mediated penetration, while Bip1 controls a distinct sub-set of effector genes deployed during invasion of plant tissue. When considered together, these findings define a Pmk1-dependent transcriptional network required for plant infection by the blast fungus. ### Competing Interest Statement The authors have declared no competing interest. Gatsby Charitable Foundation, https://ror.org/0290hax27 Biotechnology and Biological Sciences research council (BBSRC), BB/T008717/1

DNA methylation is an important epigenetic mechanism involved in gene regulation. Most methods focus on analysing DNA methylation averaged from multiple reads, yet these average methylation profiles obscure heterogeneity between individual DNA molecules and coordinated methylation states across loci. Native Oxford Nanopore Technology (ONT) sequencing directly captures long, native DNA molecules together with their base modifications, allowing methylation to be studied at single-molecule resolution. Here, we present a scalable framework for genome-wide methylation analysis using ONT sequencing at single-molecule resolution, focused on two features that site-level summaries cannot recover. First, it quantifies molecule-to-molecule heterogeneity in DNA methylation by detecting Variable Methylated Domains (VMDs) and Variable Methylated Regions (VMRs). Second, it identifies coordinated methylation, as co-methylated positions (CMPs) and regions (CMRs), from the states observed on the same individual DNA molecules. Using data from human LCL cells, we demonstrate that substantial molecule-level methylation heterogeneity is masked by site-level summaries. Co-methylation analysis reveals coordinated patterns between CpG sites and genomic regions, including shared and sex-specific patterns, uncovering methylation organisation not apparent from average methylation levels. We also show that CMPs can be used to detect TF-pairs that are predicted to have coordinated binding. This framework is integrated within the DMRcaller R/Bioconductor package. ### Competing Interest Statement The authors have declared no competing interest.

Researchers identify CAIR1 as a redox-responsive regulator that promotes catalase localization and activity, helping plants maintain hydrogen peroxide balance and cellular redox homeostasis.

Most organisms are well adapted to the environment they have been exposed to for many generations. However, changing environments pose existential threats to populations, unless they are able to adapt. Hence, a central challenge in evolutionary genetics is to understand the adaptation to complex environmental changes. As most traits are controlled by a large number of loci with varying effects on a trait, it is challenging to understand the explicit role of genetic changes during such polygenic adaptation. We use forward-in-time simulations to investigate the evolutionary dynamics of phenotypic and genetic adaptation in populations facing different environmental shifts. Specifically, we simulated sudden, gradual, and fluctuating environmental shifts for multiple trait architectures. Our results show distinct evolutionary paths across different types of environmental shifts and a higher extinction risk during sudden and fluctuating environmental shifts than during gradual shifts. Comparing the contribution of mutations from different sources highlights the critical role of standing genetic variation in driving phenotypic adaptation. We summarize allele frequency trajectories by clustering them by their temporal pattern and reveal how large- and small-effect mutations jointly shape the successful adaptation to changing environments. Additionally, we trained a convolutional neural network (CNN) on "genetic architecture matrices" of populations to jointly infer the type and magnitude of environmental changes and the mutational effect size distribution. The CNN was able to predict all three input parameters with very high accuracy, even on unseen parameter combinations. Our results demonstrate the impact of ecological change on the evolutionary outcome and the assorted mutational changes that enable successful adaptation. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft, https://ror.org/018mejw64, 456082119 – TRR 341 subproject B6

A mechanistic basis for how the hormone salicylic acid promotes transcriptional activation during plant immune responses is described.

A study reveals an independent case of plastid loss and a metabolic partnership with a bacterial endosymbiont in an understudied lineage of non-photosynthetic ochrophytes.

The diversity of cultivated bananas remains partially unknown, whereas cultivars with suitable adaptive traits could address the drastically increasing biotic and abiotic constraints on banana production. This partial knowledge also impacts our understanding of domestication processes, although replicating these processes is an endorsed strategy for banana varietal improvement. To address this gap, 91 specimens were collected during a collecting mission across northern Vietnam, northern Laos, and China’s Yunnan region, an underexplored area at the northern limit of the Musa natural range. Native wild relatives were also collected (Musa acuminata subsp. burmannica, M. balbisiana, M. itinerans, M. yunnanensis) to assess their potential contributions to cultivated crops. SNP polymorphisms revealed that, beyond the globally cultivated sweet or starchy cultivars, farmers cultivate numerous previously undescribed landraces. SNP-based chromosome paintings further showed that all these landraces carry genomic signatures from endemic wild Musa relatives. Notably, Musa acuminata subsp. burmannica, typically regarded as a minor contributor to cultivated bananas, was detected in several M. acuminata derived diploids (AA) and triploids (AAA) as well as M. acuminata × M. balbisiana derived AAB and ABB landraces. Remarkably, we also report here for the first time polyploid landraces containing a complete haplotype of the local M. itinerans. Crucially, we showed that these landraces were not directly domesticated from the endemic wild Musa. They appear to result from local hybridizations of endemic wilds with exogenous AA diploids introduced into Mainland Southeast Asia from distant regions and originating from earlier domestication farther south. In addition, the various M. acuminata subspecies contributing to these exogenous diploids, provide arguments for an alternative eastern route of introduction via southern China or Taiwan and through the Philippines, distinct from the previously described western route via the Malay Peninsula, through Java, and Sumatra. We highlight an accumulation of genomic introgressions from native wild relatives, suggesting that banana diversity was shaped by an atypical process of cumulative diversification. This ‘post-domestication’ process is thought to enhance local adaptation through genes pyramiding. This multi-level genetic stacking is strengthened in bananas by polyploidy and vegetative propagation fixing any valuable combinations.

The PLANT CYSTEINE OXIDASE (PCO) N-degron pathway contributes to oxygen sensing in plants. Here the authors identify HYPOXIA TRANSDUCER1 (HYT1) as a substrate of PCO and show it forms a coherent feed-forward loop with ERFVII transcription factors to ensure a robust response to reduced oxygen.

The pathogen Pseudomonas aeruginosa uses a membrane complex, PelBC, to produce exopolysaccharides for biofilm formation. Here the authors combine structural analysis, simulations and single-channel recordings of PelBC to provide a detailed view on its unique architecture and dynamics, and reveal the export route for the polysaccharide.

The ornamental chrysanthemum (Chrysanthemum × morifolium) is the world’s second favourite cut flower after roses, cultivated across some 30,000...

A mechanistic basis for how the hormone salicylic acid promotes transcriptional activation during plant immune responses is described.

Structural, genetic, functional and biochemical analyses of the complex flagellar motor of Campylobacter jejuni reveal structural adaptations with an ancient origin also found more widely across bacterial species, including elements exapted from the type IV pilus machinery.