Genomes of autotetraploid wild and cultivated Ziziphus mauritiana reveal polyploid evolution and crop domestication.

Indian jujube (Ziziphus mauritiana) holds a prominent position in the global fruit and pharmaceutical markets. Here, we report the assemblies of haplotype-resolved, telomere-to-telomere genomes of autotetraploid wild and cultivated Indian jujube plants using a two-stage assembly strategy. The generation of these genomes permitted in-depth investigations into the divergence and evolutionary history of this important fruit crop. Using a graph-based pan-genome constructed from eight monoploid genomes, we identified structural variation (SV)-FST hotspots and SV hotspots. Gap-free genomes provide a means to obtain a global view of centromere structures. We identified presence-absence variation-related genes in four monoploid genomes (cI, cIII, wI, and wIII) and resequencing populations. We also present the population structure and domestication trajectory of the Indian jujube based on the resequencing of 73 wild and cultivated accessions. Metabolomic and transcriptomic analyses of mature fruits of wild and cultivated accessions unveiled the genetic basis underlying loss of fruit astringency during domestication of Indian jujube. This study reveals mechanisms underlying the divergence, evolution, and domestication of the autotetraploid Indian jujube and provides rich and reliable genetic resources for future research.

Mercaptoimidazole-capped gold nanoparticles as a potent agent against plant pathogenic fungi.

Plant pathogenic fungi pose a substantial challenge to agricultural production, but the conventional fungicide-based approaches are losing importance. As agents with broad-spectrum antibacterial effects, gold nanoparticles (Au NPs) are found to have antifungal effects; however, no study has examined their application in agriculture as fungicides. Accordingly, this study investigates the activity of 2-mercaptoimidazole-capped Au NPs (MI-Au NPs) against the 'top' plant pathogenic fungi, finding that they could inhibit Magnaporthe oryzae, Botrytis cinerea, Fusarium pseudograminearum and Colletotrichum destructivum by inducing cytoplasmic leakage. Moreover, MI-Au NPs are found to protect plants from infection by B. cinerea. Specifically, pot experiments demonstrate that MI-Au NPs decrease the incidence rate of B. cinerea infection in Arabidopsis thaliana from 74.6% to 6.2% and in Solanum lycopersicum from 100% to 10.9%, outperforming those achieved by imazalil. Furthermore, the biosafety assays reveal that MI-Au NPs cannot penetrate the cuticle of plant cells or negatively influence plant growth, and it is safe to mammalian cells. In summary, the findings of this study will support the development of NP-based antifungal agents for use in agriculture.

Heterologous synthesis of poly-γ-glutamic acid enhanced drought resistance in maize (Zea mays L.).

Drought stress is the main factor restricting maize yield. Poly-γ-glutamic acid (γ-PGA), as a water-retaining agent and fertilizer synergist, could significantly improve the drought resistance and yield of many crops. However, its high production costs and unclear long-term impact on soil ecology limit its large-scale application. In this study, an environmentally friendly green material γ-PGA was heterologous synthesized in maize for the first time using the synthetic biology method. The genes (PgsA, PgsB, PgsC) participated in γ-PGA synthesis were cloned from Bacillus licheniformis and transformed into maize to produce γ-PGA for the first time. Under drought stress, transgenic maize significantly increased the ear length, ear weight and grain weight by 50 % compared to the control, whereas the yield characteristic of ear weight, grain number per ear, grain weight per ear and 100-grain weight increased by 1.67 %-2.33 %, 3.78 %-13.06 %, 8.41 %-22.06 %, 6.03 %-19.28 %, and 11.85 %-18.36 %, respectively under normal growth conditions. γ-PGA was mainly expressed in the mesophyll cells of maize leaf rosette structure and improved drought resistance and yield by protecting and increasing the expression of genes for the photosynthetic and carbon fixation. This study is an important exploration for maize drought stress molecular breeding and building resource-saving agriculture.

