dataesr/scientific-paragraphs-categorization huggingface dataset:
The visualization and clustering (based on pearson's correlation) of these indicator OTUs were conducted using aheatmap function in the "NMF" package  (Gaujoux, 2014). Co-occurrence patterns in microbial communities were assessed by performing network analyses using Random Matrix Theory (RMT)-based methods. This method identified the appropriate similarity threshold automatically for network construction  (Deng et al. , 2012). Four separate co-occurrence networks were constructed based on four groups of samples: those taken during the rain-exclusion period and those taken after roof removal, split by rainexclusion or control plots. To reduce rare OTUs in the dataset, the taxa with relative abundance < 0. 1 % were excluded for each network construction. A cutoff value (similarity threshold) for the similarity matrix was automatically generated using default settings.
Acknowledgments The authors acknowledge funding by the  University of Antwerp BOF/GOA -project  REGIME SHIFT. This work further benefited from an  Investissements d'Avenir grant  managed by  Agence Nationale de la Recherche  (CEBA, ref. ANR-10-LABX-25-01 ) and was supported by the  European Research Council Synergy  grant  ERC-2013-SyG-610028-IMBALANCE-P. We are grateful to  Thomas Saint-Germain ,  Jocelyn Cazal ,  Maricar Aguillos ,  Benoit Burban ,  Jean-Yves Goret ,  Baptiste Rabineau  and the master students of the Module FTH for their help in the field. Downloaded from https://academic. oup. com/femsec/advance-article/doi/10. 1093/femsec/fiab116/6348091 by IFREMER user on 01 September 2021.
The use of global alignment-derived pairwise identity values can result in the deflation of the sequence identity values due to fixed gaps. This becomes problematic, especially when diverse sequences are included in such alignments. Thus, here, we use true pairwise sequence identity values to determine their distribution in order to establish species demarcation thresholds. We analysed the annotated ORF1 coding (complete ORF1) regions of complete anellovirus genome sequences (n = 749) available in the GenBank database (downloaded 10 July 2020). We determined the pairwise identity values for all the ORF1 nucleotide sequences using SDT v1. 2  [37]. The plot of the distribution of the pairwise identity values (Fig. 1 ) revealed a trough at ~69%. Using 69% as a species demarcation threshold, of the 75 currently established species, viruses in only 10 species did not fit this criterion, and thus these species were abolished and the corresponding viruses were reassigned to already established species (see Table  2  for abolished species and the reassignment of viruses).
The 69% species demarcation threshold has also been used for the classification of the viruses in the genus Gyrovirus, which now has nine new species (see Kraberger et al. [30] ). To establish genus demarcation criteria, since the pairwise identity plot does not give a clear demarcation threshold, we opted for a phylogeny-based approach using the ORF1 amino acid sequences. A dataset of the ORF1 amino acid sequences of a representative member of each species was assembled, and this was then aligned using MAFFT  [28]. The alignment was trimmed with TrimAL  [11]  using the gappyout option, and the alignment was used to infer a maximum-likelihood tree with IQTree  [35]  with the LG+F+G4 substitution model. The TrimAL alignment contained 361 amino acid sites in the final alignment. The resulting maximum-likelihood phylogenetic tree was rooted at the midpoint and edited in iTOL v4  [31].
Based on the phylogeny (Fig. 2 ), we established a total of 16 new genera (Table  1 ). We used the Greek alphabet for naming new genera. In the spirit of using ancient alphabets, we adopt the Phoenician alphabet for an additional six new genera in series without using 'bet' (to avoid confusion with "beta"). In the future, the following letters of the Phoenician alphabet can be used for new genus names with minimal conflict with current names: yod, lamed, mem, samek, ayin, pe, sade, qop, res, sin, taw. Furthermore, based on the criteria discussed above, we have established 80 new species (see Table  3 ). A comprehensive list of the new classification of anelloviruses is provided in Supplementary Table  S1. This includes all sequences with sufficient information for their classification available in GenBank on 20 May 2021.
White/blue colonies selection and mutation frequency DNA extracted from embryos was transformed in electrocompetent indicator bacteria (MBM7070 strain bearing an amber mutation in the lacZ gene) for white/blue screening and plated on selective petri dishes (40 μg mL -1 Xgal,; 200 μM IPTG). Over one thousand colonies were scored at least for each condition in each replicate. Plasmid DNA was isolated from mutant clones using a standard protocol (QIAGEN). After paired-end Sanger sequencing, polymorphisms were filtered for sequencing quality > 30 and analyzed on both strands using Geneious or Snapgene softwares. Mutation rates were estimated from the proportion of blue colonies observed (P0). Before calculating the proportion of blue colonies observed (P0), the basal percentage of white colonies prior to microinjection was subtracted from the percentage of white colonies in each experimental condition.
