High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar.

Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid "84K" (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.

High-resolution genome mapping and functional dissection of chlorogenic acid production in Lonicera maackii.

Amur honeysuckle (Lonicera maackii) is a widely used medicinal plant of the Caprifoliaceae family that produces chlorogenic acid. Research on this plant mainly focuses on its ornamental value and medicinal compounds, but a reference genome sequence and molecular resources for accelerated breeding are currently lacking. Herein, nanopore sequencing and high-throughput chromosome conformation capture (Hi-C) allowed a chromosome-level genome assembly of L. maackii (2n = 18). A global view of the gene regulatory network involved in the biosynthesis of chlorogenic acid and the dynamics of fruit coloration in L. maackii was established through metabolite profiling and transcriptome analyses. Moreover, we identified the genes encoding hydroxycinnamoyl-CoA quinate transferase (LmHQT) and hydroxycinnamoyl-CoA shikimic/quinate transferase (LmHCT), which localized to the cytosol and nucleus. Heterologous overexpression of these genes in Nicotiana benthamiana leaves resulted in elevated chlorogenic acid contents. Importantly, HPLC analyses revealed that LmHCT and LmHQTs recombinant proteins modulate the accumulation of chlorogenic acid (CGA) using quinic acid and caffeoyl CoA as substrates, highlighting the importance of LmHQT and LmHCT in CGA biosynthesis. These results confirmed that LmHQTs and LmHCT catalyze the biosynthesis of CGA in vitro. The genomic data presented in this study will offer a valuable resource for the elucidation of CGA biosynthesis and facilitating selective molecular breeding.

Boosted Mg-CO2 Batteries by Amine-Mediated CO2 Capture Chemistry and Mg2+ -Conducting Solid-electrolyte Interphases.

Mg-CO2 battery has been considered as an ideal system for energy conversion and CO2 fixation. However, its practical application is significantly limited by the poor reversibility and sluggish kinetics of CO2 cathode and Mg anode. Here, a new amine mediated chemistry strategy is proposed to realize a highly reversible and high-rate Mg-CO2 battery in conventional electrolyte. Judiciously combined experimental characterization and theoretical computation unveiled that the introduced amine could simultaneously modify the reactant state of CO2 and Mg2+ to accelerate CO2 cathodic reactions on the thermodynamic-kinetic levels and facilitate the formation of Mg2+ -conductive solid-electrolyte interphase (SEI) to enable highly reversible Mg anode. As a result, the Mg-CO2 battery exhibits boosted stable cyclability (70 cycles, more than 400 h at 200 mA g-1 ) and high-rate capability (from 100 to 2000 mA g-1 with 1.5 V overpotential) even at -15 °C. This work opens a newly promising avenue for advanced metal-CO2 batteries.

Zinc ion Batteries: Bridging the Gap from Academia to Industry for Grid-Scale Energy Storage.

Zinc ion batteries (ZIBs) exhibit significant promise in the next generation of grid-scale energy storage systems owing to their safety, relatively high volumetric energy density, and low production cost. Despite substantial advancements in ZIBs, a comprehensive evaluation of critical parameters impacting their practical energy density (Epractical) and calendar life is lacking. Hence, we suggest using formulation-based study as a scientific tool to accurately calculate the cell-level energy density and predict the cycling life of ZIBs. By combining all key battery parameters, such as the capacity ratio of negative to positive electrode (N/P), into one formula, we assess their impact on Epractical. When all parameters are optimized, we urge to achieve the theoretical capacity for a high Epractical. Furthermore, we propose a formulation that correlates the N/P and Coulombic efficiency of ZIBs for predicting their calendar life. Finally, we offer a comprehensive overview of current advancements in ZIBs, covering cathode and anode, along with practical evaluations. This Minireview outlines specific goals, suggests future research directions, and sketches prospects for designing efficient and high-performing ZIBs. It aims at bridging the gap from academia to industry for grid-scale energy storage.

Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata.

Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein-protein and DNA-protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.

Monolithic Phosphate Interphase for Highly Reversible and Stable Zn Metal Anode.

