dataesr/scientific-paragraphs-categorization huggingface dataset:
Characteristic of the genes strongly differentiated between Coenonympha macromma and C. gardetta that show the sharpest clines across the hybrid zone and that match other lepidopteran genes in ncbi database Locus ID Organism Gene (predicted) Putative function Locus accession % identity E-value CLocus_1159 Papilio machaon G protein-coupled Mth Olfactory receptor XM_014503013. 1 83. 824 8. 70E-10 2-like CLocus_1160 Galleria mellona Baculoviral IAP repeat- Immunity XM_026902591. 1 83. 333 2. 66E-16 containing protein 6 like (BIRC6) CLocus_5199 Bicyclus anynana Protein AF-10 Eyespot development XM_024081740. 1 84. 783 6. 26E-18 CLocus_4520 Bicyclus anynana Secreted protein Immunity XM_024088674. 1 94. 118 3. 69E-27 acidic rich in cysteine (SPARC) CLocus_3650 Bicyclus anynana Rapamycin-insensitive Cell growth regulation XM_024085403.
Phylogeny and Structural Investigation Aspergillus chevalieri TM2-S6 was isolated from the sponge Axinella collected on the upper mesophotic zone off Tel Aviv-Jaffa, Israeli Mediterranean coast (32°1′42. 431″ N 34°46′42. 323″ E). The sponge was collected at 38 m depth by a ROV (Remote Operating Vehicle) equipped with a collection arm (Figure  1 ). According to the phylogenetic analyses of ITS rDNA sequence, the isolate TM2-S6 described in this study belongs to the Aspergillus Restricti section of the Aspergillus genus. Based upon blast search against the "rRNA_typestrains/ITS_RefSeq_Fungi" database and subsequent phylogeny analyses, TM2-S6 isolate was assigned as Aspergillus chevalieri with the GenBank number MT256106 (Figure  2 ). According to the phylogenetic analyses of ITS rDNA sequence, the isolate TM2-S6 described in this study belongs to the Aspergillus Restricti section of the Aspergillus genus.
Based upon blast search against the "rRNA_typestrains/ITS_RefSeq_Fungi" database and subsequent phylogeny analyses, TM2-S6 isolate was assigned as Aspergillus chevalieri with the GenBank number MT256106 (Figure  2 ). S1. Scale represents substitutions per site. The strain was cultivated in PDB medium (Potato Dextrose Broth) composed of ingredients of plant origin. This medium is classified non-hazardous and is compatible with cosmetic formulations. After 9 days of culture, the medium was filtered, sterilized and lyophilized. The obtained powder was directly diluted to the desired concentration in the bioassay buffers, leading to the ACCB solution. Sample of ACCB solution was extracted with ethyl acetate and analyzed by HPLC coupled to a PhotoDiode Array detector (PDA), an evaporative light-scattering detector (ELSD) and a mass detector (MS).
The obtained powder was directly diluted to the desired concentration in the bioassay buffers, leading to the ACCB solution. Sample of ACCB solution was extracted with ethyl acetate and analyzed by HPLC coupled to a PhotoDiode Array detector (PDA), an evaporative light-scattering detector (ELSD) and a mass detector (MS). Figure  3  shows the presence of two peaks at 23,8 and 24,6 min. The peaks were dereplicated according to their 1 H-NMR and HRMS spectra, and submitted to Antibase database of microbial compounds (Wiley-VCH) and natural compounds Reaxys database (Elsevier). Compound 1 was identified as tetrahydroauroglaucin and compound 2 as flavoglaucin (Supplementary Table  S2 , Figures  S1  and S2 ). Both compounds have previously been isolated from Aspergillus strains; some are used in the preparation of the traditional Katsuobushi in Japanese cuisine  [15, 16].
FUNDING MR was supported by the  Spanish MINECO Ministry , project  AGL2011-26490  and the  Generalitat Valenciana  grant  DOCV [2010/8910 ]. JO and JS were supported by the " Innov'agrumes " project funded by  FEDER  and the  "Collectivité de Corse. " RM was supported by the " CAVALBIO " project funded by  FEDER  and the  Guadeloupe Region  and by the " TROPICSAFE " project funded by  European Union 's  Horizon 2020 research and innovation programme  under grant agreement No. 727459.
The most abundant one was used for quantification while the other one was used for confirmation. The ratio of quantification transition area to the confirmation transition area was compared to that obtained with an authentic standard (margin applied: 20%). Data were collected using Mass Hunter software from Agilent Technologies, which was also used for analyte quantification. To correct potential analyte losses, matrix effect or volume variation, ISs were used to quantify one or several analytes: Atrazine ring 13 C3 was used for atrazine, simazine and S-Metolachlor, HA 13 C3 was used for HA, and DEA 13 C3 was used for DEA and DIA. Quantification was carried out by calculating the response factor of each analyte relative to its corresponding IS and the concentrations were determined using a least-square linear regression analysis of the peak area ratio versus the concentration ratio.
