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Glyphosate has been widely used to control Eleusine indica and other weeds in South China for many years. Among the most troublesome weeds in South China, E. indica can remain alive all year round. However, the influence of temperature on glyphosate efficacy on E. indica , especially under days with fluctuating temperature, is unknown. This study evaluated the influence of two temperature regimes on glyphosate efficacy on glyphosate-resistant (R) and -susceptible (S) E. indica biotypes. Plants of the R and S biotypes were cultivated under two temperature regimes (high: 30°C/20°C day/night; low: 20°C/15°C day/night). Dose-response experiments showed improved efficacy of glyphosate at the low temperature compared with that at the high temperature for both biotypes. Based on the LD 50 values, the R biotype was 8.9 times more resistant to glyphosate than the S biotype at the high temperature; however, the resistance index (R/S) decreased to 3.1 at the low temperature. At 4 days after glyphosate application, shikimic acid accumulation was greater at the low temperature than at the high temperature in plants of both biotypes, and the increase was higher in plants of the R biotype than in the S biotype. At a sublethal glyphosate dose (R: 400 g ai ha −1 ; S: 200 g ai ha −1 ), plants grown at the low temperature showed a strong decrease in leaf chlorophyll content and Fv/Fm value compared with those of plants grown at the high temperature and the untreated control. At 3 days after treatment, glyphosate absorption was similar between biotypes at the high temperature, but absorption decreased to 64.9% and 53.1% at the low temperature for the R and S biotypes, respectively. For both biotypes, glyphosate translocation from the leaf to the remainder of the plant was reduced at the low temperature compared with that at the high temperature. No differences in glyphosate translocation were observed between biotypes within each temperature regime. This is the first report on the effect of temperature on glyphosate efficacy on E. indica , and provides important insights for glyphosate application and resistance management.

Non-target-site resistance (NTSR) to herbicides is a worldwide concern for weed control. However, as the dominant NTSR mechanism in weeds, metabolic resistance is not yet well-characterized at the genetic level. For this study, we have identified a shortawn foxtail ( Sobol.) population displaying both TSR and NTSR to mesosulfuron-methyl and fenoxaprop- -ethyl, yet the molecular basis for this NTSR remains unclear. To investigate the mechanisms of metabolic resistance, an RNA-Seq transcriptome analysis was used to find candidate genes that may confer metabolic resistance to the herbicide mesosulfuron-methyl in this plant population. The RNA-Seq libraries generated 831,846,736 clean reads. The transcriptome assembly yielded 95,479 unigenes (averaging 944 bp in length) that were assigned putative annotations. Among these, a total of 29,889 unigenes were assigned to 67 GO terms that contained three main categories, and 14,246 unigenes assigned to 32 predicted KEGG metabolic pathways. Global gene expression was measured using the reads generated from the untreated control (CK), water-only control (WCK), and mesosulfuron-methyl treatment (T) of R and susceptible (S). Contigs that showed expression differences between mesosulfuron-methyl-treated R and S biotypes, and between mesosulfuron-methyl-treated, water-treated and untreated R plants were selected for further quantitative real-time PCR (qRT-PCR) validation analyses. Seventeen contigs were consistently highly expressed in the resistant plants, including four cytochrome P450 monooxygenase (CytP450) genes, two glutathione S-transferase (GST) genes, two glucosyltransferase (GT) genes, two ATP-binding cassette (ABC) transporter genes, and seven additional contigs with functional annotations related to oxidation, hydrolysis, and plant stress physiology. These 17 contigs could serve as major candidate genes for contributing to metabolic mesosulfuron-methyl resistance; hence they deserve further functional study. This is the first large-scale transcriptome-sequencing study to identify NTSR genes in that uses the Illumina platform. This work demonstrates that NTSR is likely driven by the differences in the expression patterns of a set of genes. The assembled transcriptome data presented here provide a valuable resource for biology, and should facilitate the study of herbicide resistance at the molecular level in this and other weed species.

