dataesr/scientific-paragraphs-categorization huggingface dataset:
Development of Illumina transcriptomes Two mRNA libraries were built and sequenced in one lane as described. 24 The Illumina paired-end sequencing technology generated 2Â 100 bp independent reads from the 200 bp insert libraries. RNAseq data were processed for the de novo transcriptome assemblies using the Velvet 1. 2. 07 and CAP3 08/06/13 softwares and orthologous relationships between contigs of the two transcriptome assemblies were identified by best reciprocal hit search. To evaluate the quality of the assembly, all usable reads were realigned to the contigs using BWA-MEM 0. 7. 12-r1039 and SAMtools idxstats 1. 1. To assess the depth of gene coverage through comparative genome analysis, ORFs were searched in A. evenia transcripts with TransDcoder_r20140704 and used for BLASTX alignment (E value < 10 À20 ) with Blastall 2.
2. 26 onto the protein database of A. duranensis (Araip. V14167. a1. M1. peptide. fa file downloaded from www. peanut. org). Raw Illumina sequence data have been deposited in the NCBI Sequence Read Archive (SRA) under the accession numbers SRR3276128 and SRR3285082, for the CIAT8232 and CIAT22838 lines respectively.
Sequence search and comparison Symbiotic gene sequences were obtained from M. truncatula and L. japonicus by searching in the NCBI database. These sequences were used to find orthologous unigenes in an A. evenia local database developed with a Galaxy work bench (INRA, Toulouse, France) (https:// bbric-pipelines. toulouse. inra. fr/galaxy/) and containing the CIAT8232 and CIAT22838 transcriptome data (Supplementary Tables  S1, S3 ; Files S1, S2). For estimation of divergence time, single-copy genes identified in the CIAT8232 and CIAT22838 transcriptomes were used to obtain orthologous sequences for A. evenia IRLFL6945 from its transcriptome database (http://esttik. cirad. fr) and for A. duranensis and A. ipaensis from their genome sequence database (http://peanutbase. org/) (Supplementary Table  S5 ).
SSR and INDEL genotyping Detection of microsatellites in the transcriptome data were performed using the SPUTNIK software by searching for di-to hexanucleotide SSRs with a minimum of three to six repetitions depending on the motifs. Orthologous sequences in the two transcriptome assemblies comprising different lengths of the same SSR motif, with a contig length over 500 nt and with at least 50 nt surrounding the SSR motifs were selected as in silico polymorphic SSRs (Supplementary Table  S1 ). For specific gene mapping, SSR and INDELs were searched by sequence comparison from the two transcriptomes. Primer pairs were designed using Primer3 with tree parameters: (i) a primer length of 20 bp with an annealing temperature of 55 C, (ii) three ranges of PCR product size of 90-120, 150-180 and 220-250 bp, (iii) the addition of a 5 0 -end M13 tail (5 0 -CACGACGTTGTAAAACGAC-3 0 ) on the forward primer (Supplementary Table  S2 ).
SNP genotyping To detect single nucleotide polymorphisms for a set of target genes, sequences of orthologous contigs identified in the two transcriptome datasets were aligned with the MUSCLE program (Supplementary Table  S3 ). Positions of the SNPs were determined by examining the intron/exon structure of orthologous genes in Arachis (http://peanut base. org/). Whenever necessary, additional SNPs were searched by intron sequencing. Up to three SNPs were selected for each target gene and flanking sequences 50 bp both upstream and downstream each target SNP were sent to KBioscience for primer design (Supplementary Table  S4 ). Genotyping of the F 2 mapping population was performed with the KASP genotyping chemistry (KBioscience Ltd. , Hoddesdon, UK) on Fluidigm 96. 96 Dynamic Arrays using the BioMark HD system (Fluidigm Corp, San Francisco, CA).
