The water lily genome and the early evolution of flowering plants.

Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms1-3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.

First Report of Colletotrichum aenigma Causing Anthracnose on Bromus japonicus in Tianjin, China.

Japanese brome (Bromus japonicus Thunb.) is a weed commonly found in roadsides, floodplain wetlands, and farmlands. During September 2020 and 2021, a leaf spot disease was observed on B. japonicus in greenhouses of Baodi district, Tianjin, China (117°15'E, 39°47'N). More than 10% of the weeds were infected. Initial irregular brown spots on leaf apices continued to expand until adjacent spots coalesced. Eventually, severely infected leaves became yellow, thinner, drier and withered. Small patches (3×3 mm) were cut from symptomatic leaves, sterilized with 75% ethanol for 30s, rinsed three times with sterile water and incubated on Petri dishes with potato dextrose agar at 25°C in darkness for 7 days. Three isolates, with uniform morphology were selected for further analysis. Colonies were cottony with entire edges and aerial white mycelia; and average growth rate of 4.5 mm/day. The upper side was pale white, and the reverse side was grayish-green. Conidia were aseptate, hyaline, subcylindrical with rounded ends, 8.6 to 18.7×4.4 to 8.3 µm (n = 50). Appressoria were dark brown, oval or irregular shaped with a few lobes, 5.7 to 9.4×4.5 to 7.8 µm (n = 50). Total genomic DNA of isolates was extracted with Fungal DNA Kit (GBCBIO, Guangzhou, China). Primers for sequences of internal transcribed spacer (ITS) regions, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ß-tubulin (TUB2), and calmodulin (CAL) genes were amplified and sequenced (Weir et al., 2012). After aligned and trimmed, the sequences of TJBDA1, TJBDA2, and TJBDA3 were identical. TJBDA1 representative isolate sequences were deposited in GenBank ITS OP247554 with 99.83% (576/577) similarity to MT476809, GAPDH OP414834 with 99.59% (244/245) similarity to MT501009, TUB2 OP414836 with 100% (703/703) to MT501053, and CAL OP414835 with 100% (601/601) to MT500921. Maximum likelihood trees based on concatenated sequences of the four genes were constructed using MEGA7.0. The results showed that the strains isolated from B. japonicus were closely related to C. aenigma with 99% bootstrap support. Pathogenicity tests were conducted on 3-leaf stage B. japonicus seedlings. Conidial suspension of TJBDA1 (1×106 conidia/ml) brushed from a 7-day-old culture of the fungus were sprayed on 9 B. japonicus seedlings. Control plants were sprayed with sterile water. All treatments were replicated four times. The treatment plants were placed in an incubator (25°C, relative humidity > 80%, 12-h photoperiod). Typical leaf spot symptoms resembling ones in the fields were observed on inoculated leaves after 7 days, but control leaves remained symptomless. The fungi reisolated from diseased leaves were morphologically and molecularly identical to the inoculated isolatescompleting Koch's postulates. According to morphological, pathological characteristics and multilocus phylogenetic analysis, the isolated strains from B. japonicus were identified as C. aenigma. To our knowledge, this is a new host record for C. aenigma causing anthracnose on B. japonicus in China. Currently, B. japonicus has evolved a high level of resistance to herbicides in some regions of China (Li et al, 2022) and C. aenigma caused serious disease to B. japonicus. We hope to discover a biocontrol method against weed on non-host cultivated plants through the production of secondary metabolites by C. aenigma.

Florasulam resistance status of flixweed (Descurainia sophia L.) and alternative herbicides for its chemical control in the North China plain.