Juglandaceae species are plants of great economic value and have been cultivated, domesticated, and utilized by human society for a long time. Their edible, nutrient-rich nuts and tough, durable wood have attracted the attention of botanists and breeders. With the advent of the genomics era, genome sequencing of the Juglandaceae family has been greatly accelerated, and a large amount of data has been generated. In this paper, we introduce the Portal of Juglandaceae (PJU), a tool to bring all these data together. The PJU contains genomes, gene-coding sequences, protein sequences, various types of annotation information, expression data, and miRNA data, which are configured with BLAST, JBrowse, and our self-developed synteny analysis tool. The PJU has a user-friendly and straightforward interface that performs a variety of query tasks with a few simple operations. In the future, we hope that the PJU will serve as a hub for the study of the Juglandaceae family.

Hickory ( Carya cathayensis ) is a critical tree species of the genus Carya from the Juglandaceae family that contains nutrient-rich nuts. Due to large-scale soil degradation, the pests and diseases of hickory are becoming more and more serious. Thaumatin-like proteins (TLPs) are vital proteins involved in the complex defense process of plant pathogens. In this study, 40 CcTLP genes were identified genome-widely and phylogenetically grouped into three subfamilies. The sequence of CcTLPs had a conservative pattern, such as eight stable disulfide bonds, REDDD, and G-X-[GF]-X-C-X-T-[GA]-D-C-X(1,2)-G-X-(2,3)-C structure. In total, 57 cis -elements related to stress-responsive, light-responsive, phytohormone-responsive, and plant-responsive were discovered. Under salicylate (SA), methyl jasmonate (MeJA), and ethephon (ETH) treatments, the expressions of CcTLP28, CcTLP29, CcTLP30, CcTLP31, CcTLP32, CcTLP33, CcTLP37, CcTLP38 , and CcTLP39 had different patterns. This is an indication that most of the TLP genes were upregulated by SA and downregulated by MeJA. Notably, seven TLP genes were significantly upregulated under the Botryosphaeria dothidea inoculation, especially CcTLP31 , with an over 20-fold change. Nine genes were shown by subcellular localization analysis to be located at the plasma membrane and cytoplasm. The knowledge of the disease-resistant function of the CcTLP family in hickory is promoted by these results. A foundation reference for the molecular breeding of this plant in the future is provided by our findings.

The evolved resistance of Bromus japonicus Houtt. to ALS-inhibiting herbicides is well established. Previous studies have primarily focused on target-site resistance; however, non-target-site resistance has not been well characterized. This investigation demonstrated that ALS gene sequencing did not detect any previously known resistance mutations in a mesosulfuron-methyl-resistant (MR) population, and notably, treatment with the P450 monooxygenase (P450) inhibitor malathion markedly heightened susceptibility to mesosulfuron-methyl. Utilizing UPLC-MS/MS analysis confirmed elevated mesosulfuron-methyl metabolism in MR plants. The integration of Isoform Sequencing (Iso-Seq) and RNA Sequencing (RNA-Seq) facilitated the identification of candidate genes associated with non-target sites in a subpopulation with two generations of herbicide selection. Through qRT-PCR analysis, 21 differentially expressed genes were characterized, and among these, 10 genes (comprising three P450s, two glutathione S-transferases, one glycosyltransferase, two ATP-binding cassette transporters, one oxidase, and one hydrolase) exhibited constitutive upregulation in resistant plants. Our findings substantiated that increased herbicide metabolism is a driving force behind mesosulfuron-methyl resistance in this B. japonicus population.

