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Abstract BackgroundAnalysis of the relationship between chromosomal structural variation (synteny breaks) and 3D-chromatin architectural changes among closely related species has the potential to reveal causes and correlates between chromosomal change and chromatin remodeling. Of note, contrary to extensive studies in animal species, the pace and pattern of chromatin architectural changes following the speciation of plants remain unexplored; moreover, there is little exploration of the occurrence of synteny breaks in the context of multiple genome topological hierarchies within the same model species. ResultsHere we used Hi-C and epigenomic analyses to characterize and compare the profiles of hierarchical chromatin architectural features in representative species of the cotton tribe (Gossypieae), includingGossypium arboreum,Gossypium raimondii, andGossypioides kirkii, which differ with respect to chromosome rearrangements. We found that (i) overall chromatin architectural territories were preserved inGossypioidesandGossypium, which was reflected in their similar intra-chromosomal contact patterns and spatial chromosomal distributions; (ii) the non-random preferential occurrence of synteny breaks in A compartment significantly associate with the B-to-A compartment switch in syntenic blocks flanking synteny breaks; (iii) synteny changes co-localize with open-chromatin boundaries of topologically associating domains, while TAD stabilization has a greater influence on regulating orthologous expression divergence than do rearrangements; and (iv) rearranged chromosome segments largely maintain ancestralin-cisinteractions. ConclusionsOur findings provide insights into the non-random occurrence of epigenomic remodeling relative to the genomic landscape and its evolutionary and functional connections to alterations of hierarchical chromatin architecture, on a known evolutionary timescale. 

Abstract Achieving durable lithium (Li) metal anodes in liquid electrolytes remains challenging, primarily due to the instability of the formed solid‐electrolyte interphases (SEIs). Modulating the Li‐ion solvation structures is pivotal in forming a stable SEI for stabilizing Li metal anodes. Here a strategy is developed to fine‐tune the Li‐ion solvation structures through enhanced dipole–dipole interactions between the Li‐ion‐coordinated solvent and the non‐Li‐ion‐coordinating diluent, for creating a stable SEI in the developed binary salt electrolyte. The enhanced dipole–dipole interactions weaken the coordination between Li‐ions and the solvents while strengthening the interaction between Li‐ions and dual anions, thereby facilitating the Li‐ion transport and a robust anion‐derived SEI with a distinct bilayer structure. Consequently, the developed electrolyte exhibited exceptional electrochemical performance in high energy‐density Li||LiNi_0.8Mn_0.1Co_0.1O₂ (NMC811) cells, with long calendar life, stable cyclability at 1 C, and reliable operation between 25 and −20 °C, and it also demonstrat remarkable cycling stability for a Li||NMC811 pouch cell with projected energy density of 402 Wh kg⁻¹, maintaining 80% capacity retention over 606 cycles under practical conditions. 

Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends ver- sus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently chal- lenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two F. oxysporum strains share a core genome of about 46 Mb, in addition to 1,229 and 5,415 unique accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (about 80%) in responding to both fungal inoculums at all timepoints from 12 to 96 h postinoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the path- ogenic interaction activates plant stress responses and sup- presses functions related to plant growth and development, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest timepoint sampled, and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interac- tion displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine- tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens. 

Abstract Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed ‘subgenome dominance’ remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations. 

Abstract Cytonuclear coordination between biparental-nuclear genomes and uniparental-cytoplasmic organellar genomes in plants is often resolved by genetic and transcriptional cytonuclear responses. Whether this mechanism also acts in allopolyploid members of other kingdoms is not clear. Additionally, cytonuclear coordination of interleaved allopolyploid cells/individuals within the same population is underexplored. The yeast Saccharomyces pastorianus provides the opportunity to explore cytonuclear coevolution during different growth stages and from novel dimensions. Using S. pastorianus cells from multiple growth stages in the same environment, we show that nuclear mitochondria-targeted genes have undergone both asymmetric gene conversion and growth stage-specific biased expression favoring genes from the mitochondrial genome donor (Saccharomyces eubayanus). Our results suggest that cytonuclear coordination in allopolyploid lager yeast species entails an orchestrated and compensatory genetic and transcriptional evolutionary regulatory shift. The common as well as unique properties of cytonuclear coordination underlying allopolyploidy between unicellular yeasts and higher plants offers novel insights into mechanisms of cytonuclear evolution associated with allopolyploid speciation. 