Zinc metal battery (ZMB) is promising as the next generation of energy storage system, but challenges relating to dendrites and corrosion of the zinc anode are restricting its practical application. Here, to stabilize Zn anode, we report a controlled electrolytic method for a monolithic solid-electrolyte interphase (SEI) via a high dipole moment solvent dimethyl methylphosphonate (DMMP). The DMMP-based electrolytes can generate a homogeneous and robust phosphate SEI (Zn3 (PO4 )2 and ZnP2 O6 ). Benefiting from the protecting impact of this in situ monolithic SEI, the zinc electrode exhibits long-term cycling of 4700 h and a high Coulombic efficiency 99.89 % in Zn|Zn and Zn|Cu cell, respectively. The full V2 O5 |Zn battery with DMMP-H2 O hybrid electrolyte exhibits a high capacity retention of 82.2 % following 4000 cycles under 5 A g-1 . The first success in constructing the monolithic phosphate SEI will open a new avenue in electrolyte design for highly reversible and stable Zn metal anodes.

Organic pH Buffer for Dendrite-Free and Shuttle-Free Zn-I2 Batteries.

Aqueous Zn-Iodine (I2 ) batteries are attractive for large-scale energy storage. However, drawbacks include, Zn dendrites, hydrogen evolution reaction (HER), corrosion and, cathode "shuttle" of polyiodines. Here we report a class of N-containing heterocyclic compounds as organic pH buffers to obviate these. We evidence that addition of pyridine /imidazole regulates electrolyte pH, and inhibits HER and anode corrosion. In addition, pyridine and imidazole preferentially absorb on Zn metal, regulating non-dendritic Zn plating /stripping, and achieving a high Coulombic efficiency of 99.6 % and long-term cycling stability of 3200 h at 2 mA cm-2 , 2 mAh cm-2 . It is also confirmed that pyridine inhibits polyiodines shuttling and boosts conversion kinetics for I- /I2 . As a result, the Zn-I2 full battery exhibits long cycle stability of >25 000 cycles and high specific capacity of 105.5 mAh g-1 at 10 A g-1 . We conclude organic pH buffer engineering is practical for dendrite-free and shuttle-free Zn-I2 batteries.

Electrolyte Engineering Enables High Performance Zinc-Ion Batteries.

Zinc-ion batteries (ZIBs) feature high safety, low cost, environmental-friendliness, and promising electrochemical performance, and are therefore regarded as a potential technology to be applied in large-scale energy storage devices. However, ZIBs still face some critical challenges and bottlenecks. The electrolyte is an essential component of batteries and its properties affect the mass transport, energy storage mechanisms, reaction kinetics, and side reactions of ZIBs. The adjustment of electrolyte formulas usually has direct and obvious impacts on the overall output and performance. In this review, advanced electrolyte strategies are overviewed for optimizing the compatibility between cathode materials and electrolytes, inhibiting anode corrosion and dendrite growth, extending electrochemical stability windows, enabling wearable applications, and enhancing temperature tolerance. The underlying scientific mechanisms, electrolyte design principles, and recent progress are presented to provide a better understanding and inspiration to readers. In addition, a comprehensive perspective about electrolyte design and engineering for ZIBs is included.

SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers.

With advanced sequencing technology, dozens of complex polyploid plant genomes have been characterized. However, for many polyploid species, their diploid ancestors are unknown or extinct, making it impossible to unravel the subgenomes and genome evolution directly. We developed a novel subgenome-phasing algorithm, SubPhaser, specifically designed for a neoallopolyploid or a homoploid hybrid. SubPhaser first searches for the subgenome-specific sequence (k-mer), then assigns homoeologous chromosomes into subgenomes, and further provides tools to annotate and investigate specific sequences. SubPhaser works well on neoallopolyploids and homoploid hybrids containing subgenome-specific sequences like wheat, but fails on autopolyploids lacking subgenome-specific sequences like alfalfa, indicating that SubPhaser can phase neoallopolyploid/homoploid hybrids with high accuracy, sensitivity and performance. This highly accurate, highly sensitive, ancestral data free chromosome phasing algorithm, SubPhaser, offers significant application value for subgenome phasing in neoallopolyploids and homoploid hybrids, and for the subsequent exploration of genome evolution and related genetic/epigenetic mechanisms.

A High-Performance Alginate Hydrogel Binder for Aqueous Zn-Ion Batteries.