Comparative genomics Gene sequences underlying the molecular marker loci assigned to the linkage map were blasted against the A. duranensis and A. ipaensis genome sequences (http://peanutbase. org/) to detect significant matches at minimum threshold E values < 10 À60 (Supplementary Table  S6 ). For the purpose of graphic preparation, cM distance on the A. evenia linkage groups were scaled by factors calculated on the basis of the genome size of A. ipaensis, to provide matching chromosomal lengths in base pairs. The graphical comparative maps were drawn using the Circos program (http://circos. ca/) and the SpiderMap software (JF Rami, unpublished).
Illumina paired-end sequencing and de novo transcriptome assembly High-throughput transcriptomic sequencing allows generating a large transcript sequence dataset for gene discovery and development of molecular markers that serve for gene-based map construction. To be able to achieve a broad survey of genes associated with symbiosis, RNA was extracted and pooled from various organs: roots, leaves and nodules at 4, 7 and 14-dpi. In addition, to increase the efficiency of molecular marker development by prior in silico polymorphic analysis, a RNA library was developed for each parental genotype. Using Illumina paired-end sequencing and after stringent quality check of the raw data, $72 million reads were kept for the Mbao genotype and $66 million for the Bahia genotype. Based on these highquality reads, a total of 51,763 and 52,648 contigs were assembled respectively, with a common N50 of 1,800 bp and a consistent contig size distribution (Table  1 ).
A few additional markers were also used, notably to locate the 5S and 45S loci that were previously identified on A. evenia chromosomes by cytogenetics (Supplementary Tables  S1, S2 ). 21 3 Construction of the genetic map and mapping of symbiotic genes   mapping population. DNAs were extracted from the 220 F 2 individuals and were genotyped for the selected 318 SSR markers by capillary sequencing. Multiplexes of 12 SSR markers were chosen so as to combine both three ranges of fragment sizes and four fluorochromes (FAM, VIC, NED and PET). 46 additional markers comprising SSRs, INDELs and SNPs, which target notable putative symbiotic genes, were also used for genotyping by capillary sequencing or KASPAR technology. This genotyping generated a matrix with <0. 6% of missing data for the 364 co-dominant markers used.
Building of the genetic map The A. evenia genetic map was built using the JOINMAP software with a minimum LOD score value of 6. The markers were assembled into 10 linkage groups, corresponding to the haploid chromosome set of A. evenia (2n ¼ 20). Interestingly, no marker remained unlinked and no linkage group could be split by increasing the LOD score value up to a LOD of 15. In addition, manual checking of the marker positions using colormapping revealed no discrepancy in the genotyping data, thus corroborating the robustness of the 10 linkage groups obtained. They were thus numbered AeLG1 to AeLG10 and orientated as explained below (Fig. 5 ). The resulting genetic map spans 1,036 Kosambi cM, with an average of 400 kb/cM. The 10 linkage groups have different genetic sizes ranging from 82 to 130.
Estimate of time divergences With the aim of fostering genomic and symbiotic comparative analysis, we wanted to further our knowledge of the genetic differentiation in A. evenia and of the evolution within the Dalbergioid clade that contains Aeschynomene and Arachis. A $49 MYA divergence of Aeschynomene and Arachis was previously estimated from chloroplast gene phylogenies (Fig  2A ). 6 Using this date for calibration and assuming a simple molecular clock, we made a rough estimate for the divergence times between different A. evenia genotypes and between the two Arachis ancestral species of peanut. The coding reading frame of seven single-copy nuclear genes was obtained from the transcript databases available for A. evenia genotypes Bahia (CIAT8232), Goias (IRFL6945) and Mbao (CIAT22838) and their Arachis orthologs in the genome sequences of A.
