dataesr/scientific-paragraphs-categorization huggingface dataset:
These gaps were filled with the Platanus gap_close function using the original reads (Table  S3A ). Then, the scaffolding of the assembled genome was improved using the proteins described for the AgamP4 reference in VectorBase (www. vectorbase. org). Blat 76 was used to map the proteins to the assembled scaffolds and to reorder and join scaffolds accordingly with PEP_scaffolder 77. For the second round of gap filling, and due to format incompatibilities, the GapCloser tool from the SOAPdenovo package  78  was used (Table  S3A ). To evaluate the assembly quality, the presence of conserved genes among the Diptera order was assessed using the BUSCO software  79. The 2,799 gene models conserved among Diptera species were classified as: i) completely found in a single sequence, ii) fragmented in different sequences, or iii) completely missing.
10  made a whole multiple genome alignment using ROAST  80  that represents approximately 40% of the euchromatic genome. The resulting MAF based on field-collected samples was downloaded from http://datadryad. org/resource/doi:10. 5061/dryad. f4114  10. Then, this MAF was added to our An. fontenillei assembly, and the highest coverage An. bwambae genome sequences available (see below). Anopheles fontenillei sp. n. First, a database was generated with the scaffolds of the An. fontenillei assembly. Then, blastn was run for each region in the MAF using AgamP3 as query sequence against the An. fontenillei scaffold database. This blastn analysis was repeated using other species of the MAF regions as query: An. arabiensis, An. quadriannulatus, An. melas, and An. merus (Text S2. 1. 1-Text S2. 1. 4), but not An.
Windows with less than 10% of informative base pairs (e. g. , <5,000 bp) were excluded (following 10 ). The different topologies obtained were sorted, counted, and analysed using ad-hoc perl scripts (Text S2. 6. 3). pairwise distance and bootstrapping. The R package ' APE' (v4. 1  88  ) was used to estimate pairwise genetic distances based in the ML phylogenetic trees. Then, the bootstrap analysis was performed using the 'boot' package in R 89 (Text S2. 7). centromeric region alignment quality. For each chromosomal arm, 30 windows were randomly chosen from centromeric regions, and 30 from other genomic regions. Centromeric regions were defined based on the observed ancestry pattern in Fig. 3 : 2L: 0 to 10 Mb, 2R: 50 to 61. 3 Mb, 3L: 0 to 10 Mb, 3R: 40 to 53. 1 Mb, and X: 15 to 20. 2 Mb. For these 60 windows, the alignment length, the alignment length without completely undetermined characters and gaps, the proportion of gaps, and the alignment patterns were extracted from the RAxML information file.
Acknowledgements We are grateful to  P. Nosil  and  G. Lanzaro  for comments on the manuscript. We thank the  "Agence Nationale de la Preservation de la Nature" (ANPN) , the  "Station d'Etudes des Gorilles et Chimpanzes" (SEGC)  and the  "Centre National de la Recherche Scientifique et Technologique of Gabon" (CENAREST)  that authorized this study and facilitated the access to the national parks of  La Lopé. We specially thank  Vincenzo Petrarca  for its help interpreting chromosome polymorphisms. Finally, we greatly thank  Maureen Coetzee  for revising the taxonomic description. Funding was provided by the  "Institut de Recherche pour le Developpément" , the  "Agence Universitaire de la Francophonie " (grant OKANDA), the  "Agence Nationale de Recherche"  ( ANR-18-CE35-0002-01 -WILDING ), the  "Consejo Superior de Investigaciones Cientificas"  and the  "Centre National de la Recherche Scientifique" (PICS ANCESTRAL) , and the  "Ministerio de Ciencia, Innovación y Universidades/ AEI/FEDER " ( BFU2017-82937-P ) and the  "Secretaria d'Universitats i Recerca.
Total RNA was isolated from peripheral blood mononuclear cells (PBMCs) using a PAXgene Blood RNA Kit (Qiagen) and stored at -80 • C. cDNA synthesis was performed using a High Capacity RNA-to-cDNA kit (Applied Biosystems). Sequencing of the transcripts was performed as previously explained with specific primers for RT-PCR products. CLUSTAL multiple sequence alignment was performed with MUSCLE (V. 3. 8) software  [10]  for the amino acidic sequences of KL wild-type and deletion variant. The potential pathogenic impact of the new allele identified on KL was investigated in silico with the MutationTaster software (http://www. mutationtaster. org/) [11].
