dataesr/scientific-paragraphs-categorization huggingface dataset:
Other glycoside hydrolases likely involved in degradation of cell wall hemicelluloses include GH5_7 endomannanases (Phlgi1_97727, Phlgi1_110296), a GH74 xyloglucanase (Phlgi1_98770), a GH27 a-galactosidase (Phlgi1_72848) and a GH10 endoxylanase (Phlgi1_85016). Expression of oxidative enzymes implicated in lignocellulose degradation was also influenced by growth on LP-media (NELP or ELP) relative to Glc-containing media. Transcripts corresponding to five LPMO-encoding genes showed significant regulation (P, 0. 01) in LP-medium, and three LPMO proteins were detected (Phlgi1_227588, Phlgi1_227560, Phlgi1_37310). An AAD-like oxidoreductase (Phlgi1_30343), possibly involved in the transformation of lignin metabolites, was also upregulated. However, we did not observe high expression of class II peroxidases under the conditions tested (Dataset S2).
On the other hand, a DyP (Phlgi1_85295) was significantly upregulated in certain LPcontaining media (Table  1 ). The importance of these peroxidases is further supported by the high protein levels of another DyP, Phlgi1_122124. Specifically, the latter protein showed emPAI values. 17 after 5 days growth on LP media and, relative to Glc medium, its transcript ratios were. 5-fold higher (p,0. 04) (Dataset S2). High DyP gene expression has been observed in white-rot fungi Trametes versicolor and Dichomitus squalens  [21] , but no genes for these proteins are present in P. chrysosporium and C. subvermispora (Figure  4 ). The P. gigantea DyP (Phlgi1_122124) was also abundant in media containing microcrystalline cellulose (Avicel) as the sole carbon source (Dataset S2). To identify enzymes involved in tolerance to and/or degradation of extractives, comparisons were made of gene expression in ground loblolly pine wood that had been extensively extracted with acetone (ELP) versus non-extracted loblolly pine wood (NELP) (Figure  7A ).
2  and 3. doi:10. 1371/journal. pgen. 1004759. t001 extract-induced genes, lipases Phlgi1_19028 and Phlgi1_36659 likely hydrolyze the significant levels of triglycerides. The substrate specificity of aldehyde dehydrogenases such as Phlgi1_115040 is difficult to assess based on sequence, although several have been implicated in the degradation of pine wood resins by bacteria  [56]. Secretome patterns in media containing microcrystalline cellulose (Avicel) as sole carbon source generally supported the importance of the same proteins in the metabolism of pine wood extractives (Table  3 , Dataset S2). Specifically, lipases Phlgi1_19028 and Phlgi1_36659 and aldehyde dehydrogenase Phlg1_115040 were more abundant in loblolly pine wood and in Avicel media relative to the same media without extractives.
The distribution and expression of DyP-encoding genes are notable; with no genes present in P. chrysosporium and C. subvermispora but several highly expressed genes in T. versicolor, D. squalens  [21]  and P. gigantea (Table  2 ). Physiological roles of DyP are likely diverse, but oxidation of lignin-related aromatic compounds has been demonstrated  [59]. In addition to lignin, oxidative mechanisms likely play a central role in P. gigantea cellulose attack. Of 15 LPMO-encoding genes, transcripts of six genes were regulated (. 2-fold; p,0. 01) and peptides corresponding to three were unambiguously identified in NELP-or ELP-containing media. Our inability to detect any LPMO proteins in Avicel media (Dataset S2) suggests induction by substrates other than cellulose  [60]. Beyond this, the CDH gene was highly expressed (transcripts and protein) in LP media.
