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Plants are associated with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals, including maize. We studied an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe region of Oaxaca, Mexico. This landrace is characterized by the extensive development of aerial roots that secrete a carbohydrate-rich mucilage. Analysis of the mucilage microbiota indicated that it was enriched in taxa for which many known species are diazotrophic, was enriched for homologs of genes encoding nitrogenase subunits, and harbored active nitrogenase activity as assessed by acetylene reduction and 15N2 incorporation assays. Field experiments in Sierra Mixe using 15N natural abundance or 15N-enrichment assessments over 5 years indicated that atmospheric nitrogen fixation contributed 29%-82% of the nitrogen nutrition of Sierra Mixe maize.

Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops. Pecan is an important specialty crop that has experienced extensive interspecific hybridization and nearly-obligate outcrossing. Here, the authors assemble diploid genomes of four outbred genotypes, identify interspecific introgressions through comparative genomics analyses, and map QTLs associated with pest resistance.

The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.The genome of the model fern species Ceratopteris richardii reveals a history of remarkably dynamic genome evolution, including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago.

As the human population grows from 7.8 billion to 10 billion over the next 30 years, breeders must do everything possible to create crops that are highly productive and nutritious, while simultaneously having less of an environmental footprint. Rice will play a critical role in meeting this demand and thus, knowledge of the full repertoire of genetic diversity that exists in germplasm banks across the globe is required. To meet this demand, we describe the generation, validation and preliminary analyses of transposable element and long-range structural variation content of 12 near-gap-free reference genome sequences (RefSeqs) from representatives of 12 of 15 subpopulations of cultivated Asian rice. When combined with 4 existing RefSeqs, that represent the 3 remaining rice subpopulations and the largest admixed population, this collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to map resequencing data to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice.Measurement(s)genome • DNA • sequence_assembly • sequence feature annotation • physical mapTechnology Type(s)DNA sequencing • PacBio Sequel System • sequence assembly process • transposable elements annotation • Optical Mapping Illumina sequencingFactor Type(s)Oryza sativa cv. varietySample Characteristic - OrganismOryza sativaMachine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11950596

A proteomic atlas of a model legume and its rhizobial symbiont provides a resource for understanding symbiotic nitrogen fixation. Legumes are essential components of agricultural systems because they enrich the soil in nitrogen and require little environmentally deleterious fertilizers. A complex symbiotic association between legumes and nitrogen-fixing soil bacteria called rhizobia culminates in the development of root nodules, where rhizobia fix atmospheric nitrogen and transfer it to their plant host. Here we describe a quantitative proteomic atlas of the model legume Medicago truncatula and its rhizobial symbiont Sinorhizobium meliloti , which includes more than 23,000 proteins, 20,000 phosphorylation sites, and 700 lysine acetylation sites. Our analysis provides insight into mechanisms regulating symbiosis. We identify a calmodulin-binding protein as a key regulator in the host and assign putative roles and targets to host factors (bioactive peptides) that control gene expression in the symbiont. Further mining of this proteomic resource may enable engineering of crops and their microbial partners to increase agricultural productivity and sustainability.

Background: Seagrasses (Alismatales) are the only fully marine angiosperms.  Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass  Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings.   Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding.  Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins.  Conclusions: As an important marine angiosperm, the improved  Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.

Exploring natural diversity for biological nitrogen fixation in maize and its progenitors is a promising approach to reducing our dependence on synthetic fertilizer and enhancing the sustainability of our cropping systems. We have shown previously that maize accessions from the Sierra Mixe can support a nitrogen-fixing community in the mucilage produced by their abundant aerial roots and obtain a significant fraction of their nitrogen from the air through these associations. In this study, we demonstrate that mucilage production depends on root cap and border cells sensing water, as observed in underground roots. The diameter of aerial roots correlates with the volume of mucilage produced and the nitrogenase activity supported by each root. Young aerial roots produce more mucilage than older ones, probably due to their root cap’s integrity and their ability to produce border cells. Transcriptome analysis on aerial roots at two different growth stages before and after mucilage production confirmed the expression of genes involved in polysaccharide synthesis and degradation. Genes related to nitrogen uptake and assimilation were up-regulated upon water exposure. Altogether, our findings suggest that in addition to the number of nodes with aerial roots reported previously, the diameter of aerial roots and abundance of border cells, polysaccharide synthesis and degradation, and nitrogen uptake are critical factors to ensure efficient nitrogen fixation in maize aerial roots.