1041delT variant. Sequencing of the cDNA from PBMCs of the patient did not show the presence of this deletion in KL transcripts suggesting that effectively the mRNA product of this allele is degraded by the NMD pathway (Figure  1C ). In order to study the pathogenic potential of the variant detected in the KL gene, we evaluated in silico its functional effect on the protein by using the MutationTaster software  [11]. This program checks if the resulting protein of a particular genetic variant will be elongated, truncated, or whether nonsense-NMD is likely to occur. If the software concludes that a variant causes NMD, this alteration is automatically regarded as a disease mutation. In our new identified variant, the prediction resulted in a protein regulated by an NMD mechanism and, hence, to be "disease-causing" under a model of complex change of the amino acid sequence (i.
60 mmol/L) or high (>1. 60 mmol/L) serum phosphate levels. The serum levels of FGF23 and KL were similar between both groups. In this study, we identified a previously unknown genetic variant in the KL gene in a 67-year-old hyperphosphatemic woman consisting of a heterozygous deletion of a T at position 1041 in exon 2 (c. 1041delT). Such variant causes a shift in the open reading frame and generates a PTC downstream. At the protein level, the isoleucine at position 348 of the wild-type protein is substituted by a phenylalanine and the new stop codon establishes the early termination of the protein 28 amino acids downstream (p. Ile348Phefs*28). This variation is present at low frequency in control DNA databases (ExAC, MAF: 0. 00001647). The appearance of a PTC in exon 2 makes plausible the idea that the putative transcript carrying the deletion allele is susceptible to be degraded by the NMD pathway.
Sequencing of the cDNA obtained from these cells revealed the exclusive presence of transcripts with the wild-type allele, supporting the idea of degradation of deletion-carrier mRNAs. Another interesting approach would have been to study if the putative truncated form of KL protein was produced by the patient and if this coexisted with wild-type forms. Unfortunately, by the time we were developing the experimental work of this study, the patient had already died. Therefore, it was not possible to obtain new samples (this approach was not originally conceived for the purposes of the study). This fact is a limitation regarding the conclusion about whether the deletion variant was translated or not. Additionally, we further evaluated the potential effects of this new genetic variant in silico by testing it with MutationTaster, a software designed to predict functional consequences of amino acid substitutions, intronic and synonymous alterations, short indels and variants spanning intron-exon borders  [11].
Funding: This work was supported by  Instituto de Salud Carlos III (ISCIII) : ( PI13/01726 ,  PI16/00024  and  REDINREN RD16/0009/0022 ) and  Sociedad Española de Nefrología. We acknowledge co-funding by  Fondo Europeo de Desarrollo Regional, Unión Europea ("Una forma de hacer Europa"). E. M. -N. is recipient of a PFIS research contract from  ISCIII  ( FI14/00033 ). J. D. -C. is recipient of a Sara Borrell contract from  ISCIII  ( CD16/00165 ). V. G. T. is recipient of a research grant " Stop Fuga de Cerebros " from  Roche España  and  FUNCANIS  ( C16/004 ).
PCR reactions contained 7. 5 µl of 2× SYBR Green supermix, 500 nM of each primer and 1 µl of cDNA in a final volume of 15 µl. All PCR reactions were performed in duplicate. The PCR protocol used was as follows: 95 • C for 5 min followed by 35 cycles of 95 • C (10 s) and 60 • C (30 s) and melting curve analysis from 55 to 95 • C, with an increment of 0. 5 • C/10 s. The primers were designed using the Primer3 Plus software  (Untergasser et al. , 2012)  and are listed in Table  3. Standard curves for each primer pair were generated with serial dilutions of genomic DNA and cDNA to determine PCR efficiency and each product was verified by melting curve analysis. The transcript level data were normalized to that of the reference gene rpoD and relative to the control sample using the Bio-Rad iQ5 software.