GH11 endoxylanase and CE carbohydrate esterase peptides were also detected in the pine wood-containing media, but not in Avicel cultures (Dataset S2). In aggregate, these results demonstrate P. gigantea adaptation to conifer hemicellulose degradation. P. gigantea's gene expression patterns reveal multiple strategies for overcoming the challenging composition of resinous sapwood. Tolerance to monoterpenes may be mediated in part by a putative ABC efflux transporter (Phlbi1_130987, Figure  9 ). Of the 51 ABC proteins of P. gigantea, this protein is most closely related to the GcABC-G1 gene of the ascomycete Grosmannia clavigera, a pathogen of Pinus contorta  [63]. The GcABC-G1 gene is upregulated in response to various terpenes and appears to be a key element against the host defenses. Consistent with a similar function, our analysis showed the P.
gigantea homolog to be upregulated. 4. 9-fold (p = 0. 02) in NELP relative to ELP media (Dataset S2). Other transcripts accumulating in NELP-derived mycelia included three CYPs (Table  2 ) potentially involved in the hydroxylation of diterpenoids and related resin acids  [55]. Differential regulation also implicates glutathione S-transferase, aldehyde dehydrogenase and peroxiredoxin in the transformation and detoxification of extractives (Table  2 ). Three putative transcription regulators were similarly regulated (Table  3 ). Aldehyde dehydrogenase-and AAD-encoding genes, some of which are upregulated in P. gigantea LP cultures relative to Glc cultures (Tables 1), are induced by aromatic compounds in P. chrysosporium  [64, 65]. Predicted to degrade triglycerides, a total of nine lipaseencoding genes were identified in the P.
gigantea genome and four of these were upregulated. 2-fold (p,0. 01) in LP media compared to Glc medium (Dataset S2). Two lipases displayed similar patterns of transcript and protein upregulation on NELP relative to ELP (Table  3 ), and the pine wood extractive also induced accumulation of these lipases in Avicel media (Table  3 ). Further metabolism of triglycerides is uncertain, although a putative glycerol uptake facilitator (Phlbi1_99331) was highly expressed (RPKM value of 2532) and significantly (p,0. 02) upregulated (2. 1-fold) in NELP compared to ELP (Dataset S2). Fatty acids activation and b-oxidation can be inferred by the expression of fatty acid CoA ligase (Phlgi1_107548, Phlgi1_126556, Phlgi1_89325), b-ketothiolase (Phlgi1_27649, Phlgi1_130767), and fatty acid desaturase (Phlgi1_100083, Phlgi1_115799).
For example MOX (Phlgi1_120749) is among the most abundant transcripts in both NELP and ELP (Dataset S2), suggesting an important role in H 2 O 2 production associated with lignin demethylation  [53]. Extracellular peroxide generation is key to peroxidase activity, and MOX fulfills this role along with CRO, AAO, and P2O. Along these lines, we also observed high extracellular protein levels of DyP (Phlgi1_122124) under all culture conditions. Most problematic, many P. gigantea genes and proteins exhibited little or no homology to NCBI NR or Swiss-Prot entries. Some of these 'hypothetical' or 'uncharacterized' proteins are undoubtedly important, particularly those that are highly expressed, regulated and/or secreted. For example, of 92 genes upregulated (. 2-fold; p,0. 01) in NELP relative to ELP, 51 were designated as hypothetical (Table  2 ; Dataset S2).
Sequencing and annotation The genome was sequenced using Illumina and annotated using the JGI Annotation Pipeline  [69]. Assembly and annotations are available from JGI portal MycoCosm  [38]  and deposited to DDBJ/EMBL/GenBank under accession AZAG00000000. The version described in this paper is version AZAG01000000. The completeness of the P. gigantea genome was assessed by finding 99. 1% of CEGMA proteins conserved across sequenced genomes of eukaryotes  [70] (Text S1; Tables  S1, S2 ).
