Resultados totales (Incluyendo duplicados): 45302
Encontrada(s) 4531 página(s)
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330547
Dataset. 2022

SUPPLEMENTARY MATERIAL. EFFECTS OF CONSERVATION TILLAGE, CONTROLLED TRAFFIC AND REGULATED DEFICIT IRRIGATION ON SOIL CO2 EMISSIONS IN A MAIZE-BASED SYSTEM IN MEDITERRANEAN CONDITIONS

  • Salamanca-Fresno, Carlos
  • Soriano, Mª Auxiliadora
  • Testi, Luca
  • Gómez Macpherson, H.
Figure S1. Weekly average of maximum and minimum daily temperatures (ºC) and weekly-accumulated rainfall and ETo (mm) during the two agricultural seasons of this study (2016/17-2017/18) at the experimental site. Figure S2. A) Scheme of the experimental design, showing the distribution of tillage system (CTR and ZTR) and irrigation strategy (FI and RDI) treatments in each block. B) Arrangement of the three consecutive PVC collars in an elementary plot. Each group of three collars [+F, L, -F] in consecutive positions constitutes a measuring site, or unit of measure, for the two main factors (tillage system and irrigation strategy). Table S1. Number of irrigations and fortnight irrigation amount for FI and RDI treatments during the 2016 and 2017 irrigation seasons. Table S2. Daily mean, and minimum and maximum diurnal soil C-CO2 effluxes (mg m-2 h-1) measured during the three diurnal cycles in the CTR and ZTR tillage systems, and relative difference in relation to the 24-h mean for the minimum and maximum diurnal values (%; negative value = underestimation; positive values = overestimation). CV = coefficient of variation (%)., Peer reviewed

Proyecto: //
DOI: http://hdl.handle.net/10261/330547
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330547
HANDLE: http://hdl.handle.net/10261/330547
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330547
PMID: http://hdl.handle.net/10261/330547
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330547
Ver en: http://hdl.handle.net/10261/330547
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330547

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330548
Dataset. 2022

TABLE_5_IMPACTS OF THE BIOCONTROL STRAIN PSEUDOMONAS SIMIAE PICF7 ON THE BANANA HOLOBIONT: ALTERATION OF ROOT MICROBIAL CO-OCCURRENCE NETWORKS AND EFFECT ON HOST DEFENSE RESPONSES.XLSX

  • Gómez-Lama Cabanás, Carmen
  • Wentzien, Nuria M.
  • Zorrilla-Fontanesi, Yasmín
  • Valverde-Corredor, Antonio
  • Fernández-González, Antonio José
  • Fernández-López, Manuel
  • Mercado-Blanco, Jesús
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

Proyecto: //
DOI: http://hdl.handle.net/10261/330548
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330548
HANDLE: http://hdl.handle.net/10261/330548
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330548
PMID: http://hdl.handle.net/10261/330548
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330548
Ver en: http://hdl.handle.net/10261/330548
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330548

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330549
Dataset. 2022

TABLE_4_IMPACTS OF THE BIOCONTROL STRAIN PSEUDOMONAS SIMIAE PICF7 ON THE BANANA HOLOBIONT: ALTERATION OF ROOT MICROBIAL CO-OCCURRENCE NETWORKS AND EFFECT ON HOST DEFENSE RESPONSES.XLSX

  • Gómez-Lama Cabanás, Carmen
  • Wentzien, Nuria M.
  • Zorrilla-Fontanesi, Yasmín
  • Valverde-Corredor, Antonio
  • Fernández-González, Antonio José
  • Fernández-López, Manuel
  • Mercado-Blanco, Jesús
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

Proyecto: //
DOI: http://hdl.handle.net/10261/330549
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330549
HANDLE: http://hdl.handle.net/10261/330549
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330549
PMID: http://hdl.handle.net/10261/330549
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330549
Ver en: http://hdl.handle.net/10261/330549
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330549

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330550
Dataset. 2022

DATA_SHEET_1_IMPACTS OF THE BIOCONTROL STRAIN PSEUDOMONAS SIMIAE PICF7 ON THE BANANA HOLOBIONT: ALTERATION OF ROOT MICROBIAL CO-OCCURRENCE NETWORKS AND EFFECT ON HOST DEFENSE RESPONSES.DOCX

  • Gómez-Lama Cabanás, Carmen
  • Wentzien, Nuria M.
  • Zorrilla-Fontanesi, Yasmín
  • Valverde-Corredor, Antonio
  • Fernández-González, Antonio José
  • Fernández-López, Manuel
  • Mercado-Blanco, Jesús
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

Proyecto: //
DOI: http://hdl.handle.net/10261/330550
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330550
HANDLE: http://hdl.handle.net/10261/330550
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330550
PMID: http://hdl.handle.net/10261/330550
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330550
Ver en: http://hdl.handle.net/10261/330550
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330550

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330551
Dataset. 2022

OPTIMIZED DEGRADATION OF BISPHENOL A BY IMMOBILIZED LACCASE FROM TRAMETES VERSICOLOR USING BOX-BEHNKEN DESIGN (BBD) AND ARTIFICIAL NEURAL NETWORK (ANN) [DATASET]