This will allow much better comparison with Arachis to characterize genome evolution within the Dalbergioid clade. In particular, microsynteny analysis will allow investigating if chromosome rearrangements and transposable elements had an impact on certain symbiotic genes as suspected for the AeCCaMK gene and those that could not be found in the transcriptome datasets. Understanding how these symbiotic genes evolved (by changes of gene expression or by gene loss) in a NF-independent context would be an important advance in understanding the evolution of nodulation. In addition, an a priori identification of symbiotic genes in A. evenia using a mutagenesis approach should be a powerful tool. ] [45] [46]  New methods, such as SHOREmap and MutMap, now integrate simultaneous mapping and mutation identification in a single step by deep whole-genome resequencing of pooled DNA from a F 2 mutant population.
Funding This work was supported by  Agropolis Fondation  through the  « Investissements d'avenir » programme  ( ANR-10-LABX-0001-01 ) under the reference ID "AeschyMap"  AA1202-009 , and by a grant from the  French National Research Agency  ( ANR-AeschyNod-14-CE19-0005-01 ). Funding to pay the Open Access publication charges for this article was provided by the  French National Research Agency.
Sequencing of gene fragments for phylogenetic analysis PCR products used for DNA sequencing were purified with QIAquick PCR purification kit (QIAGEN Sciences, Maryland) and sequencing was done using a fluorescence-based automated sequencing system (Retrogen Sequencing, San Diego, CA). For the phylogenetic analysis, forward and reverse direction sequences of the 379 bp gltA gene fragment, 935 bp ftsZ gene fragment, 893 bp rpoB gene fragment, and the various sized fragments (721 bp to 723 bp) of the 16S-23S ITS region were joined to form a concatenated sequence. Sequence data were imported into MEGA version 5. 0 software (http://www. megasoftware. net) and aligned by the Clustal W program. A neighbor-joining tree was constructed  [27]  and bootstrap replicates were performed to estimate node reliability of the phylogenetic tree, with values obtained from 1000 randomly selected samples of the aligned sequence data.
Serology results of samples from bobcats and mountain lions All bacteremic bobcats and mountain lions were seropositive (titer 1:64), using an IFA with B. henselae genotype II antigen (strain U4, U. C. Davis). In addition, four of the 10 non-bacteremic mountain lions and six of the 12 non-bacteremic bobcats were seropositive (Tables  1  and 2 ). For mountain lion L-42-94, a decrease of the antibody titer was concomitant with a decline in the level of bacteremia (Table  1 ). IFA titers were identical or very close (within one dilution factor) when using either B. henselae or L-42-94 strain as the antigen (data not shown).
Pulsed field Gel Electrophoresis (PFGE) The sequence of 379 bp in the 3'-end of the gltA gene was determined for the strains isolated from mountain lions and for the strains isolated from bobcats (Fig  3     L-17-96, DS08, L-10-97, L-11-97 and DS507 matched 100% (GenBank accession numbers: KF246538, KF246537, KF246533, KF246536, KF246535 and KF246534, respectively, Table  6 ). Alignment between mountain lion and bobcat isolate sequences showed two bp substitutions, which translated to a synonymous amino acid sequence. The ftsZ sequences for mountain lion isolate FM98061 (GenBank #KF466250) and bobcat isolate SC443 (GenBank #KF466251) matched 100%, and the ftsZ sequence of both isolates had one bp substitution compared to the corresponding ftsZ fragment in B. henselae. However, the substitution still translated to the same amino acid as B.
henselae ftsZ. Sequences for the 16S-23S ITS region from mountain lion isolates L-42-94, l-27-96 and l-39-97 matched 100% (GenBank #KF437493, KF437495, and KF437494, respectively), and sequences from bobcat isolates L-08-96, L-17-96, L-10-97, L-11-97 and DS507 matched 100% (GenBank #KF437501, KF437500, KF437499, KF437498, and KF437497, respectively, Table  6 ). However, bobcat isolate DS08 had one mutation compared to the other bobcat isolates. Mountain lion isolate FM98061 and bobcat isolate SC443 16S-23S ITS region sequences matched 100% (GenBank #KF466254 and KF466255, respectively). When compared to the corresponding 16S-23S ITS fragment sequence in B. henselae, the 16S-23S ITS sequences of both these isolates had three bp substitutions. Insertions and deletions (five total) in the 16S-23S ITS region sequence resulted in a fragment of: 723 bp in size for bobcat isolates L-08-96, L-17-96, L-10-97, L-11-97, DS507 and DS08; 722 bp for mountain lion isolate FM98061 and bobcat isolate SC443; and 721 bp for mountain lion isolates L-42-94, L-27-96, L-39-97.
