Volatile guest molecule mediated strategy to convert covalent organic framework into nitrogen, sulfur-doped carbon as metal-free oxygen reduction electrocatalysts.

Covalent organic framework (COF) derived metal-free carbon materials have emerged as promising electrocatalysts for the oxygen reduction reaction (ORR). Herein, a volatile guest molecule mediated-pyrolysis strategy was explored on a designed thiophene-rich and imine-linked COF. Through the modulation of guest mediators (iodine and sulfur), the properties of the as-obtained carbon materials can be well regulated. The optimized nitrogen and sulfur dual-doped carbon electrocatalyst demonstrates remarkable ORR activity with a half-wave potential of 0.87 V and impressive durability, with only an 8% current loss over 21 h. The corresponding assembled zinc-air battery has a comparable power density (60 mW cm-2) to that of the commercial Pt/C. It is proposed that the coexistence of the guest mediators iodine and sulfur in the channels of COFs could prevent the loss of N species. The enhanced N content and N/S ratio are assumed to be responsible for the ORR performance. This study puts forward a novel strategy to prepare COF-derived carbon materials mediated by volatile guest molecules, which may provide new insights into the development of metal-free ORR catalysts.

A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera.

Ancient whole-genome duplication (WGD) or polyploidization is prevalent in plants and has played a crucial role in plant adaptation. However, the underlying genomic basis of ecological adaptation and subsequent diversification after WGD are still poorly understood in most plants. Here, we report a chromosome-scale genome assembly for the genus Orinus (Orinus kokonorica as representative) and preform comparative genomics with its closely related genus Cleistogenes (Cleistogenes songorica as representative), both belonging to a newly named subtribe Orininae of the grass subfamily Chloridoideae. The two genera may share one paleo-allotetraploidy event before 10 million years ago, and the two subgenomes of O. kokonorica display neither fractionation bias nor global homoeolog expression dominance. We find substantial genome rearrangements and extensive structural variations (SVs) between the two species. With comparative transcriptomics, we demonstrate that functional innovations of orthologous genes may have played an important role in promoting adaptive evolution and diversification of the two genera after polyploidization. In addition, copy number variations and extensive SVs between orthologs of flower and rhizome related genes may contribute to the morphological differences between the two genera. Our results provide new insights into the adaptive evolution and subsequent diversification of the two genera after polyploidization.

Multi-omics data provide insight into the adaptation of the glasshouse plant Rheum nobile to the alpine subnival zone.

Subnival glasshouse plants provide a text-book example of high-altitude adaptation with reproductive organs enclosed in specialized semi-translucent bracts, monocarpic reproduction and continuous survival under stress. Here, we present genomic, transcriptomic and metabolomic analyses for one such plant, the Noble rhubarb (Rheum nobile). Comparative genomic analyses show that an expanded number of genes and retained genes from two recent whole-genome duplication events are both relevant to subnival adaptation of this species. Most photosynthesis genes are downregulated within bracts compared to within leaves, and indeed bracts exhibit a sharp reduction in photosynthetic pigments, indicating that the bracts no longer perform photosynthesis. Contrastingly, genes related to flavonol synthesis are upregulated, providing enhanced defense against UV irradiation damage. Additionally, anatomically abnormal mesophyll combined with the downregulation of genes related to mesophyll differentiation in bracts illustrates the innovation and specification of the glass-like bracts. We further detect substantial accumulation of antifreeze proteins (e.g. AFPs, LEAs) and various metabolites (e.g. Proline, Protective sugars, procyanidins) in over-wintering roots. These findings provide new insights into subnival adaptation and the evolution of glasshouse alpine plants.

A chromosome-scale Rhubarb (Rheum tanguticum) genome assembly provides insights into the evolution of anthraquinone biosynthesis.

Rhubarb is the collective name for various perennial plants from the genus Rheum L. and the Polygonaceae family. They are one of the most ancient, commonly used, and important herbs in traditional Chinese medicine. Rhubarb is a major source of anthraquinones, but how they are synthesized remains largely unknown. Here, we generate a genome sequence assembly of one important medicinal rhubarb R. tanguticum at the chromosome level, with 2.76 Gb assembled into 11 chromosomes. The genome is shaped by two recent whole-genome duplication events and recent bursts of retrotransposons. Metabolic analyses show that the major anthraquinones are mainly synthesized in its roots. Transcriptomic analysis reveals a co-expression module with a high correlation to anthraquinone biosynthesis that includes key chalcone synthase genes. One CHS, four CYP450 and two BGL genes involved in secondary metabolism show significantly upregulated expression levels in roots compared with other tissues and clustered in the co-expression module, which implies that they may also act as candidate genes for anthraquinone biosynthesis. This study provides valuable insights into the genetic bases of anthraquinone biosynthesis that will facilitate improved breeding practices and agronomic properties for rhubarb in the future.