Samples were mounted in coverslips using Vectashield. Images were acquired with a Zeiss Axiovert Apotome microscope at 5X using Coolsnap HQ CDD camera (Photometrics) and processed using Omero 5. 2. 0 software. P-values were obtained using a two-tailed, unpaired Student's t-test. Drosophila embryo protein lysates preparation 60 females and 10 males were incubated together inside embryo's collectors with embryo dishes for a certain number of hours according to the desired stage of embryos to be harvested. Collected embryos were gently rinsed off the medium with embryo collection buffer (Triton X-100 0,03 %; NaCl 68 mM). Embryos were removed from the medium using a brush and poured into a sieve (Falcon Cell Strainer 40 µM Nylon 352340). Harvested embryos were washed again and collected in a fresh tube (up to 50 µL -1 of embryos corresponding to 100 embryos).
Illumina Next Generation Sequencing Two genomic DNA samples per condition (extracted from single heterozygous dpolη EXC215/+ males either dPolη maternally-depleted or maternally-provided, see text ) were sequenced by Illumina NGS. After library construction and shotgun, whole Drosophila genomes were pairedend sequenced and assembled as previously described  (30). Data were filtered for Genotype Quality > 35 and Depth > 10 before sequences alignment against the Drosophila reference genome (Flybase release 6). Variant calling was done using Freebayes software version 0. 9. 20. Genotype ratio was not changed from recommended settings. Alignment was performed with BWA version 0. 7. 12-r1039. Variant calling was performed using Freebayes version 0. 9. 20 and then annotated with Ensembl VEP version 82.
We have observed that Polη mutagenic activity may be important to maintain the stability of centromeric DNA sequences in the Drosophila pre-blastoderm embryo, thus being good for life. Genome-wide association studies have implicated hundreds of thousands of single-nucleotide polymorphisms (SNPs) in human diseases and traits  (66). In the future, it will be important to explore which is the level of DNA damage inherited in the post-MBT embryo, and its contribution to the polymorphisms that characterize each individual. by ANR (ANR-12-BSV2-0022) and MSD Avenir grants to D. M. E. L. F. was supported by a 3-year PhD fellowship from the "Ligue contre le Cancer" and 1-year fellowship from "Fondation ARC contre le cancer". (B) Mutation frequency and (C) mutagenesis rate (measured as described in Figure  1 ) of lacZ recovered from embryos co-injected with the indicated RAD18 mRNAs, or lacZ injected alone.
The mutation frequency of lacZ recovered from embryos injected with a post-MBT amount of plasmid DNA (post-MBT) is also included as comparison. RAD18 WT , RAD18 C28F n=3; RAD18 C207F , RAD18 C28FC207F n=2. (D) Western blot of total protein extracts obtained from Xenopus embryos subjected to the indicated experimental conditions, n=3. (E) Mutation spectrum of lacZ recovered from embryos injected with the indicated RAD18 variants, or lacZ injected alone. Data are presented as means ± SD. Means were compared using analysis of one-way ANOVA, followed by unpaired Student's t test. (B) Genetic crosses set up to generate either maternally-depleted or maternally-provided dPolη adult flies. The first two crosses generated a balanced stock over TM3 marked with Sb with a isogenic 3rd chromosome carrying the dpolη Exc2.
6. 2 [31]. Putative virus reads and plant virus reads obtained using either BLASTn or BLASTx  [32]  from sugarcane and wild Poaceae with e-values < 0. 001 were retained. Finally, only putative plant viruses with more than 10 reads per sample were taken into consideration for further analysis. Cleaned reads have been deposited in the sequence read archive of GenBank (accession number PRJNA721112).
Phylogenetic Analyses Contigs produced by assembly of Illumina reads were utilized as queries to perform BLASTn and BLASTx searches  [32]  using the NCBI database (https://blast. ncbi. nlm. nih. gov/Blast. cgi, accessed on 31 March 2021). Forty-eight contigs assigned to plant viruses obtained from both compartments (within and outside the quarantine) were selected for further comparisons. These 48 sequences were subsequently aligned to reference genomes using ClustalW with default settings  [33]. Visual inspection of alignment quality and BLAST graphic summaries was done and one contig presenting one chimeric end was trimmed. The resulting alignments were used to infer neighbor-joining phylogenetic trees using the MegaX software  [34]. The Jukes-Cantor nucleotide substitution model with 1000 bootstrap replicates for branch support was applied.