RNA-seq Mycelium was derived from triplicate cultures of 250 ml basal salts containing: i. 1. 25 g freshly-harvested, ground (1mm mesh) loblolly pine wood that had been 'spiked' with acetone and thoroughly dried (NELP); or ii. the same material following extended acetone extraction in a Soxhlet apparatus and drying (ELP). The composition of the extract (Text S1) was determined by GC-MS  [51]. Duplicate cultures of basal salts medium with glucose as sole carbon source served as a reference. After 5 days incubation, total RNA was purified from frozen mycelium as described  [22, 71]. Multiplexed libraries were constructed and sequenced on an Illumina HiSeq2000. DNAStar Inc (Madison, WI) modules SeqNGen and Qseq were used for mapping reads and statistical analysis. Transcriptome data was deposited to the NCBI Gene Expression Omnibus (GEO) database and assigned accession GSE53112 (Reviewer access via http://www.
The evolutionary distances were computed using the Poisson correction method  [79]  and are in the units of the number of amino acid substitutions per site. The ME tree was searched using the Close-Neighbor-Interchange (CNI) algorithm  [4]  at a search level of 1. The Neighbor-joining algorithm  [80]  was used to generate the initial tree. All positions containing gaps and missing data were eliminated from the dataset (Complete deletion option). There were a total of 183 positions in the final dataset. Phylogenetic analyses were conducted in MEGA4  [81]. (EPS) Ligninolytic peroxidases, including LiP models -A) 150531 peroxidase, B) 121662 peroxidase and C) 30372 peroxidaseharboring an exposed tryptophan potentially involved in oxidation of high redox-potential substrates, and MnP models -D) 75566 peroxidase, E) 75572 peroxidase, F) 115591 peroxidase, G) 115592 peroxidase and H) 117668 peroxidase -harboring a putative Mn 2+ oxidation site (formed by two glutamates and one aspartate); and I) manually curated GP (32509).
ID numbers refer to protein models in the JGI MycoCosm (http://genome. jgi-psf. org/programs/fungi/ index. jsf), other accession numbers to the NCBI database (http:// www. ncbi. nlm. nih. gov/), specific names to proteins specified with accession numbers in Hoegger et al. [29]  and Lettera et al. [87]. Blue coloring marks enzymes with laccase activity experimentally shown, light brown enzymes with proven ferroxidase activity, purple enzymes with ascorbate activity, olive enzymes acting in fungal pigment synthesis, and two colors dual enzymatic activities with the left color marking the respective major performance (  [88, 89]  and references in the review of Ku ¨es and Ru ¨hl 2011  [90] ). Proteins from P. gigantea are highlighted in red. (EPS) Figure  S21  Sequence alignment for four regions of S.
CDS sequences were obtained from each genome database according to assigned protein IDs. Incomplete CDS sequences (partial fragments) were eliminated from the analysis. For each CE family, a multiple alignment was performed using MegAlign version 10 software. The phylogenetic tree was then constructed from the multiple alignment using Clustal W  [85]   Figure  S31  Phylogenetic tree of the cytochrome P450 proteins (P450ome) in P. gigantea. Tree was constructed using 124 P450 sequences (which were full-length or near full-length) and evolutionary history was inferred using bootstrap Neighbor-Joining method. Phylogenetic analyses were conducted using MEGA4  [81]. The P450 listing in the tree is based on the corresponding protein ID with the CYP name in parenthesis. P450s that belong to a new subfamily are indicated with the abbreviation NS.
(Acr), Aspergillus nidulans (Ani), Cryptococcus neoformans (Cne), Coprinopsis cinerea (Cci), Pleurotus ostreatus (Pos), Phanerochaete carnosa (Pca), Phanerochaete chrysosporium (Pch), Phanerochaete flavido-alba (Pfa), Phlebiopsis gigantea (Pgi), Postia placenta (Ppl), Saccharomyces cerevisiae (Sce), Schizophyllum commune (Sco), Serpula lacrymans (Sla), Sporobolomyces roseus (Sro), Tremella mesenterica (Tme), and Ustilago maydis (Uma). Alignments were produced in program ClustalW, manually adjusted in Genedoc and computed in MEGA4. 0 for phylogenetic tree production (neighbourjoining, bootstrap values 500). ID numbers refer to protein models in the JGI MycoCosm (http://genome. jgi-psf. org/programs/fungi/ index. jsf), other accession numbers to the NCBI database (http:// www. ncbi. nlm. nih.