Flixweed (Descurainia sophia L.) is widely distributed in winter wheat (Triticum aestivum L.) fields in the North China Plain and has evolved resistance to herbicides, including the acetolactate synthase (ALS) inhibitor florasulam. However, the florasulam resistance status of flixweed in the North China Plain is poorly understood, which hinders the integrated management of this weed in winter wheat production systems. Thus, 45 flixweed populations were collected in wheat fields in these areas, and their sensitivity to florasulam and ALS-inhibitor-resistant mutation diversity were assessed. Meanwhile, alternative herbicides/herbicide mixtures for the control of florasulam-resistant flixweed were screened and evaluated under greenhouse and field conditions. Of the populations, 30 showed florasulam resistance (RRR and RR), 9 had a high risk of evolving florasulam resistance (R?) and 6 were susceptible. These populations had 5.3 to 345.1-fold resistance to florasulam, and 4 ALS resistance mutations (P197H, P197S, P197T and W574L) were observed. The subsequent herbicide sensitivity assay showed that the SD-06 population (with ALS1 P197T and ALS2 W574L mutations) exhibited cross-resistance to all ALS inhibitors tested, but was sensitive to MCPA-Na, fluroxypyr, carfentrazone-ethyl and bipyrazone. Meanwhile, the other HN-07 population with non-target-site resistance (NTSR) also showed resistance to all tested ALS inhibitors, and it was "R?" to MCPA-Na while sensitive to fluroxypyr, carfentrazone-ethyl and bipyrazone. The field experiments were conducted at the research farm where the SD-06 population was collected, and the results suggested that florasulam at 3.75-4.5 g ai ha-1 had little efficacy (0.6-12.1%), whereas MCPA-Na + carfentrazone-ethyl (87.1-91.2%) and bipyrazone+fluroxypyr (90.1-97.8%) controlled the resistant flixweed.

Silica-Mediated Formation of Nickel Sulfide Nanosheets on CNT Films for Versatile Energy Storage.

An effective, nondestructive, and universal strategy to homogeneously modify freestanding carbon nanotube (CNT) films with various active species is essential to achieve functional electrodes for flexible electrochemical energy storage, which is challenging and has attracted considerable research interest. In this work, a generalizable concept, to utilize silicon oxide as the intermediate to uniformly decorate various metal sulfide nanostructures throughout CNT films is reported. Taking nickel sulfide nanosheet/CNT (NS/CNT) films, in which the NS nanosheets are homogeneously attached on the intact few-walled CNTs, as an example, the sheet-like NS provides sufficient active sites for redox reactions and the CNT network acts as an efficient electron highway, maintaining the structural integrity of the composite and also buffering volume changes. These merits enable NS/CNT films to meet the requirements of versatile energy storage applications. When used for supercapacitors, a high specific capacitance (2699.7 F g-1 /10 A g-1 ), outstanding rate performance at extremely high rates (1527 F g-1 /250 A g-1 ), remarkable cycling stability, and excellent flexibility can be achieved, among the best performance so far. Moreover, it also delivers excellent performance in the storage of Li and Na ions, meaning it is also potentially suitable for Li/Na ion batteries.

Method validation and dissipation kinetics of the new HPPD inhibitor QYR301 in rice, paddy water and paddy soil using a QuEChERS-based method and LC-MS/MS.

A rapid and simple method based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) of sample preparation using QuEChERS was developed for detecting residues of QYR301, a new HPPD-inhibiting herbicide, in rice plant (straw), water, soil, rice hull and brown rice (BR). To eliminate matrix interference, matrix-matched calibrations with satisfactory linearity (R2 > 0.99) were used for accurate quantification. The method showed recoveries of 90.3-108.1% and relative standard deviations (RSDs) < 11%. The limits of quantification (LOQ) for QYR301 were 0.005 mg kg-1 in all five matrixes. Furthermore, the dissipation kinetics and terminal residues of QYR301 were determined at two sites in 2018. The days for 50% dissipation (DT50) of QYR301 in rice plants, water and soil were 3.6-4.4, 0.7-3.0 and 4.3-8.0 d, respectively, which indicated that QYR301 is a short-persistence herbicide. Moreover, no QYR301 residues were detected in BR, rice hull and straw collected at harvest following its application at 1.0 or 1.5 × of the recommended high rate. These results will help organizations and governments establish related principles/laws regarding the use of QYR301 in terms of environmental protection, food safety and other potential aspects.

Fenoxaprop-P-ethyl and mesosulfuron-methyl resistance status of shortawn foxtail (Alopecurus aequalis Sobol.) in eastern China.