Developing a multi-modular assembled prime editing (mPE) system improved precise multi-base insertion efficiency in dicots.

INTRODUCTION: The Prime Editing (PE) system is a precise and versatile genome editing tool with great potential in plant breeding and plant synthetic biology. However, low PE efficiency severely restricts its application, especially in dicots. PE can introduce small tags to trace target protein or cis-element to regulate gene transcription which is an expertise superior to other gene editing tools. Owing to low efficiency, PE adaption in stably transformed Arabidopsis is lacking. OBJECTIVES: This study aimed to investigate the issue of low PE efficiency in dicots and develop systematic solutions to improve it. Currently, PE in dicots is undetectable and inconsistent, and this study seeks to address it. Split PE into several parts showed better performance in some target sites in mammal cells. We plan to discover the optimal split PE combination in dicot. METHODS: We conducted large-scale transformation experiments in dicot model plants Arabidopsis thaliana (At) and Nicotiana benthamiana (Nb) by Agrobacterium-mediated transformation with deep amplicon sequencing (0.2-0.5 million clean total reads). RESULTS: The editing efficiency decreased upon using a fused reverse transcriptase (RT) or an extended pegRNA separately and further decreased dramatically when these were used together. With the help of the pol II strategy to express PE gRNA (pegRNA), we named the most effective split PE combination as a multi-modular assembled prime editing system (mPE). mPE exhibited improved precise editing efficiency on most gene sites with various editing types, ranging from 1.3-fold to 1288.5-fold and achieved PE on some sites that could not be edited by original PE2. Especially, mPE showed superiority for multi-base insertion with an average improvement of 197.9-fold. CONCLUSION: The original PE architecture strongly inhibited the cleavage activity of Cas9. Split PE improved PE efficiency extensively and was in favor of introducing small insertions in dicot plants, indicating that different PE variants might have their own expertise.

Designing a synthetic moss genome using GenoDesigner.

The de novo synthesis of genomes has made unprecedented progress and achieved milestones, particularly in bacteria and yeast. However, the process of synthesizing a multicellular plant genome has not progressed at the same pace, due to the complexity of multicellular plant genomes, technical difficulties associated with large genome size and structure, and the intricacies of gene regulation and expression in plants. Here we outline the bottom-up design principles for the de novo synthesis of the Physcomitrium patens (that is, earthmoss) genome. To facilitate international collaboration and accessibility, we have developed and launched a public online design platform called GenoDesigner. This platform offers an intuitive graphical interface enabling users to efficiently manipulate extensive genome sequences, even up to the gigabase level. This tool is poised to greatly expedite the synthesis of the P. patens genome, offering an essential reference and roadmap for the synthesis of plant genomes.

The high-quality genome of Grona styracifolia uncovers the genomic mechanism of high levels of schaftoside, a promising drug candidate for treatment of COVID-19.

Recent study has evidenced that traditional Chinese medicinal (TCM) plant-derived schaftoside shows promise as a potential drug candidate for COVID-19 treatment. However, the biosynthetic pathway of schaftoside in TCM plants remains unknown. In this study, the genome of the TCM herb Grona styracifolia (Osbeck) H.Ohashi & K.Ohashi (GSO), which is rich in schaftoside, was sequenced, and a high-quality assembly of GSO genome was obtained. Our findings revealed that GSO did not undergo recent whole genome duplication (WGD) but shared an ancestral papilionoid polyploidy event, leading to the gene expansion of chalcone synthase (CHS) and isoflavone 2'-hydroxylase (HIDH). Furthermore, GSO-specific tandem gene duplication resulted in the gene expansion of C-glucosyltransferase (CGT). Integrative analysis of the metabolome and transcriptome identified 13 CGTs and eight HIDHs involved in the biosynthetic pathway of schaftoside. Functional studies indicated that CGTs and HIDHs identified here are bona fide responsible for the biosynthesis of schaftoside in GSO, as confirmed through hairy root transgenic system and in vitro enzyme activity assay. Taken together, the ancestral papilionoid polyploidy event expanding CHSs and HIDHs, along with the GSO-specific tandem duplication of CGT, contributes, partially if not completely, to the robust biosynthesis of schaftoside in GSO. These findings provide insights into the genomic mechanisms underlying the abundant biosynthesis of schaftoside in GSO, highlighting the potential of GSO as a source of bioactive compounds for pharmaceutical development.