Phylogenetic Relationships of Plant Viral Sequences Assigned to the Closteroviridae, Luteoviridae, and Potyviridae Families While the 101 Closteroviridae contigs obtained from seven quarantined sugarcane varieties (Q112, B46364-USA51/1, B46364-PAK155, BJ790038, X, LF653661, and NA021668) were assigned to the Ampelovirus genus, one Closteroviridae contig obtained from a grassland sample of Brachypodium phoenicoides was assigned to the Closterovirus genus using BLASTx searches (Figure  2A  and Table  S2 ). The highest identity score for this 535-nt-long contig obtained from B. phoenicoides was obtained with raspberry leaf mottle virus (accession number QOS14265, highest percent identity = 36%, e-value = 3 × 10 -10 ), suggesting that it represented a novel closterovirus that needs further characterization.
The phylogenetic analyses also showed that the sugarcane Ampelovirus contigs grouped together but were also distributed into several subgroups, thus indicating that sugarcane-associated am-peloviruses are diverse and may represent several divergent variants of the same species, or even several species (Figure  2A ). Two contigs from an Aegilops triuncialis plant, one contig from a Bothriochloa barbinodis plant, and two large contigs from two sugarcane varieties (B46364-USA51/1 and B46364-PAK155) were assigned to the Luteoviridae family using BLAST searches (Table  S3 ). The large contig from each sugarcane variety shared 99% identity with sugarcane yellow leaf virus (SCYLV, accession number KY052166) and represented 97. 7% of the com- Two contigs from an Aegilops triuncialis plant, one contig from a Bothriochloa barbinodis plant, and two large contigs from two sugarcane varieties (B46364-USA51/1 and B46364-PAK155) were assigned to the Luteoviridae family using BLAST searches (Table  S3 ).
The large contig from each sugarcane variety shared 99% identity with sugarcane yellow leaf virus (SCYLV, accession number KY052166) and represented 97. 7% of the complete genome sequence of this SCYLV isolate. The two overlapping contigs from A. triuncialis and B. barbinodis shared 71% identity among each other, suggesting that they could be variants of the same virus. Identities of the three wild Poaceae contigs with SCYLV (accession number KY052166) ranged from 39 to 43% and from 70. 8 to 74. 9% with unclassified luteoviruses isolated from insects (Fagle virus, accession number MK440658 and Norway luteo-like virus 1, accession number MF141065). The phylogenetic analysis allowed us to confirm that the Luteoviridae contigs obtained from the two wild grasses were highly divergent from plant luteoviruses (Figure  2B ).
The two complete genome sequences recovered from a sloped land sample of Brachypodium phoenicoides and a grassland sample of Gastridium ventricosum shared 99% nucleotide identity. This suggested that both sequences belonged to the same Tritimovirus species. Furthermore, these two Poaceae tritimovirus sequences shared 67. 6% nucleotide identity with oat necrotic mottle virus (accession number AY377938), which is below the species demarcation (<76% nucleotide identity) of the Potyviridae family  [35]. Consequently, these sequences could represent a novel species of the Tritimovirus genus.
For the wild Poaceae, only one sample of B. phoenicoides collected from grassland contained four badnavirus contigs (Table  S6 ) that shared 74. 5-77% nucleotide identity with canna yellow leaf mottle virus (CaYMV, accession number KX255725) and 30 to 72% nucleotide identity with the badnavirus contigs obtained from quarantined sugarcane varieties. Based on phylogenetic analyses, the two longest contigs of B. phoenicoides clustered with CaYMV and formed a group that was apart from any of the badnaviruses currently known to infect sugarcane (Figure  4A  and Figure  S1 )  [37]. The contigs produced from sugarcane varieties R579, B46364 USA51/1, B46364 PAK155, and BJ79038 were related to sugarcane baciliform Guadeloupe A virus (SCBGAV, accession number NC_038382) (Figure  4A ). The contigs obtained from the variety X clustered with sugarcane bacilliform Guadeloupe D virus (SCBGDV, accession number NC_013455) (Figure  4A  and Figure  S1 ) and contigs obtained from varieties KN88104, KN8843, and LF653661 grouped with banana streak CA virus (accession number HQ593111) (Figure  4A  and Figure  S1 ).
