dataesr/scientific-paragraphs-categorization huggingface dataset:
In the case of ID, data points are below this solid line. [48, 55] , resulting in higher mortality between fertilization and seed maturation for selfed zygotes than for outcrossed zygotes. Lifetime estimates of ID in natura were very high (mean: 0. 9), not significantly affected by patch size, and well above the threshold value of 0. 5 below which selfing is favored due to its transmission advantage  [13, 56]. This threshold, which was proposed for annuals  [6] , applies to perennials only for lifetime estimates of ID, such as those obtained here  [29]. Our results suggest that there is strong selective pressure against selfed progenies, as already reported for other perennials  [8, 57, 58 ]. An association of strong ID with high levels of self-incompatibility and a predominance of outcrossing is commonly observed in long-lived species  [59] [60] [61] , due to the accumulation of somatic mutations over the lifetime of the organism (  [29, 62]  but see also  [63].
We carried out linear regression analyses to investigate the relationship between R. ferrugineum floral display and reproductive and pollination estimates (fruit and seed sets, reproductive assurance and selfcompatibility). The analysis was based on mean values for each patch. R. ferrugineum floral display was logtransformed to reduce the impact of very large floral displays (>30 million inflorescences) with respect to that of other patches in the model. Fruit and seed set were arcsine square root-transformed before analysis, to obtain a Gaussian distribution. Statistical analyses were performed with PROC REG in SAS (version 9. 2; SAS Institute, Cary, North Carolina, USA).
Acknowledgments We thank  P. Buscail ,  M. Ferval , and  L. Verneuil  for help with data collection and  O. Charrier  and  C. Le Corre  for help with DNA extraction. This work was supported by  COMBIO  project No. AAP-IN-2009-013  (FRB funds) and is part of the  TULIP "Laboratoire d'Excellence (LABEX) " ( ANR -10-LABX-41 ).
mRNA-seq analysis For each sample, ten micrograms of RNA was sequenced to a depth of ,20M reads using Illumina Hi-Seq contracted through Macrogen (Seoul, Korea; www. macrogen. com). Frequency counts were obtained using Bowtie2  [28]  to align reads to the predicted gene models detailed below. Reads Per Kilobase per Million (RPKM) mapped reads were extracted from the BAM files using the 'DEseq' library in Bioconductor (www. bioconductor. org) in the statistical software package 'R'. Quantitative PCR (qPCR) was performed as described in  [29] , with Actin as a control, using primers MdEXPA2F (TTCCAAGACAGGGTGGCAAG) and MdEXPA2R (TGCCCTCAAATGTTTGTCCG) for apple and PcEXP2F (GGCAAGCCCTGTCAAGAAAT) and PcEXP2R (GCCCTCAAATGTTTGTCCG) for pear.
Genome assembly GS FLX+ reads were assembled with the Roche GS De Novo Assembler (version 2. 7; http://454. com/products/analysissoftware/index. asp), using both the large and heterozygous genome modes and 8 CPUs. All other assembler configuration settings were left at their default settings. The completeness of the assembly was estimated by Core Eukaryotic Genes Mapping Approach (CEGMA) analysis (version 2. 4. 010312) [30].
Gene prediction and annotation De novo assembly of 'Comice' transcripts was performed using trans-ABySS (v1. 3. 2)  [35]. Briefly, 58,026,953 Illumina HiSeq RNASeq reads were trimmed by 15 bases at their 59 ends, filtered to remove reads containing ambiguities using an in-house PERL script. The RNASeq reads were subsequently trimmed to a minimum quality score of 20 using the program fastq-mcf from the ea-utils package (http://code. google. com/p/ea-utils). Transcript contigs resulting from de novo assembly using every second kmer from 35 to 69 were then merged in to a single transcript set with the program abyss-rmdups-iterative from the trans-ABySS software distribution. Gene prediction used a hybrid prediction approach, combining ab initio gene prediction and homology searching. Specifically Augustus (Augustus 2.