Characterization and heterologous reconstitution of Taxus biosynthetic enzymes leading to baccatin III.

Paclitaxel is a well known anticancer compound. Its biosynthesis involves the formation of a highly functionalized diterpenoid core skeleton (baccatin III) and the subsequent assembly of a phenylisoserinoyl side chain. Despite intensive investigation for half a century, the complete biosynthetic pathway of baccatin III remains unknown. In this work, we identified a bifunctional cytochrome P450 enzyme [taxane oxetanase 1 (TOT1)] in Taxus mairei that catalyzes an oxidative rearrangement in paclitaxel oxetane formation, which represents a previously unknown enzyme mechanism for oxetane ring formation. We created a screening strategy based on the taxusin biosynthesis pathway and uncovered the enzyme responsible for the taxane oxidation of the C9 position (T9αH1). Finally, we artificially reconstituted a biosynthetic pathway for the production of baccatin III in tobacco.

Near telomere-to-telomere genome of the model plant Physcomitrium patens.

The model plant Physcomitrium patens has played a pivotal role in enhancing our comprehension of plant evolution and development. However, the current genome harbours numerous regions that remain unfinished and erroneous. To address these issues, we generated an assembly using Oxford Nanopore reads and Hi-C mapping. The assembly incorporates telomeric and centromeric regions, thereby establishing it as a near telomere-to-telomere genome except a region in chromosome 1 that is not fully assembled due to its highly repetitive nature. This near telomere-to-telomere genome resolves the chromosome number at 26 and provides a gap-free genome assembly as well as updated gene models to aid future studies using this model organism.

ORPA: a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes.

Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually, a process that can be time-consuming and prone to errors. The HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual operations. The processing of a large number of sequences, however, remains a time-consuming task. To conquer this challenge, we develop a speedy and efficient method called Organelle Genomes for Phylogenetic Analysis (ORPA). ORPA can quickly generate multiple sequence alignments for whole-genome comparisons by parsing the result files of NCBI BLAST, completing the task just in 1 min. With increasing data volume, the efficiency of ORPA is even more pronounced, over 300 times faster than HomBlocks in aligning 60 high-plant chloroplast genomes. The phylogenetic tree outputs from ORPA are equivalent to HomBlocks, indicating its outstanding efficiency. Due to its speed and accuracy, ORPA can identify species-level evolutionary conflicts, providing valuable insights into evolutionary cognition.

The Jasmine (Jasminum sambac) Genome Provides Insight into the Biosynthesis of Flower Fragrances and Jasmonates.

Jasminum sambac (jasmine flower), a world-renowned plant appreciated for its exceptional flower fragrance, is of cultural and economic importance. However, the genetic basis of its fragrance is largely unknown. Here, we present the first de novogenome assembly of J. sambac with 550.12 Mb (scaffold N50 = 40.10 Mb) assembled into 13 pseudochromosomes. Terpene synthase (TPS) genes associated with flower fragrance are considerably amplified in the form of gene clusters through tandem duplications in the genome. Gene clusters within the salicylic acid/benzoic acid/theobromine (SABATH) and benzylalcohol O-acetyltransferase/anthocyanin O-hydroxycinnamoyltransferases/anthranilate N-hydroxycinnamoyl/benzoyltransferase/deacetylvindoline 4-O-acetyltransferase (BAHD) superfamilies were identified to be related to the biosynthesis of phenylpropanoid/benzenoid compounds. Several key genes involved in jasmonate biosynthesis were duplicated, causing an increase in copy numbers. In addition, multi-omics analyses identified various aromatic compounds and many genes involved in fragrance biosynthesis pathways. Furthermore, the roles of JsTPS3 in ß-ocimene biosynthesis, as well as JsAOC1 and JsAOS in jasmonic acid biosynthesis, were functionally validated. The genome assembled in this study for J. sambac offers a basic genetic resource for studying floral scent and jasmonate biosynthesis, and provides a foundation for functional genomic research and variety improvements in Jasminum.