Biomass energy is an essential component of the agriculture economy and represents an important and particularly significant renewable energy source in the fight against fossil fuel depletion and global warming. The recognition that many plants naturally synthesize hydrocarbons makes these oil plants indispensable resources for biomass energy, and the advancement of next-generation sequencing technology in recent years has now made available mountains of data on plants that synthesize oil. We have utilized a combination of bioinformatic protocols to acquire key information from this massive amount of genomic data and to assemble it into an oil plant genomic information repository, built through website technology, including Django, Bootstrap, and echarts, to create the Genomic Information Repository for Oil Plants (GROP) portal ( http://grop.site/ ) for genomics research on oil plants. The current version of GROP integrates the coding sequences, protein sequences, genome structure, functional annotation information, and other information from 18 species, 22 genome assemblies, and 46 transcriptomes. GROP also provides BLAST, genome browser, functional enrichment, and search tools. The integration of the massive amounts of oil plant genomic data with key bioinformatics tools in a database with a user-friendly interface allows GROP to serve as a central information repository to facilitate studies on oil plants by researchers worldwide.

Widespread herbicide-resistant weeds and severe insect pest infestations pose a challenge to the preplant pest management (PPPM) strategy currently in use in leaf vegetable fields in southern China. The aim of this study was to develop a new weed and insect control method for use before planting leaf vegetables in southern China. Two flaming machines (a tractor mounted and a trolley flaming machine) were designed, and their efficacies for the control of insect and weed pests were evaluated and compared in two field trials. With liquefied petroleum gas (LPG) at 101 kg·ha −1 , flaming machines reduced plant numbers by 86.7% to 98.8% 2 days after treatment (DAT), which was equal to or higher than the reduction after application of paraquat at 900 g·ha −1 . Some weed species, especially awnless barnyard grass ( Echinochloa colona ) and goosegrass ( Eleusine indica ), regrew at 7 DAT, resulting in a decrease in control efficacy. Flaming machines also reduced the number of diamondback moth ( Plutella xylostella ) larvae by 83.0% to 88.2% and the number of adult striped flea beetles ( Phyllotreta striolata ) by 64.9% to 80.9%. This is the first report on flaming treatment in China to show that this method is a promising alternative to chemical pesticides for PPPM in leaf vegetable fields.

Due to its peculiar morphological characteristics, there is dispute as to whether the genus of Annamocarya sinensis, a species of Juglandaceae, is Annamocarya or Carya. Most morphologists believe it should be distinguished from the Carya genus while genomicists suggest that A. sinensis belongs to the Carya genus. To explore the taxonomic status of A. sinensis using chloroplast genes, we collected chloroplast genomes of 16 plant species and assembled chloroplast genomes of 10 unpublished Carya species. We analyzed all 26 species’ chloroplast genomes through two analytical approaches (concatenation and coalescence), using the entire and unique chloroplast coding sequence (CDS) and entire and protein sequences. Our results indicate that the analysis of the CDS and protein sequences or unique CDS and unique protein sequence of chloroplast genomes shows that A. sinensis indeed belongs to the Carya genus. In addition, our analysis shows that, compared to single chloroplast genes, the phylogeny trees constructed using numerous genes showed higher consistency. Moreover, the phylogenetic analysis calculated with the coalescence method and unique gene sequences was more robust than that done with the concatenation method, particularly for analyzing phylogenetically controversial species. Through the analysis, our results concluded that A. sinensis should be called C. sinensis.

In the original publication [...]

Broomcorn millet ( Panicum miliaceum L.) is an orphan crop with the potential to improve cereal production and quality, and ensure food security. Here we present the genetic variations, population structure and diversity of a diverse worldwide collection of 516 broomcorn millet genomes. Population analysis indicated that the domesticated broomcorn millet originated from its wild progenitor in China. We then constructed a graph-based pangenome of broomcorn millet based on long-read de novo genome assemblies of 32 representative accessions. Our analysis revealed that the structural variations were highly associated with transposable elements, which influenced gene expression when located in the coding or regulatory regions. We also identified 139 loci associated with 31 key domestication and agronomic traits, including candidate genes and superior haplotypes, such as LG1 , for panicle architecture. Thus, the study’s findings provide foundational resources for developing genomics-assisted breeding programs in broomcorn millet. Population analysis of 516 wild and domesticated broomcorn millet genomes and a graph-based pangenome based on de novo assemblies of 32 representative accessions identify genomic variations associated with domestication traits.