Resistance to the acetyl-coenzyme A carboxylase (ACCase)- and acetolactate synthase (ALS)- inhibiting herbicides in shortawn foxtail (Alopecurus aequalis) has been reported in wheat fields of eastern China. To better understand the distribution of the resistant populations and the occurrence of the target-site mutations, 74 populations collected from Anhui, Jiangsu and Shandong province were surveyed, and the ACCase and ALS gene fragments, encompassing all the documented mutant codon positions, were amplified and sequenced. Plants from 37 and 34 populations survived fenoxaprop-P-ethyl and mesosulfuron-methyl treatment at 62.1 g a.i. ha-1 and 9 g a.i. ha-1 respectively, with different survival rates. Twenty-seven populations exhibited multiple resistance to fenoxaprop-P-ethyl and mesosulfuron-methyl. Whole-plant dose-response experiments showed that the resistance index ranged from 6.2 to 167.8 for fenoxaprop-P-ethyl, and from 7.8 to 139.5 for mesosulfuron-methyl. Four ACCase (I1781L, I2041N, I2041T and D2078G) and four ALS (P197R, P197S, P197T and W574 L) resistance mutations were detected respectively. Individuals containing two amino acid substitutions were also found. D2078G and W574 L were predominant ACCase and ALS gene mutations respectively. This study has shown that fenoxaprop-P-ethyl and mesosulfuron-methyl resistance was prevalent in A. aequalis in eastern China, and target site mutations in the ACCase and ALS gene were one of the most common mechanisms.

Comparison of ALS functionality and plant growth in ALS-inhibitor susceptible and resistant Myosoton aquaticum L.

Herbicide target-site resistance mutations may cause pleiotropic effects on plant ecology and physiology. The effect of several known (Pro197Ser, Pro197Leu Pro197Ala, and Pro197Glu) target-site resistance mutations of the ALS gene on both ALS functionality and plant vegetative growth of weed Myosoton aquaticum L. (water chickweed) have been investigated here. The enzyme kinetics of ALS from four purified water chickweed populations that each homozygous for the specific target-site resistance-endowing mutations were characterized and the effect of these mutations on plant growth was assessed via relative growth rate (RGR) analysis. Plants homozygous for Pro197Ser and Pro197Leu exhibited higher extractable ALS activity than susceptible (S) plants, while all ALS mutations with no negative change in ALS kinetics. The Pro197Leu mutation increased ALS sensitivity to isoleucine and valine, and Pro197Glu mutation slightly increased ALS sensitivity to isoleucine. RGR results indicated that none of these ALS resistance mutations impose negative pleiotropic effects on relative growth rate. However, resistant (R) seeds had a lowed germination rate than S seeds. This study provides baseline information on ALS functionality and plant growth characteristics associated with ALS inhibitor resistance-endowing mutations in water chickweed.

Tribenuron-methyl resistance and mutation diversity of the AHAS gene in shepherd's purse (Capsella bursa-pastoris (L.) Medik.) in Henan Province, China.

Shepherd's purse is a troublesome dicot weed that occurs in the major wheat-producing areas in China. Twenty-eight shepherd's purse populations were collected from winter wheat-planting areas in Henan Province and used to evaluate tribenuron-methyl resistance and acetohydroxyacid synthase (AHAS) gene-mutation diversity. The results indicate that all 28 shepherd's purse populations were resistant to tribenuron-methyl at different levels compared with the susceptible population. Mutation of the 197 codon (CCT) changed proline (Pro) into tyrosine (Tyr), histidine (His), leucine (Leu), serine (Ser), arginine (Arg), alanine (Ala) and threonine (Thr), whereas mutation of the 574 codon (TGG) changed tryptophan (Trp) into leucine (Leu). Among these amino acid changes, a co-concurrence of Pro197Leu and Trp574Leu substitutions was identified for the first time in resistant weed species. Furthermore, Pro197Tyr, Pro197Arg and Pro197Ala substitutions have not been previously reported in shepherd's purse. The results of the in vitro AHAS assay suggest that an insensitive AHAS is likely involved in the resistance to tribenuron-methyl in the R populations with AHAS gene mutations, and the non-target-site based resistance might exist in some populations.

Cross-resistance patterns to ACCase-inhibitors in American sloughgrass (Beckmannia syzigachne Steud.) homozygous for specific ACCase mutations.

American sloughgrass is a troublesome annual grass weed in winter wheat field rotated with rice in China. The overreliance on acetyl-coenzyme A carboxylase (ACCase) inhibiting herbicides has resulted in resistance evolution in this weed. In this study, the cross-resistance patterns to fenoxaprop-p-ethyl, clodinafop-propargyl, fluazifop-p-butyl, haloxyfop-p-methyl, sethoxydim, clethodim and pinoxaden were established using purified plants individually homozygous for specific mutant ACCase alleles. Results indicated that 1781Leu allele endows high-level resistance to APPs, CHDs and pinoxaden while confers moderate resistance to haloxyfop-p-methyl. The 2027Cys and 2041Asn alleles endow high-level resistance to APPs and pinoxaden and lower level resistance to CHDs. The 2078Gly allele confers high-level resistance to all herbicides tested in this study, however, moderate resistance to sethoxydim. The 2096Ala very likely endows high-level resistance to fluazifop-p-butyl, haloxyfop-p-methyl and moderate resistance to sethoxydim. In addition, one undefined resistance mechanism was involved in population SD-04.