The binder is an indispensable battery component that maintains the integrity of the electrode. Polyvinylidene fluoride (PVDF) is most commonly used as a binder in rechargeable batteries; however, it is associated with the toxic and expensive N-methyl-2-pyrrolidone organic solvent. Here, through the cross-linking of sodium alginate (SA) with metal cations, a high-performance hydrogel binder is developed that maintains the stability of MnO2 cathodes in an aqueous electrolyte. Owing to the strong adhesion, high hydrophilicity, and good mechanical stability resulting from the strong bonding of Ca2+ with SA, a commercial microsized MnO2 cathode with a Ca-SA binder delivered a capacity above 300 mAh/g at 1 C, which was larger than those of Mn-SA and Zn-SA (∼200 mAh/g) and PVDF (∼150 mAh/g) binders, and a capacity of 250 mAh/g at 3 C for over 200 cycles. These encouraging results could unlock the enormous potential of aqueous binders for practical applications in aqueous batteries.

The Acer truncatum genome provides insights into nervonic acid biosynthesis.

Acer truncatum (purpleblow maple) is a woody tree species that produces seeds with high levels of valuable fatty acids (especially nervonic acid). However, the lack of a complete genome sequence has limited both basic and applied research on A. truncatum. We describe a high-quality draft genome assembly comprising 633.28 Mb (contig N50 = 773.17 kb; scaffold N50 = 46.36 Mb) with at least 28 438 predicted genes. The genome underwent an ancient triplication, similar to the core eudicots, but there have been no recent whole-genome duplication events. Acer yangbiense and A. truncatum are estimated to have diverged about 9.4 million years ago. A combined genomic, transcriptomic, metabonomic, and cell ultrastructural analysis provided new insights into the biosynthesis of very long-chain monounsaturated fatty acids. In addition, three KCS genes were found that may contribute to regulating nervonic acid biosynthesis. The KCS paralogous gene family expanded to 28 members, with 10 genes clustered together and distributed in the 0.27-Mb region of pseudochromosome 4. Our chromosome-scale genomic characterization may facilitate the discovery of agronomically important genes and stimulate functional genetic research on A. truncatum. Furthermore, the data presented also offer important foundations from which to study the molecular mechanisms influencing the production of nervonic acids.

Decreased HLF Expression Predicts Poor Survival in Lung Adenocarcinoma.

BACKGROUND Lung adenocarcinoma (LUAD) is a type of non-small cell carcinoma. Its pathogenesis is being explored and there is no cure for the disease. MATERIAL AND METHODS The Gene Expression Omnibus (GEO) was searched to obtain data on expression of messenger RNA. GEO2R, an interactive web tool, was used to calculate the differentially expressed genes (DEGs) in LUAD. All the DEGs from different datasets were imported into VENNY 2.1 (https://bioinfogp.cnb.csic.es/tools/venny/index.html) to identify the intersection of the DEGs. An online analysis tool, the Database for Annotation, Visualization, and Integrated Discovery (DAVID), was used to help understand the biological meaning of DEG enrichment in LUAD. Cytoscape 3.7.2 was used to perform centrality analysis and visualize hub genes and related networks. Furthermore, the prognostic value of the hub genes was evaluated with the Kaplan-Meier plotter survival analysis tool. RESULTS The GEO database was used to obtain RNA sequencing information for LUAD and normal tissue from the GSE118370, GSE136043, and GSE140797 datasets. A total of 376 DEGs were identified from GSE118370, 248 were identified from GSE136403, and 718 DEGs were identified from GSE140797. The 10 genes with the highest degrees of expression - the hub genes - were CAV1, TEK, SLIT2, RHOJ, DGSX, HLF, MEIS1, PTPRD, FOXF1, and ADRB2. In addition, Kaplan-Meier survival evaluation showed that CAV1, TEK, SLIT2, HLF, MEIS1, PTPRD, FOXF1, and ADRB2 were associated with favorable outcomes for LUAD. CONCLUSIONS CAV1, TEK, SLIT2, HLF, MEIS1, PTPRD, FOXF1, and ADRB2 are hub genes in the DEG interaction network for LUAD and are involved in the development of and prognosis for the disease. The mechanisms underlying these genes should be the subject of further studies.

Effects of landscapes and range expansion on population structure and local adaptation.