Constructing single atom sites on bipyridine covalent organic frameworks for selective electrochemical production of H2O2.

We developed a series of single atom catalysts (SACs) anchored on bipyridine-rich COFs. By tuning the active metal center, the optimal Py-Bpy-COF-Zn shows the highest selectivity of 99.1% and excellent stability toward H2O2 production via oxygen reduction, which can be attributed to the high *OOH dissociation barrier indicated by the theoretical calculations. As a proof of concept, it acts as a cathodic catalyst in a homemade Zn-air battery, together with efficient wastewater treatment.

Genomic divergence between two sister Medicago species triggered by the quaternary climatic oscillations on the Qinghai-Tibet plateau and northern China.

Speciation is a central topic in evolutionary biology. However, how genomic divergence originates and accumulates in the face of gene flow during ecological adaptation remains poorly understood. Closely related species that have adapted to distinct environments but inhabit some overlapping ranges provide an ideal system to evaluate this issue. Here, we combine population genomics and species distribution models (SDMs) to examine genomic divergences between two sister plant species, Medicago ruthenica and M. archiducis-nicolai, that occur in northern China and the northeast Qinghai-Tibet Plateau, respectively, with overlapping distributions in the border of the two regions. M. ruthenica and M. archiducis-nicolai are well-delimited based on population genomic data, although hybrids exist in sympatric sampling locations. Coalescent simulations and SDMs suggest that the two species diverged from each other in the Quaternary but have been in continuous contact with gene flow occurring between the two species since then. We also discovered positive selection signatures associated with genes both outside and within genomic islands in both species that are probably involved in adaptations to arid and high-altitude environments. Our findings provide insights into how natural selection and climatic changes in the Quaternary initiated and maintained interspecific divergence of these two sister species.

Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets.

Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.

Bimetallic palladium-copper nanoplates with optimized d-band center simultaneously boost oxygen reduction activity and methanol tolerance.

The methanol-poisoning of electrocatalysts at the cathodic part of direct methanol fuel cells (DMFCs) can severely degrade the overall efficiency. Therefore, engineering cathodic catalysts with outstanding oxygen reduction activity, and simultaneously, superior methanol tolerance is greatly desired. Herein, bimetallic palladium-copper (PdCu) nanoplates with the optimized d-band center are designed as promising cathodic catalysts for DMFCs. It shows outstanding oxygen reduction activity with a mass activity (MA) of 0.522 A mgPd-1 in alkaline electrolyte, overwhelming the benchmarked commercial Pt/C and Pd/C. Meanwhile, it has prominent stability with only 4.0 % loss in MA after continuous 20 K cycles. More importantly, the PdCu nanoplates are almost inert toward methanol oxidation and show excellent anti-methanol capability. The theoretical calculations reveal that the downshift of d-band center in PdCu nanoplates and the electronic interaction between Pd and Cu atoms could effectively lower the methanol adsorption energy, thus leading to enhanced methanol tolerance. This work highlights the important role of tuning the electronic structure and optimized geometry of electrocatalysts to simultaneously boost their oxygen reduction activity, stability, and methanol tolerance for their future application in DMFCs.

Somatic mutations during rapid clonal domestication of Populus alba var. pyramidalis.

For many clonally propagated species, the accumulation of somatic mutations is the principal driver of declines in yield and quality. However, somatic mutations may also promote genetic diversification. Thus, elucidating somatic mutation rates and patterns is important to understand the genetic basis undergirding the emergence of commercially valuable traits and developmental processes. In this study, we studied the effect of short-time clonal domestication of Populus alba var. pyramidalis, a species that has been propagated by cutting for the last 67 years. We found that: (1) the somatic mutation rate for P. alba var. pyramidalis is 9.24 × 10-9, which is higher than rates observed in related species; (2) there were more mutations near heterozygous regions, and a larger proportion of CpG and CHG sites were associated with somatic mutations, which may be related to the blocking of DNA repair by methylation; and (3) deleterious mutations were not shared by multiple individuals, and all occurred in heterozygous states, demonstrating the strong selective pressures that act against deleterious mutations. Taken together, the results of our study provide a global view of somatic mutation that will aid efforts to understand the genetic basis of commercially valuable traits and to improve clonally breeding species.

A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots.