7) trained using the 'Comice' transcripts was employed for gene prediction ab initio from European pear scaffolds. Augustus predictions were performed separately on unmasked and repeat masked scaffolds. RepeatMasker (version 4-0-3  [36] ) was employed to mask known repeats in the genome scaffolds using the rosid clade of repeats from RepBase  (   [37]. Alignment results were filtered using a modified version of blast92gff3. pl (http://iubio. bio. indiana. edu/gmod/ tandy/perls/blast92gff3. pl), to identity sequences with greater than 79% identity and to mediate running GeneWise (wise-2. 4. 1;  [38] ) on the retrieved region, as well as 1000 bases upstream and downstream of the aligned regions. GeneWise predictions were assessed using evigene (http://marmot. bio. indiana. edu/ EvidentialGene/) and the best models (evigene's 'okayset') retained.
uniprot. org/downloads) [40] , RefSeq (release 54)  [41] , and Arabidopsis proteins (TAIR 10) databases using BLASTX (version 2. 2. 25)  [37]. Searching against the NCBI non-redundant (NR) DNA database (ftp://ftp. ncbi. nlm. nih. gov/blast/db/) was performed using BLASTN (version 2. 2. 25)  [37] , while Gene Ontology terms were derived following motif searching based on Inter-proScan (version 4. 8)  [42]  and Interpro Release 38 (http://www. ebi. ac. uk/interpro/). Comparison of metrics for European pear gene models to that for apple, Chinese pear and strawberry was performed as follows. Published GFF3 files describing gene models for apple and strawberry were obtained from the Genome Database for Rosaceae (GDR) (http://www. rosaceae. org/) and those for Chinese pear from http://peargenome.
03 (http://solanaceae. plantbiology. msu. edu/pgsc_download. shtml), and Arabidopsis (TAIR 10; http://www. arabidopsis. org/), to identify ortholog gene clusters. These published datasets were developed using different genome annotation strategies, utilizing different tools. Although, each plant genome may hence contain biases of various types, we consider these data acceptable for application in our comparative study. Protein sequences shorter than 10 amino acids and those containing more than 20% stop codons were excluded from the analysis. The remaining sequences were reciprocally blasted against each other using BLASTP with cut-off e value 1e-10. The similarity calculation, in-paralog and co-ortholog analyses were performed using Orthomcl-2. 0. 3  [43]  together with mcl-09-149 (http://micans.
Expansin gene family analysis The expansin gene family was chosen for further analysis, to support the completeness of the gene predictions for European pear, as well as to examine the degree of similarity in the gene space between the apple and European pear genomes. Expansin protein sequences from apple and Arabidopsis were used to perform a BLASTP search against the apple predicted peptide models, in order to identify putative expansins with a BLAST score. 50. The corresponding expansin-like genes from apple were then used in a BLASTP search against the pear peptide models. Protein sequences were aligned in Geneious 6. 1. 6 (Biomatters Ltd, Auckland, NZ) using Geneious alignment with Blosum45 cost matrix. From this alignment, genes were further filtered by selecting those containing conserved expansin domains as classified by  [48]  with a conserved region of similarity corresponding to 313 residues and used to create a phylogenetic tree derived using the maximum likelihood Geneious plug-in, PhyML with the JTT substitution model and bootstrap analysis of 1000 data sets.
Expansin genes within sub-clades showed more similarity between apple and pear orthologs, than between homeologues of the same species, confirming that speciation happened after the genome duplication event (Figure  3B ). For the rapidly softening European pear 'Comice' and crisp textured 'Nijisseki' (Japanese pear) 18. 8M and 19. 7M mRNA reads were obtained, respectively. Expression levels of the expansin class of genes determined in cold-stored 'Comice' and 'Nijisseiki' pears that were undergoing rapid softening were aligned to the phylogenetic clusters. These were compared to previously published mRNA-seq data mapped to the apple gene models  [17]  from mature, ripening 'Royal Gala' apples  [51]  (Figure  3A ). It was observed that in most cases orthologous genes were expressed in both apple and pear during fruit ripening; however, the melting texture European 'Comice' pears exhibited a considerably higher level of expression than the crisp textured apples and 'Nijisseiki' Japanese pears, with some genes (such as EXP2) showing over 20-fold higher expression in 'Comice' compared with apple and 'Nijisseiki'.
The development of a whole-genome sequence is a key milestone for research in any organism and the Bartlett v1. 0 draft genome assembly will provide a springboard to explore the genetic control of key horticultural characters such as fruit quality, pest and disease resistance, and tree architecture. The genome assembly also enables the development of genetic markers for early selection of seedlings carrying alleles conferring these traits, from breeding germplasm. This genomic resource is now available to fruit researchers at the Genome Database for Rosaceae (http:// www. rosaceae. org/species/pyrus/pyrus_communis/genome_v1. 0). The number of predicted gene models  (43, 419) , the high    [49] ). The analysis of the Chinese pear genome  [18]  indicated that there may be significantly more repeated elements in the apple genome than in Chinese pear and our results in European pear validate this hypothesis.
