Resultados de investigación

Supporting Information Table S5. RT-qPCR primers for the thirteen selected genes and the two reference genes used in this study., The impact of the versatile biocontrol and plant-growth-promoting rhizobacteria Pseudomonas simiae PICF7 on the banana holobiont under controlled conditions was investigated. We examine the fate of this biological control agent (BCA) upon introduction in the soil, the effect on the banana root microbiota, and the influence on specific host genetic defense responses. While the presence of strain PICF7 significantly altered neither the composition nor the structure of the root microbiota, a significant shift in microbial community interactions through co-occurrence network analysis was observed. Despite the fact that PICF7 did not constitute a keystone, the topology of this network was significantly modified—the BCA being identified as a constituent of one of the main network modules in bacterized plants. Gene expression analysis showed the early suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers. This outcome occurred at the time in which the highest relative abundance of PICF7 was detected. The absence of major and permanent changes on the banana holobiont upon PICF7 introduction poses advantages regarding the use of this beneficial rhizobacteria under field conditions. Indeed a BCA able to control the target pathogen while altering as little as possible the natural host-associated microbiome should be a requisite when developing effective bio-inoculants., Peer reviewed

Supplementary Table S4. Pseudomonas simiae strain PICF7 (GenBank: CP0052975.1) 16S rRNA gene sequence comparison with Amplicon Sequence Variants belonging to Pseudomonas species found in Grand Naine Control and Grand Naine PICF7 samples., The impact of the versatile biocontrol and plant-growth-promoting rhizobacteria Pseudomonas simiae PICF7 on the banana holobiont under controlled conditions was investigated. We examine the fate of this biological control agent (BCA) upon introduction in the soil, the effect on the banana root microbiota, and the influence on specific host genetic defense responses. While the presence of strain PICF7 significantly altered neither the composition nor the structure of the root microbiota, a significant shift in microbial community interactions through co-occurrence network analysis was observed. Despite the fact that PICF7 did not constitute a keystone, the topology of this network was significantly modified—the BCA being identified as a constituent of one of the main network modules in bacterized plants. Gene expression analysis showed the early suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers. This outcome occurred at the time in which the highest relative abundance of PICF7 was detected. The absence of major and permanent changes on the banana holobiont upon PICF7 introduction poses advantages regarding the use of this beneficial rhizobacteria under field conditions. Indeed a BCA able to control the target pathogen while altering as little as possible the natural host-associated microbiome should be a requisite when developing effective bio-inoculants., Peer reviewed