  • Latif, Abdul
  • Maqbool, Ahsan
  • Zhou, Runzhan
  • Arsalan, Muhammad
  • Sun, Kai
  • Si, Youbin
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

Proyecto: //
DOI: http://hdl.handle.net/10261/330551
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330551
HANDLE: http://hdl.handle.net/10261/330551
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330551
PMID: http://hdl.handle.net/10261/330551
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330551
Ver en: http://hdl.handle.net/10261/330551
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330551

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330552
Dataset. 2022

SUPPLEMENTAL INFORMATION FOR PI3KΒ-REGULATED Β-CATENIN MEDIATES EZH2 REMOVAL FROM PROMOTERS CONTROLLING PRIMED HUMAN ESC STEMNESS AND PRIMITIVE STREAK GENE EXPRESSION

  • Yadav, Sudhanshu
  • Garrido, Antonio
  • Hernández, M. Carmen
  • Oliveros, Juan C.
  • Pérez-García, Vicente
  • Fraga, Mario F.
  • Carrera, Ana C.
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

Proyecto: //
DOI: http://hdl.handle.net/10261/330552
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330552
HANDLE: http://hdl.handle.net/10261/330552
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330552
PMID: http://hdl.handle.net/10261/330552
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330552
Ver en: http://hdl.handle.net/10261/330552
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330552

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330553
Dataset. 2022

SUPPORTING INFORMATION FOR PROBING THE STRUCTURE, CYTOCOMPATIBILITY, AND ANTIMICROBIAL EFFICACY OF SILVER-, STRONTIUM-, AND ZINC-DOPED MONETITE

  • Adawy, Alaa
  • Díaz, Raquel
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

Proyecto: //
DOI: http://hdl.handle.net/10261/330553
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330553
HANDLE: http://hdl.handle.net/10261/330553
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330553
PMID: http://hdl.handle.net/10261/330553
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330553
Ver en: http://hdl.handle.net/10261/330553
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330553

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330554
Dataset. 2022

SUPPORTING INFORMATION: STRUCTURAL AND ELECTRONIC EFFECT DRIVEN DISTORTIONS IN VISIBLE LIGHT ABSORBING POLAR MATERIALS ATA2V2O11(A = SR, PB)

  • Babaryk, Artem A.
  • Odynets, Ievgen V.
  • Lobato, Álvaro
  • Adawy, Alaa
  • Recio, J. Manuel
  • García-Granda, Santiago
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

Proyecto: //
DOI: http://hdl.handle.net/10261/330554
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330554
HANDLE: http://hdl.handle.net/10261/330554
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330554
PMID: http://hdl.handle.net/10261/330554
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330554
Ver en: http://hdl.handle.net/10261/330554
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330554

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330555
Dataset. 2022

SUPPLEMENTARY DATA: SYNTHESIS AND IN VITRO ANTIBACTERIAL, ANTIFUNGAL, ANTI-PROLIFERATIVE ACTIVITIES OF NOVEL ADAMANTANE-CONTAINING THIAZOLE COMPOUNDS

  • Warda, Eman T.
  • El-Ashmawy, Mahmoud B.
  • Habib, El-Sayed E.
  • Abdelbaky, Mohammed S. M.
  • García-Granda, Santiago
  • Thamotharan, Subbiah
  • El-Emam, Ali A.
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

Proyecto: //
DOI: http://hdl.handle.net/10261/330555
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330555
HANDLE: http://hdl.handle.net/10261/330555
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330555
PMID: http://hdl.handle.net/10261/330555
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330555
Ver en: http://hdl.handle.net/10261/330555
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330555

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330558
Dataset. 2022

A COMPREHENSIVE PHYLOGENOMIC PLATFORM FOR EXPLORING THE ANGIOSPERM TREE OF LIFE [DATASET]

  • Baker, William J.
  • Bailey, Paul
  • Barber, Vanessa
  • Barker, Abigail
  • Bellot, Sidonie
  • Bishop, David
  • Botigué, Laura R.
  • Brewer, Grace
  • Carruthers, Tom
  • Clarkson, James
  • Cook, Jeffrey
  • Cowan, Robyn
  • Dodsworth, Steven
  • Epitawalage, Niroshini
  • Françoso, Elaine
  • Gallego, Berta
  • Johnson, Matthew
  • Kim, Jan
  • Leempoel, Kevin
  • Maurin, Olivier
  • McGinnie, Catherine
  • Pokorny, Lisa
  • Roy, Shyamali
  • Stone, Malcolm
  • Toledo, Eduardo
  • Wickett, Norman
  • Zuntini, Alexandre
  • Eiserhardt, Wolf
  • Kersey, Paul
  • Leitch, Ilia J.
  • Forest, Félix
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

Proyecto: //
DOI: http://hdl.handle.net/10261/330558
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330558
HANDLE: http://hdl.handle.net/10261/330558
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330558
PMID: http://hdl.handle.net/10261/330558
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/330558
Ver en: http://hdl.handle.net/10261/330558
Digital.CSIC. Repositorio Institucional del CSIC
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