Acknowledgements We thank  Imre Somssich  for providing the pGEX-TM-WRKY40 plasmid and the ChIP-seq raw datasets ahead of publication;  Robert Fischer  for providing the ros1-3 and ros1-4 alleles;  Florence Jay  for its contribution to the selection of the ros1-3 dcl2-1 dcl3-1 mutants, and all the members of the  Navarro lab  for their inputs, discussions and critical reading of the manuscript. This work was supported by a  European Research Council (ERC)   Starting Grant  " Silencing and Immunity " (281749), and an  Agence Nationale pour la Recherche (ANR)  " NEPHRON " ( ANR-18-CE20-0020 ), both granted to LN. TH received additional support by a  Marie Curie Individual Fellowship  ( EU  project  661715 -BASILA ) and a post-doc funding from the " Fondation Pierre-Gilles de Genes". JW and MSR received support from the programme "Investissements d'avenir"  implemented by  ANR  ( ANR-10-LABX-54   MEMO LIFE ,  ANR-10-IDEX-0001-02PSL ).
1. The antiplasmodial activity of all crude extracts was evaluated, the chemical profile was analysed by 1 H NMR, and a multivariate data analysis was performed to identify active compounds. The antiplasmodial potential of each leaf crude extract was determined against Plasmodium falciparum (3D7 strain) and the results are shown in Table  1. Values are the mean ± standard deviation calculated from three independent assays in duplicate for each extract; Artemisinin was used as positive control (n=3). a : After 3 months of culture in the Erlenmeyer containing the MS30 solid medium, all microshoots were subcultured in flasks containing 500 mL of MS30 solid medium until the target age was reached; the extract was realised with leaves collected from one biological replicate. b : The extract was performed with leaves collected from 4-5 biological replicates pooled together.
1 H NMR profiles and multivariate data analysis The chemical profile of all crude extracts was analysed by 1 H NMR and a multivariate data analysis was performed in order to identify the bioactive metabolites. An unsupervised Principal Component Analysis (PCA) was applied on 1 H NMR spectral data of all extracts to visualize variations between the samples (Fig. S1 , supporting information). A three-component model explained 82. 7% of the variance, with the first two components explaining 70%. From a general point of view, we noticed a trend of samples as grouping in two clusters along the first component: healthy samples (axenic and acclimatized ones) and attacked samples. In order to confirm these two groups discrimination, the orthogonal projection to latent structures discriminant analysis (OPLS-DA) was applied on the 1 H NMR spectral data of healthy and attacked samples.
92 (d, J = 6. 6 Hz) and δH 3. 69 (m) were also identified. In order to confirm those hypotheses, the 1D and 2D NMR spectra of one attacked plant crude extract were obtained (supporting information). The NMR data showed signals characteristic of the labdan bicyclic ring (Table  S1 , supporting information). Characteristic signals of the lateral chain provided evidence of compounds 1-4 in the crude extract of attacked plants. Indeed, the analysis of the 13 C and 1 H NMR spectra revealed resonances consistent with those of an acetate moiety (δC 171. 4 for C-1', δC 20. 3 for C-2' and δH 2. 0 for H-2'). In addition, the signals δC 137. 4 and δC 30. 6 associated with C-13 confirmed the presence of compounds 1 and 2, respectively. Furthermore, the HSQC cross-peaks between C-15 (δC 58. 3) and H-15 (δH 3.
Multivariate data analysis Chemometric analysis was performed with SIMCA version 12. 0 (Umetrics, Umea, Sweden) in the form of an unsupervised principal component analysis (PCA) and a supervised orthogonal partial least squares discriminant analysis (OPLS-DA). The scaling was based on Pareto method. With PCA, class differences were determined from a multivariate dataset. Rx 2 and Q 2 values described the quality of the model. Rx 2 indicated goodness of fit and is defined as the proportion of the variance in the data observed in the model. Q 2 is defined as the proportion of variance in the data that was predictable by the model.