The contigs from sugarcane variety Q112 matched with two different badnavirus genomes, i. e. , SCBGAV and sugarcane bacilliform virus isolate Iscam (accession number JN377534) (data not shown). Contigs assigned by BLAST searches to the Tombusviridae family, including members of the Umbravirus genus and unclassified umbraviruses, were obtained from five wild Poaceae species and two sugarcane varieties (BJ79038 and KN8924). These wild Poaceae samples included Trachynia distachya, Bothriochloa barbinodis, B. phoenicoides, Phalaris minor, and Festuca sp. plants from both the sloped land and the grassland areas (Table  S7 ). Umbravirus contigs recovered from wild Poaceae plants shared 45-72% nucleotide identities with a sugarcane umbra-like virus genome (accession number MN868593). Four contigs obtained from two P.
minor plants, one Festuca sp. plant, and one B. phoenicoides plant had 66-69% nucleotide identity with strawberry-associated virus A (accession number MK211274). The four contigs also clustered in a neighbor-joining phylogenetic tree, thus suggesting that a single novel umbravirus infected these wild Poaceae plants (Figure  4B ). Furthermore, while the contig recovered from the other Festuca sp. plant shared 71% nucleotide identity with Patrinia mild mottle virus (accession number MH922775), contigs from T. distachya and B. barbinodis were 100% identical and had 71-73% nucleotide identity with Ethiopia-maize-associated virus (accession number MF415880). Finally, two partial genome sequences of umbraviruses (1931 nt and 2039 nt, Table  S7 ) were recovered from sugarcane varieties (BJ79038 and KN8924), respectively, using VANA-based reads and RT-PCR assays.
These two partial genomes were 71% identical. The 2039-nt-long partial genome from the sugarcane variety KN8924 shared 97% nucleotide identity with Ethiopiamaize-associated virus (accession number MF415880), suggesting that this still-unclassified umbra-like virus, initially isolated from maize, was also infecting sugarcane. The 1931-ntlong partial genome from sugarcane variety BJ79038 shared 72% nucleotide identity with Ethiopia-maize-associated virus (accession number MF415880) and 71% with sugarcane umbra-like virus (accession number MN868593).
Statistical Analysis All the experiments were performed by using a completely randomized design (CRD) with three replicates per treatment. In each treatment, 60 explants of leaves and radicles were used. Percentage of callogenesis [(number of explants producing callus per total number of explants], percentage of embryogenic calli [(number of embryogenic calli per number of calli] and mean number of somatic embryos produced per callus (total number of somatic embryos per number of embryogenic calli) were determined. Mean numbers were calculated with their respective standard errors. Data of these observations were analyzed by using standard analysis of variance (ANOVA). The significant difference among treatments was determined using Duncan's multiple range test at p ≤ 0. 05.
Funding: This research was financially supported by the pôle  Interaction Bio-moléculaire et Fonctions Biologiques (IBFBio) in Amiens (Haut-de-France Région-France ) and was initiated as part of a research project coordinated by  Rajbir S Sangwan  ( EDYSAN-Université Picardie Jules Verne-Amiens ). A. KADRI has benefited from a 3-year thesis grant from  AUF  ( Agence Universitaire de la Francophonie ). The authors would like to thank the IFBio pôle, the  AUF (Agence universitaire de la Francophonie)  and  UniLaSalle Beauvais  for financial support. P. Ratet  was supported by the  CNRS  and the  LabEx Saclay Plant Sciences  ( ANR-10-LABX-0040-SPS ,  LabEx SPS  and  ANR-17-EUR-0007 ,  EUR SPS-GSR ) which is managed by the  Agence National de la Recherche  under the program " Investissements d'avenir"  ( ANR-11-IDEX-0003-02 ).
Pseudomolecule reconstruction To correct ordering and orientation problems, pseudomolecule scaffolds were combined with unplaced scaffolds to produce a dataset of 138 546 scaffolds (scf_v0 in Table  2  and Figure  2 ) that was aligned to the DLS and NLRS optical maps to identify scaffolds with errors in their assembly. The alignments identified 81 conflicts within 72 scaffolds covering 429. 408 Mb. The chimeric scaffolds were corrected, thereby increasing the number of scaffolds from 138 546 to 138 634, and decreasing their N50 from 6. 871 to 6. 775 Mb (scf_v1 in Table  2  and Figure  2 ). Super-scaffolds were rebuilt from scf_v1 scaffolds with the aid of the DLS map. The total length of the resulting super-scaffolds was 14. 712 Gb with an N50 of 64. 014 Mb (scf_v2 in Table  2  and Figure  2 ).