Molecular basis of multiple resistance to ACCase- and ALS-inhibiting herbicides in Alopecurus japonicus from China.

Fenoxaprop-P-ethyl-resistant Alopecurus japonicus has become a recurring problem in winter wheat fields in eastern China. Growers have resorted to using mesosulfuron-methyl, an acetolactate synthase (ALS)-inhibiting herbicide, to control this weed. A single A. japonicus population (AH-15) resistant to fenoxaprop-P-ethyl and mesosulfuron-methyl was found in Anhui Province, China. The results of whole-plant dose-response experiments showed that AH-15 has evolved high-level resistance to fenoxaprop-P-ethyl (95.96-fold) and mesosulfuron-methyl (39.87-fold). It was shown via molecular analysis that resistance to both fenoxaprop-P-ethyl and mesosulfuron-methyl was due to an amino acid substitution of Ile1781 to Leu in acetyl-CoA carboxylase (ACCase) and a substitution of Trp 574 to Leu in ALS, respectively. Whole-plant bioassays indicated that the AH-15 population was resistant to the ACCase herbicides clodinafop-propargyl, clethodim, sethoxydim and pinoxaden as well as the ALS herbicides pyroxsulam, flucarbazone-Na and imazethapyr, but susceptible to the ACCase herbicide haloxyfop-R-methyl. This work reports for the first time that A. japonicus has developed resistance to ACCase- and ALS-inhibiting herbicides due to target site mutations in the ACCase and ALS genes.

Molecular basis for resistance to ACCase-inhibiting herbicides in Pseudosclerochloa kengiana populations.

Pseudosclerochloa kengiana is a troublesome annual grass weed of wheat fields in the rice-wheat double cropping areas in China. Resistance has evolved in P. kengiana under continuously selective pressure of ACCase-inhibiting herbicides. Whole-plant experiments showed that two suspected resistant populations 12-SD-12 and 12-SD-13 were highly resistant to fenoxaprop-P-ethyl (69.9- and 57.2-fold); moderately resistant to clodinafop-propargyl (5.9- and 4.1-fold) and pinoxaden (4.4- and 3.5-fold); lowly resistant to fluazifop-P-butyl (2.2- and 2.0-fold) and sethoxydim (1.8- and 1.6-fold), but were sensitive to clethodim (1.0- and 0.9-fold) and mesosulfuron-methyl (1.1- and 0.9-fold). Molecular analyses confirmed that a Trp1999 to Ser mutation was present in the resistant populations. Two dCAPS markers were also developed to positively determine the wild type Trp and mutant Ser alleles at ACCase position 1999. All 350 individual plants of 12-SD-12 population analysed were heterozygous mutants. Meanwhile, 318 mutant heterozygotes and 32 wild types were detected from the 12-SD-13 population. In addition, the analysis of plant genotype and phenotype showed that all wild type plants were killed after treatment with any one of the ACCase-inhibiting herbicides used, while individual plants carrying the W1999S mutation survived except when treated with clethodim. To our knowledge, this is the first report of pinoxaden resistance and a Trp-1999-Ser mutation in the plastid ACCase for P. kengiana.

A novel Pro197Glu substitution in acetolactate synthase (ALS) confers broad-spectrum resistance across ALS inhibitors.

Water chickweed (Myosoton aquaticum L.), a competitive broadleaf weed, is widespread in wheat fields in China. Tribenuron and pyroxsulam failed to control water chickweed in the same field in Qiaotian Village in 2011 and 2012, respectively. An initial tribenuron resistance confirmation test identified a resistant population (AH02). ALS gene sequencing revealed a previously unreported substitution of Glu for Pro at amino acid position 197 in resistant individuals. A purified subpopulation (WRR04) that was individually homozygous for the Pro197Glu substitution was generated and characterized in terms of its response to different classes of ALS inhibitors. A whole-plant experiment showed that the WRR04 population exhibited broad-spectrum resistance to tribenuron (SU, 318-fold), pyrithiobac sodium (PTB, > 197-fold), pyroxsulam (TP, 81-fold), florasulam (TP, > 36-fold) and imazethapyr (IMI, 11-fold). An in vitro ALS assay confirmed that the ALS from WRR04 showed high resistance to all the tested ALS inhibitors. These results established that the Pro197Glu substitution endows broad-spectrum resistance across ALS inhibitors in water chickweed. In addition, molecular markers were developed to rapidly identify the Pro197Glu mutation.