BACKGROUND: Eudicots are the most diverse group of flowering plants that compromise five well-defined lineages: core eudicots, Ranunculales, Proteales, Trochodendrales, and Buxales. However, the phylogenetic relationships between these five lineages and their chromosomal evolutions remain unclear, and a lack of high-quality genome analyses for Buxales has hindered many efforts to address this knowledge gap. RESULTS: Here, we present a high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales). Our phylogenomic analyses revealed that Buxales and Trochodendrales are genetically similar and classified as sisters. Additionally, both are sisters to the core eudicots, while Ranunculales was found to be the first lineage to diverge from these groups. Incomplete lineage sorting and hybridization were identified as the main contributors to phylogenetic discordance (34.33%) between the lineages. In fact, B. austro-yunnanensis underwent only one whole-genome duplication event, and collinear gene phylogeny analyses suggested that separate independent polyploidizations occurred in the five eudicot lineages. Using representative genomes from these five lineages, we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species. Within core eudicots, we recovered one common chromosome fusion event in asterids and malvids, respectively. Further, we also found that the previously reported fused AEKs in Aquilegia (Ranunculales) and Vitis (core eudicots) have different fusion positions, which indicates that these two species have different karyotype evolution histories. CONCLUSIONS: Based on our phylogenomic and karyotype evolution analyses, we revealed the likely relationships and evolutionary histories of early eudicots. Ultimately, our study expands genomic resources for early-diverging eudicots.

Genomic divergence of Stellera chamaejasme through local selection across the Qinghai-Tibet plateau and northern China.

Understanding how populations diverge and new species arise is a central question in evolutionary biology. "Allopatric" divergence through geographical isolation is considered to be the commonest mechanism generating species biodiversity in mountain ecosystems. However, the underlying genomic dynamics, especially genomic islands of elevated divergence and genes that are highly diverged as a result of lineage-specific selection, remain poorly understood. Stellera chamaejasme has a wide geographical range across the Qinghai-Tibet Plateau and northern China, making it a good model with which to explore genomic divergence during speciation in mountain ecosystems. We assembled a high-quality, chromosome-level genome for this species and resequenced the genomes of 24 populations across its major distribution. Our population genomic analyses recovered four distinct genetic lineages corresponding to geographical distributions with contrasting environments. However, we revealed continuous gene flow during the historical divergences of these four lineages. Interlineage hybrids and plastome introgressions were frequently found in regions of contact, which further increased gene flow between two contacting lineages in the recent past. The elevated divergences were highly heterogeneous across the genome and selection of ancestral polymorphisims and divergence hitchhiking contributed greatly to the formation of genomic islands. The highly diverged and lineage-specific positively selected genes within and outside genomic islands were annotated to be mainly involved in local adaptation. Our results suggest that genomic divergence in S. chamaejasme is likely to have been triggered and maintained by local selection together with geographical isolation.

Genomes and demographic histories of the endangered Bretschneidera sinensis (Akaniaceae).

BACKGROUND: Bretschneidera sinensis is an endangered relic tree species in the Akaniaceae family and is sporadically distributed in eastern Asia. As opposed to its current narrow and rare distribution, the fossil pollen of B. sinensis has been found to be frequent and widespread in the Northern Hemisphere during the Late Miocene. B. sinensis is also a typical mycorrhizal plant, and its annual seedlings exhibit high mortality rates in absence of mycorrhizal development. The chromosome-level high-quality genome of B. sinensis will help us to more deeply understand the survival and demographic histories of this relic species. RESULTS: A total of 25.39 Gb HiFi reads and 109.17 Gb Hi-C reads were used to construct the chromosome-level genome of B. sinensis, which is 1.21 Gb in length with the contig N50 of 64.13 Mb and chromosome N50 of 146.54 Mb. The identified transposable elements account for 55.21% of the genome. A total of 45,839 protein-coding genes were predicted in B. sinensis. A lineage-specific whole-genome duplication was detected, and 7,283 lineage-specific expanded gene families with functions related to the specialized endotrophic mycorrhizal adaptation were identified. The historical effective population size (Ne) of B. sinensis was found to oscillate greatly in response to Quaternary climatic changes. The Ne of B. sinensis has decreased rapidly in the recent past, making its extant Ne extremely lower. Our additional evolutionary genomic analyses suggested that the developed mycorrhizal adaption might have been repeatedly disrupted by environmental changes caused by Quaternary climatic oscillations. The environmental changes and an already decreased population size during the Holocene may have led to the current rarity of B. sinensis. CONCLUSION: This is a detailed report of the genome sequences for the family Akaniaceae distributed in evergreen forests in eastern Asia. Such a high-quality genomic resource may provide critical clues for comparative genomics studies of this family in the future.