gov/), specific names to proteins specified with accession numbers in Hoegger et al. [29]  and Lettera et al. [87]. Blue coloring marks enzymes with laccase activity experimentally shown, light brown enzymes with proven ferroxidase activity, purple enzymes with ascorbate activity, olive enzymes acting in fungal pigment synthesis, and two colors dual enzymatic activities with the left color marking the respective major performance ( [88, 89]  and references in the review of Ku ¨es and Ru ¨hl 2011 [90] ). Proteins from P. gigantea are highlighted in red. (EPS).
The analysis involved 174 amino acid sequences. All ambiguous positions were removed for each sequence pair. There were a total of 155 positions in the final dataset. Evolutionary analyses were conducted in MEGA5 [92]. Fungal species IDs: |Cersu| (Ceriporiopsis subvermispora), |Phlgi| (Phlebiopsis gigantea), |Phchr|(Phanerochaete chrysosporium), |Gansp| (Ganoderma sp. ), |Phlbr| (Phlebia brevispora), |Serla_varsha|(Serpula lacrymans), |Wolco| (Wolfiporia cocos), |Hetan| (Heterobasidion annosum), |Schco| (Schizophyllum commune), |Copci| (Coprinopsis cinerea), |Lacbi| (Laccaria bicolor), |Ustma| (Ustilago maydis), |Acral| (Acremonium alcalophilum). The tree is rooted at Acremonium alcalophilum, representing class II of hydrophobins. (EPS) Figure S35 Chromatogram of loblolly pine wood acetone extract.
Genes encoding LC-MS/MS detected proteins and exhibiting. 2-fold regulation in comparisons of NELP and ELP cultures. 1 Listing limited to genes with RPKM values. 10 and, in comparisons of NELP and ELP cultures, with high confidence of differential expression (p,0. 01). Transcript values for cultures grown on microcrystalline cellulose (Avicel) as sole carbon source unavailable. The composition of loblolly pine wood extract (extr) is listed in Text S1. Complete listings for 11,892 genes provided in Dataset S2. doi:10. 1371/journal. pgen. 1004759. t003.
ACKNOWLEDGMENTS. We thank  Cell Imaging Core and Proteomics Facility of Turku Centre for Biotechnology. Research was financially supported by the  Academy of Finland  Projects  118637 ,  271832 , and  273870  (to E. -M. A. ),  Kone Foundation  (Y. A. ), and  Varsinais-Suomi Cultural Foundation  regional fund (M. E. ). Support was provided by the HélioBiotec platform, funded by the  European Union  ( European Regional Development Fund) , the  Région Provence Alpes Côte d'Azur , the  French Ministry of Research , and the " Commissariat à l'Energie Atomique et aux Energies Alternatives. ".
H 2 0 2 ), BFG1 carrying the HpHAP4-B gene (HpHap4-B/HpHap4-B. H 2 O 2 ). The integrity of the total RNA was determined using an Agilent Technologies 2100 Bioanalyzer and the RNA 6000 Lab-Chip kit. Total RNA concentration was determined using a NanoDrop ND-1000 spectrophotometer  [27]. For hybridization, Agilent Yeast oligomicroarrays (v2, cat # G4140B, Agilent Technologies, Palo Alto, CA) were used. Target preparation, hybridization and washing were performed according to the manufacturer's instructions. The slides were scanned using GenePix 4000B scanner at 100% laser power and the PMT voltage was automatically adjusted. The resulting 16 bit images were analysed using the GenePix Pro 6. 0 software. Data were processed using the MAnGO software  [28]. The background level was calculated using morphological operators and subtracted.