Previous studies have validated rpoD as a suitable reference gene in pseudomonads  (Savli et al. , 2003; Chang et al. , 2009). Transcript levels were determined using the relative quantity (ddCt) analysis method  (Livak and Schmittgen, 2001). Data are the means and standard deviations of at least three independent experiments. Statistical analyses (t-test) were performed using GraphPad software. qPP_0320_F ACCGGCCATTACTACAACGA RT-qPCR of PP_0320 (mcpH) qPP_0320_R ATGTTGATGAACCGTTCGGC RT-qPCR of PP_0320 (mcpH) qPP_CtpL_F TGCTGGTGACCGTGTGTATC RT-qPCR of PP_0562 (ctpL_PP) qPP_CtpL_R CCCAGATAGCGCTCCATCAG RT-qPCR of PP_0562 (ctpL_PP) qPP_McpU_F ATTGGCCTGTACCTGGTGTT RT-qPCR of PP_1228 (mcpU) qPP_McpU_R GGGACCAGTACAGCGAGAAA RT-qPCR of PP_1228 (mcpU) qPP_McpG_F CTTCCTCACGGTCTACCTGG RT-qPCR of PP_1371 (mcpG) qPP_McpG_R GTTCATGCCGTCCTTGTACC RT-qPCR of PP_1371 (mcpG) qPP_1488_F TGCTGATCAGGCATCCAGTC RT-qPCR of PP_1488 (wspA_PP) qPP_1488_R AAGCTTGGCATTGACCAGGT RT-qPCR of PP_1488 (wspA_PP) qPP_2111_F GAGATCAGCCGCAACATCAG RT-qPCR of PP_2111 (aer2) qPP_2111_R GTCAGTTCTTCGCTCAGCAG RT-qPCR of PP_2111 (aer2) qPP_CtpH_F ATGCAGCAGACCATCGACAT RT-qPCR of PP_2120 (ctpH_PP) qPP_CtpH_R TTTGCCTATCCGTGTGCTGT RT-qPCR of PP_2120 (ctpH_PP) qPP_McpA I2_F AGCAGACCAACCTGCTGGCACTGAAC RT-qPCR of PP_2249 (mcpA) qPP_McpA_R5 TGCCATCGATTTCGCCAATG RT-qPCR of PP_2249 (mcpA) qPP_2257_F4 ACTGCAATGAACCAGATGGC RT-qPCR of PP_2257 (aer1) qPP_2257_R3 CAGGTTGGTTTGCTCGGC RT-qPCR of PP_2257 (aer1) qPP_2643_F GGAGCTGAACAACAAGAGCC RT-qPCR of PP_2643 (pcaY_PP) qPP_2643_R CGTATTCGGCAAAGGTAGCC RT-qPCR of PP_2643 (pcaY_PP) qPP_McpP_F CAAGGCCATAGACACCAGCA RT-qPCR of PP_2861 (mcpP) qPP_McpP_R CGTTCAATGCGGTGAGGTTG RT-qPCR of PP_2861 (mcpP) qPP_4521_F GAAACCATCAAGCAGGGCAA RT-qPCR of PP_4521 (aer3) qPP_4521_R TGATCCGGCCTTGTTCGTAT RT-qPCR of PP_4521 (aer3) qPP_McpS_F ATCCAGTCGATGAACCAGCA RT-qPCR of PP_4658 (mcpS) qPP_McpS_R TTTGCTCTGACACATCACGC RT-qPCR of PP_4658 (mcpS) qPP_McpQ_F CCGTGATGTACTGGGTAGCA RT-qPCR of PP_5020 (mcpQ) qPP_McpQ_R CGTGCTGGTACTGGTTGATG RT-qPCR of PP_5020 (mcpQ) qPP_0584_F ATTTCAAGCAGCTGGGAAGC RT-qPCR of PP_0584 qPP_0584_R CATGTAGTGCACGCCATTGA RT-qPCR of PP_0584 qPP_0779_F AGCAAGAAATCCGGCAACTG RT-qPCR of PP_0779 qPP_0779_R TTGACCATCTCGATCCGTCC RT-qPCR of PP_0779 qPP_1819_F ACAACCTTGATGTGCTGCAG RT-qPCR of PP_1819 qPP_1819_R TTGCTCAAGAAACTCGCCAC RT-qPCR of PP_1819 qPP_1940_F CGTGTTTGAGCCGTTCTTCA RT-qPCR of PP_1940 qPP_1940_R GAACCGACCCGCTTATTGTC RT-qPCR of PP_1940 qPP_2310_F CGACAACTAGCCGAGGACAG RT-qPCR of PP_2310 qPP_2310_R GCTTCGATGGCAGCGTTAAG RT-qPCR of PP_2310 qPP_2823_F CCAGGCATAACATCGACAGC RT-qPCR of PP_2823 qPP_2823_R CTTCCAGTTGTTCCATGGCC RT-qPCR of PP_2823 qPP_3414_F AGCAGATTTCCCAGGAGCTT RT-qPCR of PP_3414 qPP_3414_R CCCGAATGGTCAGCACAATC RT-qPCR of PP_3414 qPP_3557_F AATTGGGCAGCAACGAAACC RT-qPCR of PP_3557 qPP_3557_R GTTGGCCATGTCATGTTCGG RT-qPCR of PP_3557 qPP_3950_F TACCTGTTCATGGCGCAATC RT-qPCR of PP_3950 qPP_3950_R ACCGTTCTTGAGGTTTTCGC RT-qPCR of PP_3950 qPP_4888_F CATTCAGGCGCACATTACCG RT-qPCR of PP_4888 (Continued).