A catalyst-free, additive-free, and eco-friendly method for synthesizing 1,2,4-triazolo[1,5-a]pyridines under microwave conditions has been established. This tandem reaction involves the use of enaminonitriles and benzohydrazides, a transamidation mechanism followed by nucleophilic addition with nitrile, and subsequent condensation to yield the target compound in a short reaction time. The methodology demonstrates a broad substrate scope and good functional group tolerance, resulting in the formation of products in good-to-excellent yields. Furthermore, the scale-up reaction and late-stage functionalization of triazolo pyridine further demonstrate its synthetic utility. A plausible reaction pathway, based on our findings, has been proposed.

Lignin is a cell wall polymer that reduces the enzymatic digestibility and conversion efficiency of lignocellulosic biomass to ethanol. Down-regulation of the hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT) gene reduces lignin content in alfalfa (Medicago sativa L.). The objective of this study was to evaluate HCT down-regulated alfalfa plants for their forage composition and agronomic performance in the greenhouse and under field conditions. Individual plants with two separate T0HCT down-regulation events 3a and 30a were used to make crosses with a common male sterile line to generate T1 progenies (3A and 30A, respectively). The experimental design was a randomized complete block with four replications per line and ten individuals per replication. Two-row plots with full-sib progeny rows with (+) and without (−) the transgene were planted along with commercial cultivars used as checks. Most differential responses in forage quality and agronomic characteristics between full-sib down-regulated and non-down-regulated progenies were event-specific and found mainly between the HCT30A+ and HCT30A− progenies. Variation between HCT− and HCT+ alfalfa plants was observed in the HCT gene transcript levels, acid detergent lignin (ADL), relative feed value (RFV), and saccharification efficiency. Although differential responses in agronomic performance of field-grown HCT down-regulated alfalfa plants were identified for biomass yield and plant height, HCT+ and HCT− progenies had similar spring growth and fall dormancy. The reduction in lignin content of alfalfa plants via modification of HCT transcript levels increased forage quality and efficiency of sugar release of plants grown under greenhouse and field conditions.

Pyridazine derivatives hold significant interest due to their broad applications in pharmaceuticals and materials science, where they serve as valuable scaffolds for bioactive compounds and functional materials. Here, we report a formal [4 + 2] reaction for the synthesis of 5’-sulfonyl-4’-aryl-3-cyano substituted pyridazine compounds from the reaction between vinylogous enaminonitriles and sulfonyl hydrazides. The key features of our pyridazine synthesis include the transamidation of vinylogous enaminonitriles with sulfonyl hydrazide, radical sulfonylation of the resulting intermediate, and subsequent 6-endo-trig radical cyclization. This reaction proceeds smoothly to deliver a series of pyridazine derivatives in good to high yields. We also found that the sulfonyl group of the synthesized pyridazines can be transformed into C-, O-, or N-containing functional groups. A gram-scale experiment and a diverse transformation of synthesized pyridazines were also performed to validate the practicality of our developed process. In the synthesis of sulfonyl-substituted pyridazines, a 6-endo-trig cyclization via a radical pathway is both kinetically and thermodynamically favored over the cyclization via an ionic pathway, as supported by DFT calculations. Pyridazine is an aromatic heterocyclic compound that is utilized as a bioisostere for benzene or pyridine, and is found in the core scaffold of various drug molecules, making synthetic methods to access pyridazine scaffolds of high interest. Here, the authors report the synthesis of 5’-sulfonyl-4’-aryl-3-cyano substituted pyridazine compounds from a formal [4 + 2] reaction between vinylogous enaminonitriles and sulfonyl hydrazides.