Raw data were normalized using the print-tip Loess method  [29]. The array data were submitted to the NCBI Gene Expression Omnibus public depository, entry E-MEXP-3173 for experiments in the Dhap4 background and E-MEXP-3131 for experiments in the Dyap1 background. Statistical comparisons were performed using multiple testing procedures to evaluate statistical significance for differentially expressed genes. On each slide, the normalized expression log-ratios were averaged on all replicates of each probe. A moderated t-test, e. g. a Student-like test  [30] , was computed. An error rate (pvalue) is associated with each test value. Differentially expressed genes are selected with two criteria: p-value ,0. 005 and fold-change FC. |1. 5|. To reveal the changes in gene expression in the three different contexts (ScHap4, HpHap4-A, HpHap4-B), the heat map hierarchical clustering method of the heat map function of the R package ''stats'' was applied to the normalized log2 ratios (intensity of WT versus intensity of Mutant) obtained from the whole microarray experiments in the ScDhap4 genetic background and on the normalized median signals obtained for the different conditions in the ScDyap1 background.
Acknowledgments Access to the HpHAP4-A and HpHAP4-B genes of H. polymorpha was kindly provided by  Rhein-Biotech. Our  deep thanks go to  Pr. Michael Dubow  who proofread the English language and to  Pr. F. Confalioneri ,  Dr. A. Lagorce  and  M. Dutertre  for their help in providing materials and advices for the qRT-PCR experiments.
Funding: Experiments were funded by recurrent national fundings ( CNRS and University)  to the IGM ( UMR8621 ). The  EC  contract  GARNISH QLK3-2000-174  to MBF contributed to the start of this work. NP was supported by a  French government fellowship  for joint PhD, a bilateral  CNRS-Ukrainian NAS program  and a regional support from  Ile de France  grant for joint PhD. KS was supported by a  FEBS collaborative experimental Scholarship for Central  and  Eastern Europe  and an  INTAS   fellowship grant for young Scientist  ( 05-109-4177 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Population and density per square kilometre of Camelidae in the countries of the Arabian Peninsula and African countries with over 1 million Camelidae World Health Organisation for Animal Health. World Animal Health Information Database (WAHID), Animal population, Camelidae, 2011-2013, Available from http://www. oie. int/wahis_2/public/wahid. php/ Countryinformation/Animalpopulation. Surface area and human population: World Bank, 2009-2013. http:// data. worldbank. org/.
Search strategies To identify the Lactobacillus spp. associated with weight modification, we searched PubMed database for peer-reviewed, English-language articles with no date restrictions. The search terms were combinations of 'Lactobacillus', 'probiotics', 'microbiota' and 'weight', 'weight gain', 'weight protection', 'weight loss', 'weight change', 'weight modification', 'obesity', 'growth', 'body fat' or 'adipose tissue'. We retrieved the full text of the selected studies and searched the references cited in these articles. When necessary, we contacted the corresponding authors for further clarification or additional information.
Alignment and annotation of genomes using a combination of several search tools The nucleotide sequences of strains belonging to the same species were subjected to genome alignment using Progressive Mauve software 23 using default parameters. All genomes were annotated using the Rapid Annotation using Subsystem Technology (RAST) (http://rast. nmpdr. org/). 24 he enzyme commission (EC) numbers were subsequently obtained from the RAST results (Figure  2 ). The conserved domains in protein sequences were identified using the Batch CD-Search tool. The Gene Ontology (GO) database was used for annotating and classifying gene function. 25 Using the GO data (http://www. geneontology. org), the correspondence between several identifiers obtained from CD-search and RAST were realized through manual curation between the data to obtain an accurate and non-redundant reference gene set.
The resulting annotations of the different databases were retrieved and tabulated for each genome. We focused on the proteins for which the annotated function obtained from our analysis showed involvement in carbohydrate and lipid metabolism. The maps obtained from Kyoto Encyclopedia of Genes and Genomes were used to determine the metabolic pathways in which these enzymes were involved (http://www. genome. jp/kegg/ pathway. html). 26 Moreover, Pfam HMM-profiles utilized with HMMER software package 27 facilitated the identification of genes encoding lipases.