Acknowledgments The authors thank  Darren Simpson  for trapping the mountain lions and bobcats in central California and  Dr. Pamela Swift  for allowing access to the animals kept at the  Wildlife Investigations Laboratory, California Department of Fish and Wildlife ,  Rancho Cordova , CA, as well as  Walter Boyce  and  Grace Lee  for providing the blood of the mountain lions from the  San Diego Mountains. The authors thank  K. R. Jones ,  California Department of Fish and Wildlife , and  K. A. Floyd-Hawkins ,  Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis , for their technical assistance. The authors thank  Arnold G. Steigerwalt  for performing the DNA-DNA hybridization, and  Don J. Brenner  for his thoughtful comments on the manuscript.
Importantly, we measured the iron content of the culture media 6 h after apo-pyo addition (see Fig. 6A below ). The corresponding data showed that apo-pyo addition did not result in iron enrichment in the medium, thus proving that the siderophore was purified in its ironfree structure and was not contaminated by ferri-pyo (pyoverdine chelated to iron). First, we checked that, in our experimental conditions, apo-pyo was efficiently assimilated by plants and potentially transported from roots to shoots. The presence of pyoverdine in root tissue was investigated by ELISA using rabbit polyclonal anti-pyoverdine antibodies. In root extracts of Fe 25 apo-pyo-and Fe 0 apo-pyo-treated plants, we detected 0. 64 and 0. 82 ng pyoverdine mg 21 protein, respectively (Fig. 2A ). In shoots, we were not able to discriminate a positive signal from the background (data not shown).
To strengthen the data, the presence of apo-pyo in plant tissues was further analyzed by isotope ratio mass spectrometry. Following the treatment of plants by [ 15 N]apo-pyo, approximately 4. 5 mmol 15 N h 21 g 21 dry weight was measured in the roots of Fe 25 apo-pyo-and Fe 0 apo-pyo-treated plants, thus confirming the results from the ELISA. In addition, a lower signal (0. 37 and 0. 54 mmol 15 N h 21 g 21 dry weight for Fe 25 apo-pyo and Fe 0 apo-pyo treatments, respectively) also was measured in the shoots (Fig. 2B ). These data also showed that the concentration of apo-pyo assimilated by plants did not differ according to the concentration of iron in the culture medium. Next, the impact of apo-pyo treatment on the plant macroscopic phenotype was evaluated (Fig. 3 ). Fe 25and Fe 25 apo-pyo-treated plants appeared bigger and greener compared with plants facing iron deficiency.
3 ). Genes were putatively assigned to functional categories based on the Gene Ontology annotations from The Arabidopsis Information Resource database (http://www. arabidopsis. org/tools/bulk/ go/index. jsp; Fig. 5 ). Concerning the genes whose expression was induced by apo-pyo, an overrepresentation of genes related to developmental processes (11. 7% compared with 6. 2% in the whole genome) and, in particular, to cell differentiation was observed (Fig. 5A ). These genes include a-EXPANSIN7 (AT1G12560) and a-EXPANSIN18 (AT1G62980), GLY-COSYL HYDROLASE9C1 (AT1G48930), CELLULOSE SYNTHASE-LIKE5 (AT4G15290), b-GALACTOSIDASE6 (AT5G63800), and CER4 (AT4G33790), which encodes an alcohol-forming fatty acyl-CoA reductase involved in cuticular wax biosynthesis. Moreover, this analysis revealed a predominance of genes involved in transport when comparing with the whole-genome categorization (15.