Understanding the origin and distribution of genetic diversity across landscapes is critical for predicting the future of organisms in changing climates. This study investigated how adaptive and demographic forces have shaped diversity and population structure in Pinus densata, a keystone species on Qinghai-Tibetan Plateau (QTP). We examined the distribution of genomic diversity across the range of P. densata using exome capture sequencing. We applied spatially explicit tests to dissect the impacts of allele surfing, geographic isolation and environmental gradients on population differentiation and forecasted how this genetic legacy may limit the persistence of P. densata in future climates. We found that allele surfing from range expansion could explain the distribution of 39% of the c. 48 000 genotyped single nucleotide polymorphisms (SNPs). Uncorrected, these allele frequency clines severely confounded inferences of selection. After controlling for demographic processes, isolation-by-environment explained 9.2-19.5% of the genetic structure, with c. 4.0% of loci being affected by selection. Allele surfing and genotype-environment associations resulted in genomic mismatch under projected climate scenarios. We illustrate that significant local adaptation, when coupled with reduced diversity as a result of demographic history, constrains potential evolutionary response to climate change. The strong signal of genomic vulnerability in P. densata may be representative for other QTP endemics.

An Intrinsically Non-flammable Electrolyte for High-Performance Potassium Batteries.

Potassium-ion batteries are promising for low-cost and large-scale energy storage applications, but the major obstacle to their application is the lack of safe and effective electrolytes. A phosphate-based fire retardant such as triethyl phosphate is now shown to work as a single solvent with potassium bis(fluorosulfonyl)imide at 0.9 m, in contrast to previous Li and Na systems where phosphates cannot work at low concentrations. This electrolyte is optimized at 2 m, where it exhibits the advantages of low cost, low viscosity, and high conductivity, as well as the formation of a uniform and robust salt-derived solid-electrolyte interphase layer, leading to non-dendritic K-metal plating/stripping with Coulombic efficiency of 99.6 % and a highly reversible graphite anode.

In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species' adaptability to environmental cues.

BACKGROUND: Cupressus gigantea, a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability of this extremely long-lived conifer with a large genome size. Here, we present its first de novo and multi-tissue transcriptome in-depth characterization. RESULTS: We performed Illumina paired-end sequencing and RNA libraries assembly derived from terminal buds, male and female strobili, biennial leaves, and cambium tissues taken from adult C. gigantea. In total, large-scale high-quality reads were assembled into 101,092 unigenes, with an average sequence length of 1029 bp, and 6848 unigenes (6.77%) were mapped against the KEGG databases to identify 292 pathways. A core set of 41,373 genes belonging to 2412 orthologous gene families shared between C. gigantea and nine other plants was revealed. In addition, we identified 2515 small to larger-size gene families containing in total 9223 genes specific to C. gigantea, and enriched for gene ontologies relating to biotic interactions. We identified an important terpene synthases gene family expansion with its 121 putative members. CONCLUSIONS: This study presents the first comprehensive transcriptome characterization of C. gigantea. Our results will facilitate functional genomic studies to support genetic improvement and conservation programs for this endangered conifer.

Complete plastome sequences of Picea asperata and P. crassifolia and comparative analyses with P. abies and P. morrisonicola.

Picea asperata and P. crassifolia have sympatric ranges and are closely related, but the differences between these species at the plastome level are unknown. To better understand the patterns of variation among Picea plastomes, the complete plastomes of P. asperata and P. crassifolia were sequenced. Then, the plastomes were compared with the complete plastomes of P. abies and P. morrisonicola, which are closely and distantly related to the focal species, respectively. We also used these sequences to construct phylogenetic trees to determine the relationships among and between the four species as well as additional taxa from Pinaceae and other gymnosperms. Analysis of our sequencing data allowed us to identify 438 single nucleotide polymorphism (SNPs) point mutation events, 95 indel events, four inversion events, and seven highly variable regions, including six gene spacer regions (psbJ-petA, trnT-psaM, trnS-trnD, trnL-rps4, psaC-ccsA, and rps7-trnL) and one gene (ycf1). The highly variable regions are appropriate targets for future use in the phylogenetic reconstructions of closely related, sympatric species of Picea as well as Pinaceae in general.

A Method Framework for Automatic Airspace Reconfiguration-Monte Carlo Method for Eliminating Irregular Sector Shapes Generated by Region Growth Method.