Acknowledgments DC thanks  Mr Jean-Max  and  Mr Jean-Pierre Drouilhet  for giving him his first ''poire William's'' job 20 years ago,  Drs Tony Conner  and  Andrew Granger  ( Plant & Food Research ) for originally supporting this project concept, and  Drs Jeanne Jacobs ,  David Brummel  (Plant & Food Research),  Charles-Eric Durel (INRA)  and  Pr Francesco Salamini  ( FEM-IASMA ) for comments on the manuscript. We thank  Stephen Ficklin  and  Dorrie Main  for making the Bartlett v1. 0 data publically available at the Genome Database for Rosaceae (GDR). Resources A Genome Browser  for Bartlett v1. 0 is available through the Genome Database for Rosaceae at http://www. rosaceae. org/gb/gbrowse/pyrus_communis_v1. 0/and the pear genome page with links to assembly data is at http://www. rosaceae.
Genomic sequence analysis of the QTL region Whole genome data sequences of strains SB and GN were obtained by using an Illumina pair end strategy. Briefly, genomic DNA was extracted from a saturated culture of 100 ml under anaerobic condition (YPD) using the genomic tip-100 kit (Qiagen, Courtaboeuf, FRANCE). Paired-end Illumina sequencing libraries were prepared from sonicated genomic DNA according to manufacturer protocols (Genomic DNA Sample Preparation) and were carried out by the Genomic and Transcriptomic facility of Bordeaux, FRANCE. Sequencing was performed on Illumina Genome Analyzer IIx (Illumina, CA) with a read length of 54 pb. The genome of both strains was first mapped on the reference genome using stampy program. The detection of SNP and short INDEL was carried out according to different criterions such alignment quality, read coverage, and genotype quality using the SAMtools mpileup  [45]  and vcftools programs  [46].
The SNP and their relative effect of protein sequence were determined by snpEff. De novo assembly was then carried out using mira3  [47]  with 8 iterations. In this work we specially analyzed the contigs c343 and c23 of GN as well as c9 and c7 of SB containing the genes present in the dissected QTL. The annotated contig c343 and c23 of the strain GN containing the newly described XV-t-XVI translocation was deposited on EMBL database with the following study accession number: PRJEB4706.
Statistical and graphical analyses All the statistical and graphical analyses were carried out using the R program. The variation of each trait analyzed was estimated by an analysis of variance (ANOVA) according to the model described in the result section. For each variable, the homogeneity of the variance was assessed using a Levene test by means of R's car package version 2. 15. 1  [53] , as well as the normality of residual distribution using a Shapiro test  [53]. Duncan's multiple comparison was used to determine which means differ significantly (Duncan's multiple comparison, p,0. 05) using the agricolae package. When required, pairwise comparisons were carried out using the Wilcoxon test with at least 5 independent repetitions.
A competition assay was performed with strains carrying XV-t-XVI or nt-XVI inoculated at the same rate. The strains carrying XV-t-XVI translocation clearly outcompeted their non-translocated counterparts, as more than 95% of colonies carried the XVt-XVI chromosome form at the end of the fermentation, demonstrating the translocation advantage in only five generations (data not shown). The translocation benefit was also confirmed by their prevalence in wine yeast (both grape isolate and industrial starters). These strains may have been directly or indirectly selected by human activity for their rapid colonization of grape must containing sulfur dioxide. Interestingly, the commercial starter group is the unique one carrying the translocation XV-t-XVI. Further experiments could test the relative advantage between both translocations forms in isogenic conditions.
publication were performed at the  Genomic and Transcriptomic Facility of Bordeaux  (grants from the  Conseil Regional d'Aquitaine nu20030304002FA  and  20040305003FA  and from the  European Union ,  FEDER nu2003227  and from Investissements d'avenir, Convention attributive d'aide NuANR- 10-EQPX-16-01 ). NL received a grant from  Conseil Regional d'Aquitaine (SAGESSE). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Lettuce has been used as tested plant because it is very sensitive to chemicals at low concentration, although it sometimes overestimates the actual allelopathy  [36]. Thirty swollen seeds were evenly placed on filter paper wetted with sample in each Petri dish. The germination was recorded at 24-h intervals till 144 h. A seed was considered germinated when the radical protruded ≥2 mm  [37]. Data were transformed to percent of control for further analysis. At 7th day after sowing, germination, shoot and root length of target species seedlings were measured. Data were transformed to percent of control for analysis.