Multiple resistance to ACCase and AHAS-inhibiting herbicides in shortawn foxtail (Alopecurus aequalis Sobol.) from China.

Shortawn foxtail (Alopecurus aequalis) is a troublesome grass weed infesting winter wheat and oilseed rape productions in China. Fenoxaprop-p-ethyl and mesosulfuron-methyl failed to control shortawn foxtail of AHSX-1 population collected from a wheat field in Shou County, Anhui province. Molecular analyses revealed that Asp2078Gly mutation of ACCase and Trp574Leu mutation of AHAS were present in plants of the AHSX-1 population. The homozygous plants were isolated and cultured until seed maturity. Whole-plant herbicide bioassays were conducted in the greenhouse using the purified seeds of F1 generation. Dose-response experiments showed that the AHSX-1 population has evolved a very high level resistance to fenoxaprop-p-ethyl (RI = 275) and mesosulfuron-methyl (RI = 788). To determine the sensitivity to other herbicides, assays were conducted at the single recommended rate of each herbicide. Based on the results, the AHSX-1 population was considered to be highly resistant to clodinafop-propargyl, pyroxsulam and flucarbazone-sodium, moderately or highly resistant to quizalofop-p-ethyl, clethodim, sethoxydim and pinoxaden, and susceptible to isoproturon and chlorotoluron. This is the first report of Asp2078Gly mutation in shortawn foxtail and the two robust dCAPS markers designed could quickly detect Asp2078 and Trp574 mutations in ACCase and AHAS gene of shortawn foxtail, respectively.

Metabolism-Based Herbicide Resistance to Mesosulfuron-methyl and Identification of Candidate Genes in Bromus japonicus.

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.

Temperature influences glyphosate efficacy on glyphosate-resistant and -susceptible goosegrass (Eleusine indica).

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 LD50 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.

Metabolic pathways modulated by coumarin to inhibit seed germination and early seedling growth in Eleusine indica.

Coumarin is an allelochemical that is widely present in the plant kingdom and has great potential for weed control. However, its mechanisms of action remain largely unknown. This study employed metabolomic and transcriptomic analyses along with evaluations of amino acid profiles and related physiological indicators to investigate how coumarin inhibits the germination and seedling growth of Eleusine indica by modifying metabolic pathways. At 72 h of germination at 50 and 100 mg L-1 coumarin, E. indica had lower levels of soluble sugar and activities of amylases and higher levels of starch, O2-, H2O2, auxin (IAA) and abscisic acid (ABA) compared to the control. Metabolomic analysis demonstrated that coumarin treatments had a significant impact on the pathways associated with amino acid metabolism and transport and aminoacyl-tRNA biosynthesis. Exposure to coumarin induced significant alterations in the levels of 19 amino acids, with a decrease in 15 of them, including Met, Leu and γ-aminobutyric acid (GABA). Additionally, transcriptomic analysis showed that coumarin significantly disrupted several essential biological processes, including protein translation, secondary metabolite synthesis, and hormone signal transduction. The decrease in TCA cycle metabolite (cis-aconitate, 2-oxoglutarate, and malate) contents was associated with the suppression of transcription for related enzymes. Our findings indicate that the inhibition of germination and growth in E. indica by coumarin involves the suppression of starch conversion to sugars, modification of the amino acid profile, interference of hormone signalling and the induction of oxidative stress. The TCA cycle appears to be one of the most essential pathways affected by coumarin.

Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet.

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.

Correction: Luo et al. Reassessment of Annamocarya sinesis (Carya sinensis) Taxonomy through Concatenation and Coalescence Phylogenetic Analysis. Plants 2022, 11, 52.

In the original publication [...].

GROP: A genomic information repository for oilplants.

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.

Genome-Wide Identification of TLP Gene Family and Their Roles in Carya cathayensis Sarg in Response to Botryosphaeria dothidea.

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.