Arabidopsis RESISTANCE TO POWDERY MILDEW 8.2 (RPW8.2) is specifically induced by the powdery mildew (PM) fungus (Golovinomyces cichoracearum) in the infected epidermal cells to activate immunity. However, the mechanism of RPW8.2-induction is not well understood. Here, we identify a G. cichoracearum effector that interacts with RPW8.2, named Gc-RPW8.2 interacting protein 1 (GcR8IP1), by a yeast two-hybrid screen of an Arabidopsis cDNA library. GcR8IP1 physically associated with RPW8.2 with its RING finger domain that is essential and sufficient for the association. GcR8IP1 was secreted and translocated into the nucleus of host cell infected with PM. Association of GcR8IP1 with RPW8.2 led to an increase of RPW8.2 in the nucleus. In turn, the nucleus-localised RPW8.2 promoted the activity of the RPW8.2 promoter, resulting in transcriptional self-amplification of RPW8.2 to boost immunity at infection sites. Additionally, ectopic expression or host-induced gene silencing of GcR8IP1 supported its role as a virulence factor in PM. Altogether, our results reveal a mechanism of RPW8.2-dependent defense strengthening via altered partitioning of RPW8.2 and transcriptional self-amplification triggered by a PM fungal effector, which exemplifies an atypical form of effector-triggered immunity. 

As the continuation of Fungal Diversity Notes series, the current paper is the 16th contribution to this series. A total of 103 taxa from seven classes in Ascomycota and Basidiomycota are included here. Of these 101 taxa, four new genera, 89 new species, one new combination, one new name and six new records are described in detail along with information of hosts and geographic distributions. The four genera newly introduced are Ascoglobospora, Atheliella, Rufoboletus and Tenuimyces. Newly described species are Akanthomyces xixiuensis, Agaricus agharkarii, A. albostipitatus, Amphisphaeria guttulata, Ascoglobospora marina, Astrothelium peudostraminicolor, Athelia naviculispora, Atheliella conifericola, Athelopsis subglaucina, Aureoboletus minimus, A. nanlingensis, Autophagomyces incertus, Beltrania liliiferae, Beltraniella jiangxiensis, Botryobasidium coniferarum, Calocybella sribuabanensis, Calonarius caesiofulvus, C. nobilis, C. pacificus, C. pulcher, C. subcorrosus, Cortinarius flaureifolius, C. floridaensis, C. subiodes, Crustomyces juniperi, C. scytinostromoides, Cystostereum subsirmaurense, Dimorphomyces seemanii, Fulvoderma microporum, Ginnsia laricicola, Gomphus zamorinorum, Halobyssothecium sichuanense, Hemileccinum duriusculum, Henningsomyces hengduanensis, Hygronarius californicus, Kneiffiella pseudoabdita, K. pseudoalutacea, Laboulbenia bifida, L. tschirnhausii, L. tuberculata, Lambertella dipterocarpacearum, Laxitextum subrubrum, Lyomyces austro-occidentalis, L. crystallina, L. guttulatus, L. niveus, L. tasmanicus, Marasmius centrocinnamomeus, M. ferrugineodiscus, Megasporoporia tamilnaduensis, Meruliopsis crystallina, Metuloidea imbricata, Moniliophthora atlantica, Mystinarius ochrobrunneus, Neomycoleptodiscus alishanense, Nigrograna kunmingensis, Paracremonium aquaticum, Parahelicomyces dictyosporus, Peniophorella sidera, P. subreticulata, Phlegmacium fennicum, P. pallidocaeruleum, Pholiota betulicola, P. subcaespitosa, Pleurotheciella hyalospora, Pleurothecium aseptatum, Resupinatus porrigens, Russula chlorina, R. chrysea, R. cruenta, R. haematina, R. luteocarpa, R. sanguinolenta, Synnemellisia punensis, Tenuimyces bambusicola, Thaxterogaster americanoporphyropus, T. obscurovibratilis, Thermoascus endophyticus, Trechispora alba, T. perminispora, T. subfarinacea, T. tuberculata, Tremella sairandhriana, Tropicoporus natarajaniae, T. subramaniae, Usnea kriegeriana, Wolfiporiella macrospora and Xylodon muchuanensis. Rufoboletus hainanensis is newly transferred from Butyriboletus, while a new name Russula albocarpa is proposed for Russula leucocarpa G.J. Li & Chun Y. Deng an illegitimate later homonym of Russula leucocarpa (T. Lebel) T. Lebel. The new geographic distribution regions are recorded for Agaricus bambusetorum, Bipolaris heliconiae, Crinipellis trichialis, Leucocoprinus cretaceus, Halobyssothecium cangshanense and Parasola setulosa. Corresponding to morphological characters, phylogenetic evidence is also utilized to place the above-mentioned taxa in appropriate taxonomic positions. The current morphological and phylogenetic data is helpful for further clarification of species diversity and exploration of evolutionary relationships in the related fungal groups.