Supplementary Figure 1. Principal coordinates analyses of the banana root microbial communities. PCoA of bacterial (A) and fungal (B) communities by treatment on Bray-Curtis dissimilarities. GNC: control plant, GNF7: plant inoculated with Pseudomonas simiae PICF7, DAI: days after inoculation. Supplementary Figure 2. The rarefaction curve. The abscissa is the number of sampling sequences and the ordinate is the number of Amplicon Sequence Variants (ASV) in the sampling sequences. Different colors indicate different groups. Black color indicates control and inoculated plants (GNC and GNF7) and orange color Grand Nain in vitro plants (GNI). The ASV 0 to 100 range has been magnified to show differences. Supplementary Figure 3. Box plot of α-diversity indices: InvSimpson, observed Amplicon Sequence Variants (ASV) and Shannon for the fungal community comparing Grand Nain in vitro (GNI), control (GNC) and Pseudomanas simiae PICF7-inoculated (GNF7) plants. Supplementary Figure 4. Principal coordinates analyses of the banana root microbial communities. PCoA of bacterial by treatment on Weighted Unifrac distances (A) and fungal communities by treatment on Bray-Curtis dissimilarities (B). GNI: Grand Nain in vitro, GNC: control plant, GNF7: plant inoculated with Pseudomonas simiae PICF7. Supplementary Figure 5. Relative expression levels of defence-related genes in roots at five time points upon inoculation with Pseudomonas simiae PICF7. (A) Non-expresser of PR genes 1 (NPR1) and Pathogenesis-related 1 (PR1); (B) Isochorismate synthase 1 (ICS1) and Phenylalanine ammonia-lyase (PAL); (C) Allene oxide synthase (AOS) and Jasmonic acid carboxyl methyltransferase (JMT); (D) Anthranilate synthase alpha subunit 1 (ASA1) and Polyphenol oxidase (PPO); (E) Enhanced disease susceptibility 1 (EDS1) and Phytoalexin deficient 4 (PAD4); (F) Manganese superoxide dismutase 1 (MSD1) and Coronatine insensitive 1 (COI1); (G) Ascorbate peroxidase (APX1). CNRQ: Calibrated Normalized Relative Quantity. Musa acuminata genes EF-1 and L2 were used as internal controls to normalize the expression data. Letters in black and bold type indicate significant differences based on comparison over treatments and time points (LSD; α = 0.05). Letters in grey indicate non-significant differences. Error bars: standard error of the mean (SEM). DAI: days after inoculation. GNC: non-inoculated plants; GNF7: Pseudomonas simiae PICF7-inoculated plants. N control/inoculated=4/4. Supplementary Figure 6. Relative expression levels of defence-related genes in leaves at five time points upon inoculation with Pseudomonas simiae PICF7. (A) Non-expresser of PR genes 1 (NPR1) and Isochorismate synthase 1 (ICS1), (B) Enhanced disease susceptibility 1 (EDS1) and Phytoalexin deficient (PAD4), (C) Coronatine insensitive 1 (COI1) and Anthranilate synthase alpha subunit 1 (ASA1), (D) Phenylalanine ammonia-lyase (PAL) and Polyphenol oxidase (PPO), (E) Ascorbate peroxidase (APX1) and Manganese superoxide dismutase 1 (MSD1). CNRQ: Calibrated Normalized Relative Quantity. Musa acuminata genes EF-1 and L2 were used as internal controls to normalize the expression data. Letters in black and bold type indicate significant differences based on comparison over treatments and time points (LSD; α = 0.05). Letters in grey indicate non-significant differences. Error bars: standard error of the mean (SEM). DAI: days after inoculation. GNC: non-inoculated plants; GNF7: Pseudomonas simiae PICF7-inoculated plants. N control/inoculated=4/4. Supplementary Table S1. Taxonomical profile of Amplicon Sequence Variants (ASV) present in at least 4 of the 10 Grand Nain in vitro samples analysed. Supplementary Table S2. p-values of bacterial and fungal richness (Observed Amplicon Sequence Variants; ASV), Shannon and InvSimpsom α-diversity indices for the different comparisons analysed. Significant p-values and its correspondent significant comparisons are shown in bold type and italics. GNI: Grand Nain in vitro plants, GNC: control plants, GNF7: Pseudomonas simiae-inoculated plants. Supplementary Table S3. p-values of PERMANOVA and BETADISPER analysis of quantitative β-diversity index for the different comparisons analysed. GNI: Grand Nain in vitro plants, GNC: control plants, GNF7: Pseudomonas simiae-inoculated plants. Significant p-values and its correspondent significant comparisons are shown in bold type and italics. Supplementary Table S4. Pseudomonas simiae strain PICF7 (GenBank: CP005975.1) 16S rRNA gene sequence comparison with Amplicon Sequence Variants (ASV) belonging to Pseudomonas species found in Grand Nain Control and Grand Nain PICF7 samples. Supplementary Table S5. List of defence related genes studied by real-time PCR experiments in root and aerial tissues of banana plants (cv. Grand Nain) grown under control conditions upon Pseudomonas simiae PICF7 inoculation. For all transcripts, Relative expression analysis was repeated at least two times in independent (4 replicates each one) real-time qPCR experiments. Gene names, abbreviation, Arabidopsis thaliana orthologs, Musa acuminata paralogs, primers sequences, amplicon size, annealing temperature, PCR efficiencies, correlation coefficients (R2) and linear equations are indicated. Fw: forward, Rv: reverse., The impact of the versatile biocontrol and plant-growth-promoting rhizobacteria Pseudomonas simiae PICF7 on the banana holobiont under controlled conditions was investigated. We examine the fate of this biological control agent (BCA) upon introduction in the soil, the effect on the banana root microbiota, and the influence on specific host genetic defense responses. While the presence of strain PICF7 significantly altered neither the composition nor the structure of the root microbiota, a significant shift in microbial community interactions through co-occurrence network analysis was observed. Despite the fact that PICF7 did not constitute a keystone, the topology of this network was significantly modified—the BCA being identified as a constituent of one of the main network modules in bacterized plants. Gene expression analysis showed the early suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers. This outcome occurred at the time in which the highest relative abundance of PICF7 was detected. The absence of major and permanent changes on the banana holobiont upon PICF7 introduction poses advantages regarding the use of this beneficial rhizobacteria under field conditions. Indeed a BCA able to control the target pathogen while altering as little as possible the natural host-associated microbiome should be a requisite when developing effective bio-inoculants., Peer reviewed