Jasmonate-based warfare between the pathogenic intruder and host plant: who wins?

Plants and microbial pathogens often engage in a fierce war that determines their survival. Host plants have evolved sophisticated regulatory mechanisms to fine-tune defense responses to counter attacks from pathogens, while pathogens often hijack the lipid-derived phytohormone jasmonate to cause hormonal signaling imbalances for efficient infection. This review focuses on the jasmonate-based warfare between host plants and pathogenic intruders, and further discusses approaches to uncouple plant growth and defense tradeoffs in crop breeding.

Jasmonate perception: Ligand-receptor interaction, regulation, and evolution.

Phytohormones integrate external environmental and developmental signals with internal cellular responses for plant survival and multiplication in changing surroundings. Jasmonate (JA), which might originate from prokaryotes and benefit plant terrestrial adaptation, is a vital phytohormone that regulates diverse developmental processes and defense responses against various environmental stresses. In this review, we first provide an overview of ligand-receptor binding techniques used for the characterization of phytohormone-receptor interactions, then introduce the identification of the receptor COI1 and active JA molecules, and finally summarize recent advances on the regulation of JA perception and its evolution.

The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences.

Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the evolution of seed plants. Here we report a chromosome-level genome assembly of Adiantum capillus-veneris L., a model homosporous fern. This fern genome comprises 30 pseudochromosomes with a size of 4.8-gigabase and a contig N50 length of 16.22 Mb. Gene co-expression network analysis uncovered that homospore development in ferns has relatively high genetic similarities with that of the pollen in seed plants. Analysing fern defence response expands understanding of evolution and diversity in endogenous bioactive jasmonates in plants. Moreover, comparing fern genomes with those of other land plants reveals changes in gene families important for the evolutionary novelties within the euphyllophyte clade. These results lay a foundation for studies on fern genome evolution and function, as well as the origin and evolution of euphyllophytes.

HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables.

Haplotype identification, characterization and visualization are important for large-scale analysis and use in population genomics. Many tools have been developed to visualize haplotypes, but it is challenging to display both the pattern of haplotypes and the genotypes for each single SNP in the context of a large amount of genomic data. Here, we describe the tool HAPPE, which uses the agglomerative hierarchical clustering algorithm to characterize and visualize the genotypes and haplotypes in a phylogenetic context. The tool displays the plots by coloring the cells and/or their borders in Excel tables for any given gene and genomic region of interest. HAPPE facilitates informative displays wherein data in plots are easy to read and access. It allows parallel display of several lines of values, such as phylogenetic trees, P values of GWAS, the entry of genes or SNPs, and the sequencing depth at each position. These features are informative for the detection of insertion/deletions or copy number variations. Overall, HAPPE provides editable plots consisting of cells in Excel tables, which are user-friendly to non-programmers. This pipeline is coded in Python and is available at https://github.com/fengcong3/HAPPE.

Emerging waste valorisation techniques to moderate the hazardous impacts, and their path towards sustainability.