Comparison of structural variants in the whole genome sequences of two Medicago truncatula ecotypes: Jemalong A17 and R108.

BACKGROUND: Structural variants (SVs) constitute a large proportion of the genomic variation that results in phenotypic variation in plants. However, they are still a largely unexplored feature in most plant genomes. Here, we present the whole-genome landscape of SVs between two model legume Medicago truncatula ecotypes-Jemalong A17 and R108- that have been extensively used in various legume biology studies. RESULTS: To catalogue SVs, we first resolved the previously published R108 genome assembly (R108 v1.0) to chromosome-scale using 124 × Hi-C data, resulting in a high-quality genome assembly. The inter-chromosomal reciprocal translocations between chromosomes 4 and 8 were confirmed by performing syntenic analysis between the two genomes. Combined with the Hi-C data, it appears that these translocation events had a significant effect on chromatin organization. Using both whole-genome and short-read alignments, we identified the genomic landscape of SVs between the two genomes, some of which may account for several phenotypic differences, including their differential responses to aluminum toxicity and iron deficiency, and the development of different anthocyanin leaf markings. We also found extensive SVs within the nodule-specific cysteine-rich gene family which encodes antimicrobial peptides essential for terminal bacteroid differentiation during nitrogen-fixing symbiosis. CONCLUSIONS: Our results provide a near-complete R108 genome assembly and the first genomic landscape of SVs obtained by comparing two M. truncatula ecotypes. This may provide valuable genomic resources for the functional and molecular research of legume biology in the future.

Conductive metal and covalent organic frameworks for electrocatalysis: design principles, recent progress and perspective.

Metal and covalent organic frameworks (MOFs/COFs) are emerging promising candidates in the field of catalysts due to their porous nature, chemically well-defined active sites and structural diversity. However, they are typically provided with poor electrical conductivity, which is insufficient for them to work as satisfying electrocatalysts. Designing and fabricating MOFs/COFs with high conductivity presents a new avenue towards special electrochemical reactions. This minireview firstly highlighted the origin and design principles of conductive MOFs/COFs for electrocatalysis on the basis of typical charge transfer mechanisms, that is "through space", "extended conjugation" and "through bond". An overview of conductive MOFs/COFs used in the electrocatalytic carbon dioxide reduction reaction (CO2RR), water splitting and the oxygen reduction reaction (ORR) was then made to track the very recent progress. In the final remarks, the present challenges and perspectives for the use of conductive MOFs/COFs as electrocatalysts including their structural optimization, feasible applications and structure-activity correlation are proposed.

Intercontinental transmission and local demographic expansion of SARS-CoV-2.

The global outbreak of coronavirus disease 2019 (COVID-19) is greatly threatening the public health in the world. We reconstructed global transmissions and potential demographic expansions of severe acute respiratory syndrome coronavirus 2 based on genomic information. We found that intercontinental transmissions were rare in January and early February but drastically increased since late February. After world-wide implements of travel restrictions, the transmission frequencies decreased to a low level in April. We identified a total of 88 potential demographic expansions over the world based on the star-radiative networks and 75 of them were found in Europe and North America. The expansion numbers peaked in March and quickly dropped since April. These findings are highly concordant with epidemic reports and modelling results and highlight the significance of quarantine validity on the global spread of COVID-19. Our analyses indicate that the travel restrictions and social distancing measures are effective in containing the spread of COVID-19.

A gene that underwent adaptive evolution, LAC2 (LACCASE), in Populus euphratica improves drought tolerance by improving water transport capacity.

Drought severely limits plant development and growth; accordingly, plants have evolved strategies to prevent water loss and adapt to water deficit conditions. However, experimental cases that corroborate these evolutionary processes are limited. The LACCASEs (LACs) family is involved in various plant development and growth processes. Here, we performed an evolutionary analysis of LACs from Populus euphratica and characterized the functions of LACs in Arabidopsis and poplar. The results showed that in PeuLACs, multiple gene duplications led to apparent functional redundancy as the result of various selective pressures. Among them, PeuLAC2 underwent strong positive selection. Heterologous expression analyses showed that the overexpression of PeuLAC2 alters the xylem structure of plants, including thickening the secondary cell wall (SCW) and increasing the fiber cell length and stem tensile strength. Altogether, these changes improve the water transport capacity of plants. The analysis of the physiological experimental results showed that PeuLAC2-OE lines exhibited a stronger antioxidant response and greater drought tolerance than WT. Three genes screened by transcriptome analysis, NAC025, BG1, and UGT, that are associated with SCW synthesis and drought stress were all upregulated in the PeuLAC2-OE lines, implying that the overexpression of PeuLAC2 thickened the SCW, improved the water transport capacity of the plant, and further enhanced its drought tolerance. Our study highlights that genes that have undergone adaptive evolution may participate in the development of adaptive traits in P. euphratica and that PeuLAC2 could be a candidate gene for molecular genetic breeding in trees.