Bioinformatic Analysis Repeated sequences were identified with Tandem Repeats Finder  (Benson, 1999)  using default parameters. The exact start, end, and length of repeat units were assessed from examination of the different loci harboring the satellite arrays. The monomeric consensus sequences were used as queries in Blastn searches against the entire P. parasitica INRA 310 genome, then against the various oomycete genomes available at Ensembl and GenBank. GC content was calculated using the GC content calculator online 1 , with a window size ranging from 10 to 50 nucleotides. Pairwise comparisons were performed between the consensus and the variant sequences using Blastn at the NCBI using default parameters. Searches for known repetitive sequences and transposable elements were done at Repbase using the Censor tool  (Bao et al.
A phylogenetic network of the PpSat families was conducted using the SplitsTree software with the Neighbor-Net and uncorrected p-distance parameters  (Huson and Bryant, 2006). PpSat1 and PpSat2 expression was evaluated through evaluation of the total amount of reads matching satellite sequences in Blastn searches against RNA-Seq data available at GenBank (accessions SRX1124837-SRX1124840, 1 https://en. vectorbuilder. com/tool/gc-content-calculator. html 2 http://rna. tbi. univie. ac. at SRX1124842-SRX1124845, SRX1124847-SRX1124868, SRX27 27839-SRX2727852, and SRX4902085-SRX4902107).
Yet, pairwise comparisons of these sequences allowed retrieving only four distinct families obeying to our criteria, which were provisionally designated as PpSat1 to PpSat4, according to their decreasing abundance (Table  1 ). Each sequence family was present in moderate to low copy number, the putative satellite family initially identified being the most abundant. Comparison of the consensus sequences of each family against Repbase revealed that PpSat3 derived from retrotransposons of the Gypsy lineage, whereas PpSat4 displayed the signature of a DNA transposon of the MuDR type (Table  1 ). PpSat1 and PpSat2 did not match to any repeat consensus hosted at Repbase. Further searches in GenBank assembly did not reveal significant matches so that these two families were considered as novel sequences.
The consensus sequences of PpSat1 and PpSat2 generated by TRF were used to identify homologs and possibly dispersed copies in the genome. PpSat1 was retrieved in 12 additional scaffolds, which harbored 1-34 repeats of 290-338 bp, as well as truncated repeats located at the boundaries of some arrays (Table  2 ). We then identified five scaffolds of 29. 5-2186 kb that possessed a single unit varying from 326 to 337 bp, three scaffolds (445-1715 kb) yielding 6-10 repeats, and two scaffolds of ∼26  and ∼15 kb that possessed 22 and 34 repeats (Table  2 ). Last, two scaffolds possessed 2 and 11 repeats that were located at one end of the sequence, so it was not possible to estimate the extent of the array. Discarding truncated copies led to the generation of a 504-repeat dataset consisting of single-copy (SC, 5 repeats), low-copy (LC, 24 repeats), and high-copy (HC, 463 repeats) arrays, while 12 entire monomers constituted an ambiguous group (Table  2 ).
It also confirmed that sequences retrieved in Blastn searches were actually homologs of PpSat1. In contrast, PpSat2 homologs were found only within P. nicotianae contigs, where they constituted arrays of 19-59 repeats. Single hits were observed in various P. parasitica genomes resulting from short read sequencing projects, indicating that they probably were collapsed during assembly and simply missed in the current genome assemblies. We then investigated the transcriptional profiles of PpSat1 and PpSat2 and the 1080-bp-block in P. parasitica. To this aim, we performed Blastn searches against the various RNA-Seq libraries available at GenBank. RNA-Seq reads were generated from various pre-infection stages of P. parasitica, as well as two different infected plants. We also mined two libraries enriched in small RNAs.
Distinct Trajectories Govern the Dynamics of PpSat1 and PpSat2 PpSat1 and PpSat2 diverge by several criteria, among which is their diversity. Hence, PpSat1 repeats broadly fit into two categories: a prevalent sequence, which represents 66% of the dataset, and a myriad of unique sequences differing from the primary monomer by slight differences, which overwhelmingly consist of deletions. Whether the major monomer is the founder sequence is highly probable, as it was found in all HC arrays, while all LC arrays and solo repeats constituted variants. This potential founder repeat is distributed neither equally nor randomly across HC arrays. Hence, some arrays are composed of this single sequence, while other arrays mainly contain variants. Using the PacBio technique provides reads spanning tens of contiguous monomers, so that the observed situation does not result from artifacts occurring during the assembly process, but rather corresponds to the actual organization of PpSat1.
The accumulation of differences may suggest that, if functional, PpSat1 and PpSat2 may participate to different processes. Yet, mining RNA-Seq data revealed that they display highly similar transcriptional patterns, indicative of an apparent co-expression, if not co-regulation. Hence, the two families, as well as the PpSat1-associated 1,080-bp block, present a very faint expression level in pre-infection structures, as deduced from a handful of reads in RNA-Seq experiments. Moreover, these sequences appear to be repressed during plant infection. Yet, these three sequences are clearly identified in RNA-Seq data from libraries enriched in small RNAs, although at different levels. PpSat1 is by far the most expressed sequence, while PpSat2 is largely less represented in the libraries. The 1,080-bp block displays an intermediate situation.