Due to the recent boom in urbanisation, economy, and global population, the amount of waste generated worldwide has increased tremendously. The World Bank estimates that global waste generation is expected to increase 70% by 2050. Disposal of waste is already a major concern as it poses risks to the environment, human health, and economy. To tackle this issue and maximise potential environmental, economic, and social benefits, waste valorisation - a value-adding process for waste materials - has emerged as a sustainable and efficient strategy. The major objective of waste valorisation is to transit to a circular economy and maximally alleviate hazardous impacts of waste. This review conducts bibliometric analysis to construct a co-occurrence network of research themes related to management of five major waste streams (i.e., food, agricultural, textile, plastics, and electronics). Modern valorisation technologies and their efficiencies are highlighted. Moreover, insights into improvement of waste valorisation technologies are presented in terms of sustainable environmental, social, and economic performances. This review summarises highlighting factors that impede widespread adoption of waste valorisation, such as technology lock-in, optimisation for local conditions, unfavourable regulations, and low investments, with the aim of devising solutions that explore practical, feasible, and sustainable means of waste valorisation.

H2A mono-ubiquitination differentiates FACT's functions in nucleosome assembly and disassembly.

The histone chaperone FACT (FAcilitates Chromatin Transcription) plays an essential role in transcription and DNA replication by its dual functions on nucleosome assembly to maintain chromatin integrity and nucleosome disassembly to destabilize nucleosome and facilitate its accessibility simultaneously. Mono-ubiquitination at Lysine 119 of H2A (ubH2A) has been suggested to repress transcription by preventing the recruitment of FACT at early elongation process. However, up to date, how ubH2A directly affects FACT on nucleosome assembly and disassembly remains elusive. In this study, we demonstrated that the dual functions of FACT are differently regulated by ubH2A. The H2A ubiquitination does not affect FACT's chaperone function in nucleosome assembly and FACT can deposit ubH2A-H2B dimer on tetrasome to form intact nucleosome. However, ubH2A greatly restricts FACT binding on nucleosome and inhibits its activity of nucleosome disassembly. Interestingly, deubiquitination of ubH2A rescues the nucleosome disassembly function of FACT to activate gene transcription. Our findings provide mechanistic insights of how H2A ubiquitination affects FACT in breaking nucleosome and maintaining its integrity, which sheds light on the biological function of ubH2A and various FACT's activity under different chromatin states.

Isoleucine Enhances Plant Resistance Against Botrytis cinerea via Jasmonate Signaling Pathway.

Amino acids are the building blocks of biomacromolecules in organisms, among which isoleucine (Ile) is the precursor of JA-Ile, an active molecule of phytohormone jasmonate (JA). JA is essential for diverse plant defense responses against biotic and abiotic stresses. Botrytis cinerea is a necrotrophic nutritional fungal pathogen that causes the second most severe plant fungal disease worldwide and infects more than 200 kinds of monocot and dicot plant species. In this study, we demonstrated that Ile application enhances plant resistance against B. cinerea in Arabidopsis, which is dependent on the JA receptor COI1 and the jasmonic acid-amido synthetase JAR1. The mutant lib with higher Ile content in leaves exhibits enhanced resistance to B. cinerea infection. Furthermore, we found that the exogenous Ile application moderately enhanced plant resistance to B. cinerea in various horticultural plant species, including lettuce, rose, and strawberry, suggesting a practical and effective strategy to control B. cinerea disease in agriculture. These results together showed that the increase of Ile could positively regulate the resistance of various plants to B. cinerea by enhancing JA signaling, which would offer potential applications for crop protection.

The Taxus genome provides insights into paclitaxel biosynthesis.

The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We have completed a chromosome-level genome of Taxus chinensis var. mairei with a total length of 10.23 gigabases. Taxus shared an ancestral whole-genome duplication with the coniferophyte lineage and underwent distinct transposon evolution. We discovered a unique physical and functional grouping of CYP725As (cytochrome P450) in the Taxus genome for paclitaxel biosynthesis. We also identified a gene cluster for taxadiene biosynthesis, which was formed mainly by gene duplications. This study will facilitate the elucidation of paclitaxel biosynthesis and unleash the biotechnological potential of Taxus.