Colony-Based c-di-GMP Reporter Assays Fluorescence intensity analyses using the c-di-GMP biosensor pCdrA::gfp C were carried out to determine the intracellular levels of the second messenger c-di-GMP. To this end, the reporter plasmid pCdrA::gfp C was transformed into KT2440R strains by electroporation. Subsequently, overnight bacterial cultures of the strains to be tested were adjusted to an OD 660 = 0. 05 and 20 µl aliquots were placed onto LB-agar plates containing the appropriate antibiotics. Following incubation at 30 • C for 48 h, fluorescence intensities were recorded using a Leica M165 FC stereomicroscope. Fluorescence was visualized employing a GFP filter set (emission/excitation filter 470/525 nm). Pictures were taken using Leica Application Suite software using different exposure times.
Chemotactic Responses Occur Only at Elevated Root Exudate Concentration Interestingly, above data show that the most significant increase in chemoreceptor gene transcript levels occurred at the lowest MRE concentration. Since most of these receptors mediate chemotaxis, we assessed the chemotactic behavior of P. putida KT2440 to different MRE concentrations. To this end, we have carried out quantitative capillary chemotaxis assays, which is the traditional reference assay to quantify chemotaxis. In this assay, the chemoattractant is placed into a capillary that is then submerged into the bacterial suspension. After a contact time of 30 min, the capillaries are withdrawn, emptied and the number of colony forming units is determined. The expected strong chemotaxis was observed for a 0. 2% (w/v) casamino acid solution that served as a positive control.
, 1991 pCdrA::gfp C Ap R , Gm R ; FleQ dependent c-di-GMP biosensor Rybtke et al. , 2012 pBBR1MCS-5 Gm R ; oriRK2 mobRK2 Kovach et al. , 1995 pPP4888 Km R ; pET28b(+) derivative containing DNA fragment encoding This study PP4888-LBD cloned into NdeI and BamHI sites pMAMV287 Ap R ; 2. 2-kb BamHI/HindIII PCR product containing a fragment of This study pp4338 was inserted into the same sites of pUC18Not pMAMV289 Ap Woodcock et al. , 1989v/srd/updated-databaseWoodcocket al. , 1989CC118λpir araD (ara, leu) lacZ74 phoA20 galK thi-1rspE rpoB argE recA1 λpir Herrero et al. , 1990 HB101 F -(gpt-proA)62 leuB6 supE44 ara-14 galK2 lacY1 (mcrC-mrr) rpsL20 (Sm R ) xyl-5 mtl-1 recA13 thi-1 Boyer and Roulland-Dussoix, 1969 BL21 (DE3) F -ompT gal dcm lon hsdS B (r B -m B -) λ(DE3) Jeong et al. , 2009 Pseudomonas putida KT2440 Wild type; Derivative of P.
Transcriptome analysis After quality trimming and adapter removal using Trimmomatic, reads were mapped using STAR v2. 5. 3  56  to the Drosophila genome and annotation (ENSEMBL BDGP6. 22). Reads mapping to the sense strand of the transcripts were counted with featureCounts v1. 6. 2  57  , using the Drosophila annotation files, allowing mapping to multiple genes. Differential gene expression of transcripts present in ≥20% of the libraries with at least 5 reads across all libraries was done using the deseq function of the "DESeq2" (v1. 20) package  58. Variance was estimated using the local fitting method. Read counts and normalized read counts are shown in GEO dataset GSE140955. Transcripts with log2 difference in expression ≥ 1. 5 and Benjamini & Hochberg corrected P-value < 0. 05 were considered differentially expressed.
Clustering of temporal expression profiles All differentially expressed genes between Tris and 2'3'-cGAMP injected WT flies at any time point or on average across all time points were clustered in temporal expression categories by partitioning around medoids (PAM) clustering using the pam function in the "cluster" (v2. 1. 0) package. The optimal number of clusters for either stimulated or repressed genes was determined using the gap statistic method, as implemented in the fviz_nbclust function of the "factoextra" (v1. 0. 5) package, using default parameters (100 bootstrapped replications, 10 maximum allowed clusters). Gene expression clusters were visualized using the Heatmap function of the "ComplexHeatmap" (v2. 0. 0) package and ggplot of the "ggplot2" (v3. 2. 1) package.