Twice yearly, the WHO GISRS subject matter experts meet to review data in the context of CVV selection. Seasonal influenza viruses in circulation in the months leading up to September are reviewed to identify viruses with distinct antigenic characteristics and associated epidemiological features that would justify a change in the current recommended CVVs for use in the following year in the Southern Hemisphere, and those in circulation in the months leading up to February are reviewed for the recommendation of viruses to be included in vaccines for the following winter in the Northern Hemisphere. At the same meetings, an expanded group including animal health experts also reviews comprehensive data about zoonotic influenza infections, outbreaks of influenza in animals, and virologic characteristics of corresponding influenza viruses to determine if one or more CVVs should be developed for pandemic preparedness.
ACKNOWLEDGMENTS The authors gratefully acknowledge our colleagues in the  WHO Collaborating Center for Surveillance, Epidemiology and Control of Influenza, Centers for Disease Control and Prevention, Atlanta, GA, USA. The Melbourne WHO Collaborating Centre  for Reference and Research on Influenza is supported by the  Australian Government Department of Health. The St. Jude WHO Collaborating Center is supported by  ALSAC. J. W. M. and R. S. D. are supported by  MRC  Programme number  U117512723.
Statistical analyses Log (10) transformations were used to normalize the data distribution for the amount of time spent in each mate choice zone and the amount of times hinds entered each of the mate choice zones. To retain zeros in the dataset, a value of one was added to each data point before transformation. Looking duration was normally distributed (Kolmogorov-Smirnov: P > 0. 05). Paired t-tests were used to compare looking duration, the amount of times hinds entered each of the mate choice zones, and the total amount of time spent in each mate choice zone. A binomial test was used to determine whether hinds entered either of the mate choice zones first more often than would be expected by chance. Significance levels were set at P = 0. 05 and two-tailed probability values are quoted. All data analyses were performed with IBM SPSS Statistics v20 (Chicago, IL, USA) for Mac OSX.
5B, a ). This response could be specific to N. tabacum, since no reaction was observed after leaf infiltration of Nicotiana benthamiana or Nicotiana glutinosa (data not shown). The kinetics of this necrotic response on N. tabacum was comparable to the HR response elicited by the ripAA (avrA) avirulence gene product under the same experimental conditions (Fig. 5B, g )  (18). Altogether, these data suggest that RipTPS is specifically recognized by the N. tabacum immune system. Agrobacterium-mediated transient expression assays were also performed with strains expressing RipTPS carrying single point mutations in the essential catalytic sites described above. Agrobacterium tumefaciens strain GV3101::pMP90RK containing the pAM-PAT plasmids in which the ripTPS Y154V , ripTPS W163S , and ripTPS D208G alleles were cloned induced an HR-like response similar to that induced by the strain carrying the wild-type ripTPS gene (Fig.
SUPPLEMENTAL MATERIAL Supplemental material for this article may be found at http://mbio. asm. org /lookup/suppl/doi:10. 1128/mBio. 02065-14/-/DCSupplemental. Figure  S1 , EPS file, 0. 8 MB. Figure  S2 , EPS file, 0. 2 MB. Figure  S3 , EPS file, 0. 04 MB. Table  S1 , XLSX file, 0. 02 MB. (LIPM), and Céline Remblière (LIPM) for the production of the plant material. This work was supported by the French Laboratory of Excellence project TULIP (ANR-10-LABX-41 and ANR-11-IDEX-0002-02) and by a grant from the Ministère de l'Enseignement Supérieur et de la Recherche to M. P. This work was supported in part by a grant from ANR (ANR-07-Blan-0205-01) and by a grant from Région Midi-Pyrénées (grant no. 07005583) to J. M. F.