Bacteriocins database We established a bacteriocins database (Figure  2 ). The available data were obtained from Bactibase (http://bactibase. pfba-lab-tun. org/main. php), and the sequences of all bacteriocins reported in the literature were retrieved from the NCBI database. A multi-Fasta text file containing 247 retrieved protein sequences was subsequently generated. The bacteriocin sequences were aligned using the BioEdit program (http://www. mbio. ncsu. edu/BioEdit/bioedit. html)  28  and converted into a MEGA file. A bidirectional protein BLAST 29 of whole genome sequences against the bacteriocin database was performed. The manual examination of best BLAST hits (identity over 30% and coverage over 50%) facilitated the identification of bacteriocins in the Lactobacillus genomes. The bacteriocin sequences were compared using the Artemis Comparison Tool developed by the Sanger Institute.
Clustering and statistical analysis of strains A hierarchical clustering analysis based on Pearson's correlation was performed using TIGR Multi experiment Viewer (MeV) Version 2. 2 (http:// www. tigr. org) to identify the genes present in the different species. The gene content of the strains studied was described using a two-character matrix, with 0 for an enzyme not detected and 1 for the presence of an enzyme. Principal component analyses were performed using the PRINCOMP and BIPLOT functions of the R statistical package (Vienna, Austria, http://www. R-project. org/) to infer relationships between weight gain and weight protection-associated Lactobacillus. A P-value o0. 05 was considered significant.
Lipases Lipases have an essential role in the mobilization of fatty acids from dietary or storage fats. The HMM search revealed that among the 16 lipase families identified in the libraries in this study, 3 lipases were present in at least one Lactobacillus genome (Supplementary Table  2 ). Furthermore, all genomes analyzed contain many candidate genes encoding lipases from the families PF00561 (ab hydrolase 1, including acid lipases and Pseudomonas-like lipases) and PF0785 (ab hydrolase 3 or hormone-sensitive lipase family). PF00561 was the most abundant family in the genomes analyzed, and we identified 14 corresponding genes in L. acidophilus 30SC. The second most abundant lipase family was PF0785, with 12 lipases identified in L. plantarum JDM1. The PF00561 and PF0785 lipase families belong to a superfamily of proteins characterized by an a/b hydrolase fold, representing one of the largest group of enzymes with diverse catalytic functions, such as proteases, lipases, peroxidases, esterases, epoxide hydrolases and dehalogenases.
Bacteriocins In the generated database, we observed that the sequences encoding bacteriocins differ greatly in size and composition: the sequences range from 7 amino acids (microcin C7) to 1585 amino acids (rhizobiocin), with an average length of 110 amino acids. Using BLASTp, we obtained 77 significant hits, which were subsequently compared with the annotations obtained using the RAST server. We identified 18 different types of bacteriocins in Lactobacillus spp. , among which several sequences were previously annotated as hypothetical proteins in the NCBI database (Figure  5 ). Weight gain-associated Lactobacillus spp. encoded more bacteriocins (mean ¼ 6) than weight protection-associated Lactobacillus spp. (mean ¼ 4) (Supplementary Table  3 ). Moreover, L. plantarum encoded several bacteriocin precursors (from 3 to 5 per genome).
L. acidophilus 30SC encoded the largest number of bacteriocins, with 15 putative genes. Plantaricins and colicins were the most commonly encoded bacteriocins. We identified bacteriocins annotated as colicin V proteins in L. ingluviei and L. fermentum genomes. In L. fermentum spp. , the potential colicin V gene sequences were identified in regions with high collinearity, but no synteny with the region containing the gene encoding colicin V in L. ingluviei was observed (Supplementary Figure  4 ). However, the sequence alignment of the putative colicin V with colicin V obtained from the database showed a high degree of similarity, from 21 to 100%. The clustering analysis showed that L. plantarum strains associated with weight protection are separated from the other species based on the bacteriocin content, whereas L.