Ontology analysis Differentially expressed genes between Tris and 2'3'-cGAMP injected WT flies in each temporal expression category were tested for enrichment relative to all genes passing the expression cutoff in any gene ontology type (Molecular Function, Cellular Compartment, Biological Process), using the "Generic GO subset" of gene ontology terms (downloaded from http://current. geneontology. org/ontology/subsets/index. html on 10/10/2019). Gene ontology enrichment analysis was done using the enricher function of "clusterProfiler" package (v3. 1. 12), using default parameters (Benjamini & Hochberg corrected P-value cutoff of 0. 05).
Transcription Factor Enrichment Analysis Enrichment of transcription factor binding sites (TFBS) in the regulatory regions of the differentially expressed genes was done using the cisTarget function of the "RcisTarget" package (v1. 4. 0)  59. The database "dm6-5kb-upstream-full-tx-11species. mc8nr" database was used, which includes the rankings for conserved TFBS in the non-coding regions 5 kb upstream of the transcription start site and in introns of all annotated genes in the D. melanogaster genome (r6. 02). Gene symbols were updated to the r6. 04 annotation when necessary. Transcription factor family assignment was done according to Flybase (FB2019_05).
Funding: This work was supported by the  ERANET Infect-ERA program  ( ANR-14-IFEC-0005 ), the  Agence Nationale de la Recherche  ( ANR-17-CE15-0014 ), the  Investissement d'Avenir Programs  ( ANR-10-LABX-0036  and  ANR-11-EQPX-0022 ), the  Chinese National Overseas Expertise Introduction Center for Discipline Innovation" (Project " 111" (D18010) ),  CNRS  and  INSERM. Further support was provided to R. H. by the  Novo Nordisk foundation  grant  NNF17OC0028184  and to D. C. by  Natural Science Foundation of Guangdong Province  (grant:  2016A030310278 ) and  Science and Technology Planning Project of Guangzhou  (grant:  201707010030 ). Author contributions: H. C. , A. H. , B. S. , J. S. , A. L. , J. H. , and J. H. performed experiments; N. E. M. performed bioinformatics analysis; D. C. H. H.
Summary and Conclusion The Mini-EUSO EM has been successfully tested at TurLab in 2018. This test was useful as we could confirm that the L2 trigger algorithm and L3 data acquisition are working as expected, while we found some items to be improved and debugged for L1. With a new system, which is in principle a copy of the Mini-EUSO detector, but only by the data acquisition and the processing part, we were able to perform further studies recently. A new threshold of 16 σ has been applied.
Acknowledgements This work was partially supported by  Basic Science Interdisciplinary Research Projects of RIKEN  and  JSPS KAKENHI  Grant ( JP17H02905 ,  JP16H02426  and  JP16H16737 ), by the  Italian Ministry of Foreign Affairs and International Cooperation , by the  Italian Space Agency  through the  ASI INFN  agreement n. 2017-8-H. 0and contract n. 2016-1-U. 0,by  NASA  award  11-APRA-0058  in the USA, by the  Deutsches Zentrum für Luft-und Raumfahrt , by the  French space agency CNES , the  Helmholtz Alliance for Astroparticle Physics  funded by the  Initiative and Networking Fund of the Helmholtz Association (Germany) , by  Slovak Academy of Sciences  MVTS JEMEUSO as well as  VEGA  grant agency project  2/0132/17 , by  National Science Centre in Poland  grant ( 2015/19/N/ST9/03708  and  2017/27/B/ST9/02162 ), by Mexican funding agencies  PAPIIT-UNAM ,  CONACyT  and the  Mexican Space Agency (AEM).
(ii) Polymerization of caprolactone To graft hydrophobic chains onto the oligomers, 200 mg of acetylated-oligocarrageenan were dissolved in 2 mL of toluene and 20 µL of the catalyst tin (II) ethylhexanoate was added. After 2 h of stirring at 40 °C under a nitrogen atmosphere, 330 mg of ɛ-caprolactone were added and polymerization was allowed to proceed for 20 h at 110 °C. The stability of partially acetylated oligocarrageenan and the absence of depolymerisation in these conditions was confirmed by Thermal Gravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC) and NMR analyses (data not shown). The resulting acetylated-OligoKC-g-PCL was dissolved in chloroform and precipitated in cold methanol. After freezing and lyophilization, the product was characterized by NMR.