Specimen, DNA extraction and sequencing One specimen of B. colossus was collected in French Guiana (RN2 Roura-Saint Georges) on April 20th 2010. Total genomic DNA was extracted from leg muscle tissue using the DNeasy Blood and Tissue kit (Qiagen, Valencia, CA, USA), following a protocol adapted from the manufacturer's instructions (Supplementary Data 1). The quality and quantity of extracted genomic DNA was evaluated using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and a PicoGreen double-stranded DNA quantitation assay kit (Life Technologies, Carlsbad, CA, USA). The genomic DNA was sent for library construction and sequencing to the GeT-PlaGe core facilities of Genotoul (Toulouse, France). 288 ng of DNA was used for library construction using the Illumina TruSeq Nano DNA Sample Prep Kit following the instructions of the supplier (Illumina Inc.
Sequence assembly Mitochondrial genome and nuclear ribosomal clusters were assembled using a previously described strategy  (Besnard et al. , 2013; Besnard et al. , 2014; Malé et al. , 2014). It is in essence similar to that proposed by  Hahn et al. (2013). Reads aligning with the mitochondrial protein sequences of the closely related species T. dimidiata (NC 002609,  Dotson and Beard, 2001)  were identified using the PLAST program  (Nguyen and Lavenier, 2009). For the nuclear ribosomal cluster, we started from reads aligning with the 28S and 18S rRNA genes of Eurydema maracandica  (Yu et al. , 2013). Reads with a match of at least 90% were assembled into contigs using the Velvet assembler  (Zerbino and Birney, 2008)  with a k-mer length of 81 and all the remaining parameters left at their default values.
The resulting contigs were used as seeds to initiate the genome walking strategy (iterative mapping) using the extractreads2 program (included in the Obitools package; http://metabarcoding. org/obitools). Reads sharing at least 80 consecutive bp with the seeds were selected and subsequently used as seed to repeat the operation until no new read was identified. The newly selected reads were assembled with the Velvet assembler. The few resulting contigs were assembled using Geneious 6. 0. 6 Pro (Biomatters, Auckland, New Zealand). Two regions of the genome were not assembled using this procedure, due to ambiguities in the assembling process. At these locations, repeated regions were revealed by the coexistence of two assembling paths with significant coverage support (i. e. of the same magnitude than the average coverage), one path being at the junction between two copies of the repeated element, the other being at the end of the last copy (see Fig.
Genome annotation The mitochondrial genome was first annotated using the MITOS web server  (Bernt et al. , 2013b)  applying the invertebrate mitochondrial genetic code (NCBI code Table  5 ). The annotations of tRNA genes were kept unchanged. The annotations of PCGs were refined by checking manually for consistent start/stop codons and reading frames. The annotations of rRNA genes were extended until adjacent tRNAs (tRNA Ser(TCN) , tRNA Leu(CUN) and tRNA Val ), following the punctuation model of mtDNA transcription  (Ojala et al. , 1981; Stewart and Beckenbach, 2009). The 5′ end of srRNA is not flanked by a tRNA. We adjusted it by mapping the srRNA of the A. dohrni mitogenome for which the secondary structured was predicted, and presented all expected domains  (Li et al. , 2011). We used Geneious 6.
0. 6 Pro with the following parameters: a word length of seven; maximum gap size of 15 and maximum mismatches of 40%. This approach conducted to extend lrRNA's annotation by 33 bp until tRNA Leu at its 3′ end and by 578 bp until tRNA-Val at its 5′ end. srRNA's annotation was extended by 2 bp until tRNA Val and by 47 bp at its 5′ end. We further verify the consistency of these new annotations by mapping the rRNAs of A. dohrni as described above. The remaining large non-annotated sequence was annotated as the control region in homology with other insect mitogenomes. The 18S and 28S rRNAs were annotated in comparison with that of E. maracandica  (Yu et al. , 2013). The 5. 8S rRNA was annotated in comparison with that of T. dimidiata (accession number: KF142517).
, 2013). We used the Turbofold algorithm  (Harmanci et al. , 2011) , which infers secondary structure from high base pairing probabilities using the information derived from the sequence itself via the nearest neighbor thermodynamic model and also the information computed by using pairwise-sequencealignment-based probabilities. Fifty-four additional heteropteran mitogenomes, including five assassin bugs, were downloaded from GenBank (Table  1 ). Two mitogenomes of Auchenorrhyncha were used as outgroups. The 13 PCGs were used for the analysis to allow for comparison with previous studies  (Li et al. , 2011; Yang et al. , 2013). They were first aligned separately based on amino-acid translation with translatorX  (Abascal et al. , 2010). Divergent regions were removed with Gblocks. 0. 91b before back-translation in order to conserve reading frames.