0. Issues that are more difficult to resolve remain in localized regions and will require integration of new data types, especially in areas where the resolution of optical maps was inadequate to detect or resolve discrepancies. Also, some small scaffolds could not be aligned on the optical maps and were discarded. Some optical map contigs and aligned scaffolds may have been incorporated into the pseudomolecule either arbitrarily or were kept as in IWGSC RefSeq v1. 0, because of a lack of markers or ambiguity in genetic maps. Moreover, 351. 583 Mb of assembled scaffolds remain unplaced and assigned to ChrUn. The sequences of the centromeric regions, rRNA loci, telomeric and subtelomeric regions, regions containing satellite DNA, and other hardto-assemble regions remain largely unanchored and/or collapsed.
TE annotation Intact LTR RTs were identified with the LTR_finder  (Xu and Wang, 2007). A non-redundant LTR library was generated. LTRs were annotated by searches with RepeatMasker 4. 0. 9 (http://www. repea tmasker. org) against the non-redundant LTR library, Repbase  (Bao et al. , 2015)  and TREP  (Wicker et al. , 2002)  databases. To annotate all TEs, de novo TE models were generated using CLARITE and the curated wheat TE library ClariTeRep  (Daron et al. , 2014)  as described previously  (IWGSC, 2018; Wicker al. , 2018). CLARITE uses RepeatMasker for raw similarity search, to merge adjacent TE fragments into complete TE models, and eventually identifies nested insertions. The TE content similarity between v1. 0 and v2. 1 was compared by searching for overlaps with BEDTools intersect  (Quinlan and Hall, 2010)  between v1.
ACKNOWLEDGEMENTS The authors are grateful to the  M esocentre Clermont Auvergne University (France)  and  AuBi  platform for providing computing and storage resources. The authors thank  Dr Patrick E. McGuire  for valuable suggestions and assistance with drafting the manuscript. This work was supported by the  US National Science Foundation  grant  IOS-1929053  (JD and M-CL) and  USDA Agricultural Research Service CRIS  project  2030-21430-014-00-D (YQG ). RDO was funded by a grant from the  French Government  managed by the  Research National Agency (ANR)  under the  Investment for the Future program  ( BreedWheat  project  ANR-10-BTBR-03 ).
DATA AVAILABILITY The IWGSC RefSeq v2. 1 assembly and annotations are available at the IWGSC data repository hosted by URGI-INRAE (https://wheat-urgi. versailles. inra. fr/Seq-Repository/ Assemblies) and NCBI under project PRJNA669381. The DLS optical map is available at https://doi. org/10. 25338/ B8K917.
Here, metabolomics and molecular tools provide the means to generate datasets for the study of changes in gene expression and metabolites resulting from drought stress. In this study, a holistic approach was adopted towards potato plant responses to drought, focusing on the foliar parts of the plant as well as the tubers and combining both destructive and non-destructive methods in order to investigate the effects of water stress on the whole potato plant throughout the period of its lifecycle development between planting and harvest. This approach brought together breeders, geneticists, physiologists, physicists and agronomists to pool their expertise and to unlock information on potato plant response to the multifactorial effects of water stress. The plants' physical environment was characterized by measuring air temperature and installing humidity and light sensors, while the measurement of the water deficit was finely calibrated by weighing the pots in order to quantify water use and tensiometers to monitor soil dehydration.
All of these genes showed significant induction in the transcript levels at SWD in comparison to both the Control and MWD (Fig. 2d ). However, no significant induction was observed in any of the analyzed genes at MWD in   , c, d  the hull area and projected area from the side view camera, e, f height and width from the side view camera and g the ExG index. All parameters were computed from the day of transplantation into the soil to the day of harvest. For all of the mentioned parameters, a significant difference between the three conditions was observed from 34 to 53 DASE. Additional file 1: Table  S1  for further details regarding statistical data comparison to the Control (Fig. 2d ). These results clearly suggest that drought stress perception and signaling varies widely with the degree of applied stress.
Characterization of leaf aging and senescence Changes in T 2 parameters were monitored for two leaves (Leaf Ranks (LR) 0 and + 3) throughout the six-week plant development period and under Control and SWD conditions. As expected, all T 2 distributions measured in the leaves displayed several distinct peaks (data not shown). NMR data were interpreted in line with results obtained for oilseed rape, tobacco and escarole  [13] [14] [15]. In the following, only relaxation peaks associated with the vacuole water pool (either one or two peaks characterized by the longest T 2 relaxation times, depending on leaf age and condition) are presented. In all Control plants analyzed (Fig. 4a  and b ), the progression of structural changes associated with leaf development was reflected by the pattern of T 2 evolution in accordance with previous results obtained from well-watered plants.