Diagrams were generated using http://bioinfogp. cnb. csic. es/tools/venny/index. html. apo-pyo impacts the iron homeostasis of plants grown in the iron-deficient condition. The functional categorization of the root genes whose expression was strongly modulated by apo-pyo treatment (log 2 ratio of +3 or greater or 23 or less; P # 0. 05) in plants grown in the iron-deficient condition was further assessed using AmiGO and the MapMan program. This analysis clearly confirmed an incidence of apo-pyo in the expression of genes involved in development and biotic stresses (Supplemental Fig. S2A ). The genes gathered in the biotic stress category encode proteins that play roles in hormone signaling, in cell wall dynamics, and in signaling processes (Supplemental Fig. S2B ). To complete this investigation, we performed a more systemic analysis by including root genes regulated by apo-pyo to a lower extent (log 2 ratio of +1.
Perturbations of Iron Homeostasis Induced by Apo-Pyo The impact of apo-pyo on the expression levels of genes related to iron homeostasis led us to investigate its impact on the plant iron content in our different conditions (for the experimental design, see Fig. 1 ) 6 h and 3 d after the addition of apo-pyo. First, we measured the iron content in the nutritive medium. In the Fe 25 medium, a decrease of the iron content occurred between 6 h and 3 d after the treatment, indicating that plants imported part of the iron present in the medium. When apo-pyo was added in the same medium, the concentration of iron did not decrease with time (Fig. 6A ). The measurement of iron contents in roots further supported these data (Fig. 6B ). Indeed, compared with the Fe 25 treatment, the addition of apo-pyo in the medium containing 25 mM iron (Fe 25 apo-pyo condition) strongly reduced the root iron concentration at 6 h and 3 d (Fig.
Similar to wild-type plants, apo-pyo treatment did not affect the shoot and root masses of all the mutants and overexpressors tested when grown in iron-sufficient conditions. Collectively, these data highlight an involvement of IRT1, FRO2, and, to a lower extent, NAS4 in the growth effect of apo-pyo in plants exposed to iron deficiency. Incidence of Apo-Pyo in SA, ABA, Indole-3-Acetic Acid, and Ethylene Synthesis/Accumulation The finding that apo-pyo modulated the expression of genes related to SA and ABA signaling and increased the growth of plants in medium deprived of iron prompted us to analyze the concentration of several hormones in our distinct conditions, namely SA, ABA, indole-3-acetic acid (IAA; the major endogenous auxin), and ethylene. Hormone measurements were performed 6 h and 3 d after apo-pyo treatment (for the experimental design, see Fig.
Microarray Experiment Microarray analysis was carried out at the Institute of Plant Sciences Paris-Saclay using the CATMA version 6. 2 array based on Roche-NimbleGen technology. A single high-density CATMA version 6. 2 microarray slide contains 12 chambers, each containing 219,684 primers representing all the Arabidopsis genes: 30,834 probes corresponding to CDS The Arabidopsis Information Resource version 8 annotation (including 476 probes of mitochondrial and chloroplast genes) + 1,289 probes corresponding to EUGENE software predictions. Moreover, it included 5,352 probes corresponding to repeat elements, 658 probes for microRNA/MIR, 342 probes for other RNAs (ribosomal RNA, tRNA, snRNA, and soRNA), and finally, 36 controls. Each long primer is in triplicate in each chamber for robust analysis and in both strands.
For each comparison, one technical replicate with fluorochrome reversal was performed for each biological replicate (i. e. four hybridizations per comparison). The labeling of complementary RNAs with Cy3-dUTP or Cy5-dUTP (Perkin-Elmer-NEN Life Science Products) was performed as described by  Lurin et al. (2004). The hybridization and washing were performed according to NimbleGen Arrays User's Guide version 5. 1 instructions. Two-micrometer scanning was performed with an InnoScan900 scanner (InnopsysR), and raw data were extracted using MapixR software (InnopsysR).