RNA from P. pinaster-Laccaria bicolor ectomycorrhiza, harvested three and 28 days post-infection, were gently provided by Pr F. Canavos (University of Malaga, Spain). Synthesis of these ectomycorrhizas and RNA extraction are described in Flores-Monterroso et al. (2013). PCR reactions and data analysis were performed as described in  Courty et al. (2009)  with 3 biological replicates. Primers used for control (HcTub H. cylindrosporum α-tubulin, GenBank accession number CK993737  (Tatry et al. 2009 ) and LbEf-3 L. bicolor elongation factor (F: CTCATCCTTCCTGCTCTTCTTCACG and R: CGGTGGCTTTTGTAAGTGAATCACG)) or for analysis of HcPTR2 (HcPTR2A-F (TCGTTTCCCTCTCCACTGAC) and HcPTR2A-R (GCTCGTCCTCTTTGGCATC); HcPTR2B-F (GCGTTACTCAGCACGACCT) and HcPTR2B-R (ATCAGCGGCAATCACGAC)) and of LbPTR2 (LbPTR2A-F (GGCTTGCGGAGTGTTCTG) and LbPTR2A-R (TCTTCTTGAGGGCGGTGA); LbPTR2B-F (TCCTTGTCGCTGGTCTCG) and LbPTR2B-R (CGTTTTGGTGCCTTGGTG)) had an efficiency ranging between 90 and 110%.
Phylogenetic analysis of AcrIII-1 The gene encoding AcrIII-1 is found in representatives of at least five distinct viral families, making it one of the most widely conserved of all archaeal virus proteins  29  (Extended Data Fig. 1 ; Dataset S1). The distribution of AcrIII-1 in archaea is sporadic but covers most of the main lineages (Dataset S1) and is typically adjacent to ORFs from mobile genetic elements rather than CRISPR loci. A good example is the STIV virus integrated into S. acidocaldarius genomes 30. AcrIII-1 is also present in several bacteriophages of the order Caudovirales, and there are many instances of acrIII-1 genes in sequenced bacterial genomes, with homologues found in the Firmicutes, Cyanobacteria, Proteobacteria, Actinobacteria and other phyla (Dataset S1). Maximum likelihood phylogenetic analysis of the AcrIII-1 proteins suggests multiple horizontal gene transfers between unrelated viruses as well as between bacteria and archaea (Extended Data Fig.
Viral quantification The genome sequence of SSeV is available in Genbank (accession code MN53972). To calculate the titer of SSeV, 100 µL diluted virus (10 -5 , 10 -6 , and 10 -7 ) was co-incubated with 500 µL S. islandicus Y08. 82. 36 host 20 (10-fold concentrated) without shaking at 76-78°C for 30 min. Afterwards, the virus-infected cells were transferred into a glass test tube containing 5 mL of pre-warmed Sucrose-Yeast extract (SY) and 0. 8% gelrite mixture, and plated onto SY plates. The plates were put into a plastic bag, and incubated for two days at 76-78°C. Plaques were counted in plates with proper virus dilutions, and the titer of SSeV was determined as 4. 96×10 8 plaque forming units (PFU) per ml.
2% (w/v) D-lactose and 0. 2% (w/v) L-arabinose to determine the cell density of viable transformants. Plates were incubated at 37°C for 16 -18 h; further incubation was carried out at room temperature. Colonies were counted manually and corrected for dilution and volume to obtain colony-forming units (cfu) ml -1. Raw data for plasmid counts are available in Dataset S3.
Liquid chromatography high-resolution mass spectrometry AcrIII-1 SIRV1 gp29 (40 μM dimer) was incubated with 400 μM cA 4 in Csx1 buffer for 2 min at 70°C and deproteinised by phenol-chloroform extraction followed by chloroform extraction. Liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis was performed on a Thermo Scientific™ Velos Pro instrument equipped with HESI source and Dionex UltiMate 3000 chromatography system. Compounds were separated on a Kinetex® EVO C18 column (2. 6 µm, 2. 1 × 50 mm, Phenomenex) using the following gradient of acetonitrile (B) against 20 mM ammonium bicarbonate (A): 0 -2 min 2% B, 2 -10 min 2 -8% B, 10 -11 min 8 -95% B, 11 -14 min 95% B, 14 -15 min 95 -2% B, 15 -20 min 2% B at a flow rate of 300 µl min -1 and column temperature of 40°C. UV data were recorded at 254 nm.