Fig. S1. Best topology design of the MLP based ANN algorithm. Fig. S2. impact of individual parameters on the removal of BPA from polluted water. Table S1. Enzyme kinetics constants of free laccase and Ba-alginate beads containing laccase., Peer reviewed

Document S1. Figures S1–S6 and supplemental experimental procedures. Table S1. Gene expression changes (> 1.6 and < −1.6 fold-change) in cells depleted of PIK3CB, or PIK3CA, or N/C-MYC (72 h) compared with controls cells. Document S2. Article plus supplemental information., Peer reviewed

SEM micrographs of Ag-P, Sr-P, and Zn-P (Figure S1); EDX area mapping showing the homogeneous distribution of Ag, Sr, and Zn in phosphate phases (Figure S2); powder X-ray diffraction (PXRD) patterns of Ag-P, Sr-P, and Zn-P (Figure S3); and normalized average weight and atomic percentages of phosphorus, calcium, silver, strontium, and zinc from the three highly doped phases based on EDX elemental analysis (Table S1)., Peer reviewed

Crystallographic summary and table of bond lengths: SrTa2V2O11 (CIF). Crystallographic summary and table of bond lengths: PbTa2V2O11 (CIF). The traces of (D)TG scans and the transcription of thermal effects; the final Rietveld refinement plots; supplementary HRTEM and related SAED images; equilibrium coordinates of DFT-relaxed crystal structures; principal components of Born charge and dielectric tensors; and diagrams of the electron density section of metallic subarrays for STVO and PTVO (PDF)., Peer reviewed

1. Crystal data and structure refinement parameters for compounds 5d and 5f (Table S1). 2. PASS prediction of compounds 5a-r (Table S2). 3. Molecular formulae, molecular weights and elemental analyses data of compounds 5a-r (Table S3) 4. NMR spectra of synthesised compounds 5a-r. 5. Checkcif reports for crystals 5d and 5f. 6. Determination of antimicrobial activity of compounds 5a-r (agar disc-diffusion method). 7. Determination of minimal inhibitory concentrations (MIC) and the minimal biocidal concentrations (MBC) for compounds 5a, 5c, 5g, 5l, 5m, 5o and 5q (micro-dilution susceptibility method. 8. Determination of bacterial biofilm inhibitory activity of compounds 5a, 5c, 5l and 5o (crystal violet staining method). 9. Determination of anti-proliferative activity (MTT assay, Peer reviewed

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this paper are to (i) document our methods, (ii) describe our first data release and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). A “first pass” angiosperm tree of life was inferred from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections., Calleva Foundation Sackler Trust Garfield Weston Foundation, Peer reviewed

Table S6 Candidate genes mapped within the genomic regions associated with the significantly associated SNPs detected in response to U. pisi. Chromosomal linkage disequilibrium (LD) decay was considered to limit the genomic regions were to look for candidate genes., Uromyces pisi ([Pers.] D.C.) Wint. is an important foliar biotrophic pathogen infecting grass pea (Lathyrus sativus L.), compromising their yield stability. To date, few efforts have been made to assess the natural variation in grass pea resistance and to identify the resistance loci operating against this pathogen, limiting its efficient breeding exploitation. To overcome this knowledge gap, the genetic architecture of grass pea resistance to U. pisi was investigated using a worldwide collection of 182 accessions through a genome-wide association approach. The response of the grass pea collection to rust infection under controlled conditions and at the seedling stage did not reveal any hypersensitive response but a continuous variation for disease severity, with the identification of promising sources of partial resistance. A panel of 5,651 high-quality single-nucleotide polymorphism (SNP) markers previously generated was used to test for SNP-trait associations, based on a mixed linear model accounting for population structure. We detected seven SNP markers significantly associated with U. pisi disease severity, suggesting that partial resistance is oligogenic. Six of the associated SNP markers were located in chromosomes 4 and 6, while the remaining SNP markers had no known chromosomal position. Through comparative mapping with the pea reference genome, a total of 19 candidate genes were proposed, encoding for leucine-rich repeat, NB-ARC domain, and TGA transcription factor family, among others. Results presented in this study provided information on the availability of partial resistance in grass pea germplasm and advanced our understanding of the molecular mechanisms of quantitative resistance to rust in grass pea. Moreover, the detected associated SNP markers constitute promising genomic targets for the development of molecular tools to assist disease resistance precision breeding., Peer reviewed