Microarray Data Deposition Microarray data from this article were deposited at the Gene Expression Omnibus (http://www. ncbi. nlm. nih. gov/geo/; accession no. GSE71163) and at CATdb (http://urgv. evry. inra. fr/CATdb/; project no. INRA13-03_pyo) according to Minimum Information About a Microarray Experiment standards.
Statistics One-way ANOVA was performed using XLSTAT software (Addinsoft) followed by a multiple comparison procedure with the Fisher's LSD method (at least P , 0. 05). Two-way ANOVA was performed using VassarStats online software (http://vassarstats. net/) followed by a multiple comparison procedure with Tukey's honestly significant difference method (at least P , 0. 05). Sequence data from this article can be found in the Arabidopsis Genome Initiative or GenBank/EMBL database under the following accession numbers: IRT1, AT4G19690; FRO2, AT1G015800; FER1, AT5G01600; NAS4, AT1G56430; Plant Physiol. Vol. 171, 2016.
ACKNOWLEDGMENTS We thank  Carine Fournier  for the preparation of B. cinerea spores;  Pascal Tillard  and  Alain Gojon  from the  Analytical Platform of the Biochimie et Physiologie Moléculaire des Plantes ;  Cyril Zipfel  for the gift of HBI1-ox and  HBI1 (L214E )-ox lines; and  Olivier Lamotte ,  Valérie Nicolas-Francès ,  Claire Rosnoblet , and  Hoai-Nam Truong  for careful reading of the article.
, 2013). We used the data to define aberrantly acetylated enhancer and promoters in ASD brain and thereby characterize commonly altered pathways, upstream regulatory factors, and developmental dynamics of affected loci. In addition, we used chromatin immunoprecipitation sequencing (ChIP-seq) reads to call SNPs within enhancers and promoters. We then used the genotype-independent signal correlation and imbalance (G-SCI) test  (del Rosario et al. , 2015)  to detect haQTLs in regulatory regions and assessed their relationship to known psychiatric disease-associated variants. This dataset from post-mortem human brains will provide a rich resource for future molecular analyses of ASD and serve as proof of principle for the HAWAS approach, which can be applied to a wide variety of human diseases.
In contrast, only 247 DA peaks were detected in CB. The limited molecular pathology of ASD cerebellum is consistent with results from transcriptomic studies  (Voineagu et al. , 2011; Parikshak et al. , 2016). To evaluate the likelihood of false-positive DA peaks, we repeated the entire procedure (initial DA peaks, discarding atypical samples, final DA peaks) after randomly permuting ASD and control labels. At the same false discovery rate (FDR) threshold (Q % 0. 05), permuted datasets generated fewer than 100 DA peaks, on average. Moreover, after 1,000 tries, none of the permutated datasets generated as many DA peaks as the true dataset (Figure  1B ). Thus, the chromatin changes we detected in ASD samples were far in excess of what would be expected by chance. To further characterize the overall consistency of the DA peak sets, we examined their overlaps.
Multiple gut-related gene groups such as embryonic digestive tract morphogenesis and digestive/alimentary phenotype showed significantly reduced histone acetylation in ASD cortex. These gene sets included multifunctional morphogenetic genes such as FGFR2, chemokine ligand and receptor genes (including CX3CR1), and the HDAC SALL3 (Table  S3 ). Among the individually enriched genes near downregulated peaks in TC, the behavior-related gene GRB10  (Garfield et al. , 2011)  was the most statistically significant (p < 1e-9). We hypothesized that DA peaks might act as cis-regulatory elements for some of the genes thought to be causal for ASD. We therefore analyzed a curated list of 296 ASD genes for proximity to DA peaks (SFARI database, gene score %4)  (Abrahams et al. , 2013)  (Table  S5 ). In order to control for biases in gene length and intergenic size, this analysis was performed using the same statistical procedure as in the GREAT tool  (McLean et al.