Phylogenetic analysis AcrIII-1 homologs were collected by using gp29 (NP_666617) of SIRV1 as a query and running two iterations (E=1e-05) of PSI-BLAST  39  against the non-redundant protein database at NCBI. The sequences were aligned using PROMALS3D  40. Redundant sequences (95% identity threshold) and sequences with mutated H47 active site residue were removed from the alignment. Poorly aligned (low information content) positions were removed using the gt 0. 2 function of Trimal  41. The final alignment contained 124 positions. The maximum likelihood phylogenetic tree was constructed using the PhyML program  42  with the automatic selection of the best-fit substitution model for a given alignment. The best model identified by PhyML was LG +G+I. The branch support was assessed using aBayes implemented in PhyML.
Model quality was monitored throughout using Molprobity 52 (score 1. 13; centile 99). Ramachandran statistics were 98. 5% favoured, 0% disallowed. Data and refinement statistics are shown in Extended Data Table  1. Raw data is available for the plasmid immunity analysis presented in figure  1 / ED figure  3  and the kinetic analysis presented in figure  2   Genomic neighbourhoods were analysed using the Enzyme Function Initiative-Genome Neighbourhood Tool (EFI-GNT) against the Pfam profile database  53. Gene annotations are colour coded and the key is provided on the right of the figure. for a Csx1 protein, the system can be converted from cA 6 to cA 4 -mediated immunity. (c) Plasmid transformation assay (1 day's growth) using a plasmid with a match to a spacer in the CRISPR array. If the plasmid was successfully targeted by the CRISPR system, fewer transformants were expected.
Acknowledgements This work was supported by grants from the  Biotechnology and Biological Sciences Research Council  (REF:  BB/ S000313/1  to MFW and REF:  BB/R008035/1  to TMG) and by a  NASA Exobiology and Evolutionary Biology  grant ( NNX14AK23G  to RJW). We thank  Jesse Black  and  Maria Alejandra-Bautista  for isolating and characterizing the SSeV virus, and  Rebecca Wipfler  and  Wenlong Zhu  for technical assistance.
Genetic data indicated the presence of two genetic clusters in the NEAO with a break between our collection sites in the Bay of Biscay (A, B) and sites near the Strait of Gibraltar (C, D). Similarly, we detected a shift in both cuttlebone δ 18 O CORE and δ 18 O EDGE between these two geographical areas (A, B versus C, D) (figures 4b and 5b). Genetic data also showed that sites on both sides of the Strait of Gibraltar (NEAO = C, D; W-MED = E) were part of the same subpopulation cluster, indicating that gene flow occurs through this corridor  [28]. Application of these geochemical markers was also used to investigate exchange of S. officinalis between the NEAO and Mediterranean Sea over a restricted geographical scope. Previous mark-recapture and electronic tagging studies suggest that based on observed rates of movement (km day -1 ) S.
Clotted blood samples were then centrifuged at 3000 g for15 min and 2 mL of serum were collected into cryo-tubes and stored in liquid nitrogen at -196 °C en route to the laboratory where they were stored at -20 °C until the time of analysis. As each individual animal was being sampled, epidemiological data pertaining to that individual was simultaneously collected. Among the data collected were the date and season of sample collection, interface type, owner of the animal and the village of origin, the sex and the parity in case of females and any history of previous abortion(s). All sampled animals were ear-tagged to avoid resampling them on subsequent visits.
Following immobilisation, blood was collected using jugular venipuncture and processed for laboratory analysis as described for cattle above. After sample collection from buffaloes and kudus, anaesthesia was reversed by injection of diprenorphine hydrochloride. The animals were released at the site of capture and monitored from the air or the ground until they recovered fully. Epidemiological data collected for each wild animal sampled included the date of capture, the age as estimated by dentition and the location using GPS. All sampled animals were classified as adults, subadults or juveniles.
Descriptive statistics Data recording and editing were performed in Microsoft Excel ® , and the descriptive statistics were performed using EpiCalc 2000 version 2. The overall number of seropositive animals was calculated from the total number of samples tested over the study period and expressed as a percentage. For cattle, seropositivity was examined in relation to interface type, sex, parity, abortion history and season, while seropositive wild animals were examined in relation to species, age and site. Interface type, sex, parity, abortion history and season categories were generated as follows: three for interface type (porous, non-porous and non-interface), two for sex (females and males), four for parity (heifers, 1-2, 3-4 and ≥ 5), two for abortion history (history of abortion and no history for abortion) and two for season (wet and dry).