With the growth of air traffic demand in busy airspace, there is an urgent need for airspace sectorization to increase air traffic throughput and ease the pressure on controllers. The purpose of this paper is to develop a method framework that can perform airspace sectorization automatically, reasonably, which can be used as an advisory tool for controllers as an automatic system, especially for eliminating irregular sector shapes generated by simulated annealing algorithm (SAA) based on the region growth method. The two graph cutting method, dynamic Monte Carlo method by changing location of flexible vertices (MC-CLFV) and Monte Carlo method by radius changing (MC-RC) were developed to eliminate irregular sector shapes generated by SAA in post-processing. The experimental results show that the proposed method framework of airspace sectorization (AS) can automatically and reasonably generate sector design schemes that meet the design criteria. Our methodology framework and software can provide assistant design and analysis tools for airspace planners to design airspace, improve the reliability and efficiency of airspace design, and reduce the burden of airspace planners. In addition, this lays the foundation for reconstructing airspace with the more intelligent method.

Phosphorus-Based Alloy Materials for Advanced Potassium-Ion Battery Anode.

Potassium-ion batteries (PIBs) are interesting as one of the alternative metal-ion battery systems to lithium-ion batteries (LIBs) due to the abundance and low cost of potassium. We have herein investigated Sn4P3/C composite as a novel anode material for PIBs. The electrode delivered a reversible capacity of 384.8 mA h g-1 at 50 mA g-1 and a good rate capability of 221.9 mA h g-1, even at 1 A g-1. Its electrochemical performance is better than any anode material reported so far for PIBs. It was also found that the Sn4P3/C electrode displays a discharge potential plateau of 0.1 V in PIBs, slightly higher than for sodium-ion batteries (SIBs) (0.01 V), and well above the plating potential of metal. This diminishes the formation of dendrites during cycling, and thus Sn4P3 is a relatively safe anode material, especially for application in large-scale energy storage, where large amounts of electrode materials are used. Furthermore, a possible reaction mechanism of the Sn4P3/C composite as PIB anode is proposed. This work may open up a new avenue for further development of alloy-based anodes with high capacity and long cycle life for PIBs.

Boosted Charge Transfer in SnS/SnO2 Heterostructures: Toward High Rate Capability for Sodium-Ion Batteries.

Constructing heterostructures can endow materials with fascinating performance in high-speed electronics, optoelectronics, and other applications owing to the built-in charge-transfer driving force, which is of benefit to the specific charge-transfer kinetics. Rational design and controllable synthesis of nano-heterostructure anode materials with high-rate performance, however, still remains a great challenge. Herein, ultrafine SnS/SnO2 heterostructures were successfully fabricated and showed enhanced charge-transfer capability. The mobility enhancement is attributed to the interface effect of heterostructures, which induces an electric field within the nanocrystals, giving them much lower ion-diffusion resistance and facilitating interfacial electron transport.

A strategy for characterization of persistent heteroduplex DNA in higher plants.

Heteroduplex DNA (hDNA) generated during homologous recombination (HR) is an important component that shapes genetic diversity in sexually reproducing organisms. However, studies of this process in higher plants are limited. This is because hDNAs are difficult to capture in higher plants as their reproductive developmental model only produces normal gametes and does not preserve the mitotic products of the post-meiotic segregation (PMS) process which is crucial for studying hDNAs. In this study, using the model system for tree and woody perennial plant biology (Populus), we propose a strategy for characterizing hDNAs in higher plants. We captured hDNAs by constructing triploid hybrids originating from a cross between unreduced 2n eggs (containing hDNA information as a result of inhibition chromosome segregation at the PMS stage) with normal male gametes. These triploid hybrids allowed us to detect the frequency and location of persistent hDNAs resulting from HR at the molecular level. We found that the frequency of persistent hDNAs, which ranged from 5.3 to 76.6%, was related to locations of the simple sequence repeat markers at the chromosomes, such as the locus-centromere distance, the surrounding DNA sequence and epigenetic information, and the richness of protein-coding transcripts at these loci. In summary, this study provides a method for characterizing persistent hDNAs in higher plants. When high-throughput sequencing techniques can be incorporated, genome-wide persistent hDNA assays for higher plants can be easily carried out using the strategy presented in this study.