Which factors contribute most to genome size variation within angiosperms?

Genome size varies greatly across the flowering plants and has played an important role in shaping their evolution. It has been reported that many factors correlate with the variation in genome size, but few studies have systematically explored this at the genomic level. Here, we scan genomic information for 74 species from 74 families in 38 orders covering the major groups of angiosperms (the taxonomic information was acquired from the latest Angiosperm Phylogeny Group (APG IV) system) to evaluate the correlation between genome size variation and different genome characteristics: polyploidization, different types of repeat sequence content, and the dynamics of long terminal repeat retrotransposons (LTRs). Surprisingly, we found that polyploidization shows no significant correlation with genome size, while LTR content demonstrates a significantly positive correlation. This may be due to genome instability after polyploidization, and since LTRs occupy most of the genome content, it may directly result in most of the genome variation. We found that the LTR insertion time is significantly negatively correlated with genome size, which may reflect the competition between insertion and deletion of LTRs in each genome, and that the old insertions are usually easy to recognize and eliminate. We also noticed that most of the LTR burst occurred within the last 3 million years, a timeframe consistent with the violent climate fluctuations in the Pleistocene. Our findings enhance our understanding of genome size evolution within angiosperms, and our methods offer immediate implications for corresponding research in other datasets.

The Corylus mandshurica genome provides insights into the evolution of Betulaceae genomes and hazelnut breeding.

Hazelnut is popular for its flavor, and it has also been suggested that hazelnut is beneficial to cardiovascular health because it is rich in oleic acid. Here, we report the first high-quality chromosome-scale genome for the hazelnut species Corylus mandshurica (2n = 22), which has a high concentration of oleic acid in its nuts. The assembled genome is 367.67 Mb in length, and the contig N50 is 14.85 Mb. All contigs were assembled into 11 chromosomes, and 28,409 protein-coding genes were annotated. We reconstructed the evolutionary trajectories of the genomes of Betulaceae species and revealed that the 11 chromosomes of the hazelnut genus were derived from the most ancestral karyotype in Betula pendula, which has 14 protochromosomes, by inferring homology among five Betulaceae genomes. We identified 96 candidate genes involved in oleic acid biosynthesis, and 10 showed rapid evolution or positive selection. These findings will help us to understand the mechanisms of lipid synthesis and storage in hazelnuts. Several gene families related to salicylic acid metabolism and stress responses experienced rapid expansion in this hazelnut species, which may have increased its stress tolerance. The reference genome presented here constitutes a valuable resource for molecular breeding and genetic improvement of the important agronomic properties of hazelnut.

Controlled growth of ultrafine metal nanoparticles mediated by solid supports.

As a unique class of nanomaterials with a high surface-area-to-volume ratio and narrow size distribution, ultrafine metal nanoparticles (UMNPs) have shown exciting properties in many applications, particularly in the field of catalysis. Growing UMNPs in situ on solid supports enables precise control of the UMNP size, and the supports can effectively prevent the aggregation of UMNPs and maintain their high catalytic activity. In this review, we summarize the recent research progress in controlled growth of UMNPs using various solid supports and their applications in catalysis.

Boosting oxygen evolution through phase and electronic modulation of highly dispersed tungsten carbide with nickel doping.

Exploring efficient, stable, and earth-abundant electrocatalysts for oxygen evolution reaction (OER) is of great significance for clean and renewable energy conversion technologies. In this work, in situ uniform Ni-doped tungsten carbide (Ni/WCX) nanoparticles (~3 nm) on carbon nanofibers (Ni/WCX-CNFs) that were to function as efficient OER catalysts were developed. Both the composition and electronic state of tungsten carbide (WCX: W-WC-W2C) could be regulated through varied Ni coupling. Owing to the synergistic effect between Ni and WCX, the reaction kinetics were facilitated, resulting in improved OER activity with low overpotentials of η10 = 350 mV (modified glassy carbon electrode) and η10 = 335 mV (self-supporting electrode). This work opens a facile territory for the development of cost-effective and highly promising OER electrocatalysts for use in real life applications.