Quantification was then performed by determining the mean curcumin fluorescence of 90 cells for each condition in three independent experiments using ImageJ software. 2. 12. Quantification of TNFα -induced secretion of IL-6 and MCP-1 by EA-hy926 cells The protective effect of curcumin on EA-hy926 cells was evaluated. Cells were seeded in 6-well microplates containing 2 mL of culture medium and cultured to confluency (24 h). The medium was then replaced with solutions containing empty micelles, curcumin-loaded micelles or free curcumin respectively. Two concentrations of curcumin were tested, namely 5 µM and 15 µM. After 24 h, the medium was removed, and cells were stimulated with TNFα (tumor necrosis factor-alpha) overnight, diluted in culture medium (200 µL, 10 ng/mL). The supernatants were then subjected to ELISA (e.
Acknowledgements The authors would like to thank the department of Mayotte, the  Regional Council , the  BioST federation from University of La Réunion , the  FEDER  and the  Mauritius Research Council  for their financial support. Experiments were carried out in DéTROI unit at the  CYROI biotechnologies platform (La Réunion ) and at the CBBR (Mauritius). Members of DéTROI and CBBR teams are gratefully acknowledged. TEM experiments were performed at the  TEM-SEM microscopy platform of the "Institut des Matériaux Paris Centre (IMPC)" of the Sorbonne University, Paris. The authors thank  Dr Mary Osborne-Pellegrin  for help in editing the manuscript.
Integrated analysis of genome evolution Because genome sizes vary by 2,340-fold in land plants  13  and 4,680fold in chlorophyte and streptophyte green algae  14  , we used a reducedrepresentation sequencing approach to reconstruct gene and species histories. Specifically, we generated 1,342 transcriptomes representing 1,124 species across Archaeplastida, including green plants, glaucophytes and red algae. Comparing phylogenetic inferences based on nuclear and plastid genes (Figs. 2, 3 and Supplementary Figs. 1 2 3 ), we obtained well-supported, largely congruent results across diverse datasets and analyses. Resolution of some relationships, however, was confounded by gene-tree discordance (Fig. 3 ), which is attributable to factors that include rapid diversification, reticulate evolution, gene duplication and loss, and estimation error.
Nymphaeales (2) Amborella Cupressales (  36 ) Araucariales (  23 ) Pinaceae (  15 ) Gnetales (3) Cycads and Ginkgo (5) Mosses (  42 ) Liverworts (  22 ) Hornworts (  10 ) Polypodiidae (  63 ) Marattiidae (3) Ophioglossidae (  5 ) Equisetidae (  2 ) Lycophytes (  22 ) Zygnematophyceae (  37   -3 ) with some exceptions (Supplementary Fig. 6 ). Data and analysis scripts are available at https://doi. org/10. 5281/zenodo. 3255100. for Marattiales as sister to Psilotales and Ophioglossales (Fig. 3f ). Leptosporangiate ferns (Fig. 1k ) experienced more WGD events than any other lineage of Viridiplantae outside the angiosperms, with an average of 3. 79 inferred WGDs in the history of each sampled species (Fig. 4 ). WGD was inferred in an ancestor of all extant ferns and an additional 19 putative WGDs were implicated in the ancestry of fern subclades (Ophioglossaceae and Polypodiaceae; Fig.
Data and analysis scripts are available at https://doi. org/10. 5281/zenodo. 3255100. discordance  8. Previously inferred WGDs in ancestors of Welwitschia, Pinaceae and Cupressales 18 are supported, as is a new inference of WGD in the ancestry of Podocarpaceae (Fig. 4  and Supplementary Tables 2, 5, 6). Angiosperms are by far the largest clade of green plants (more than 370,000 species 2 ) and are marked by multiple key innovations, including the carpel, double fertilization, endosperm, and for most angiosperms, vessel elements. Both nuclear and plastid phylogenomic analyses agree with previous studies  39  in providing strong support for angiosperm monophyly and in placements of Amborellales, Nymphaeales and Austrobaileyales as successive sisters to all other angiosperms (Figs. 2, 3 ). Chloranthales and magnoliids comprise a clade in the ASTRAL and supermatrix analyses, but were resolved with poor support as successive sister lineages to all other Mesangiospermae (monocots, Ceratophyllum and eudicots) in the plastome-based tree.