dataesr/scientific-paragraphs-categorization huggingface dataset:
Genome size and heterozygosity estimation The final genome assembly after Hi-C scaffolding (481,507,213 bp) anchored 97. 2% sequences of the contig-level assembly (495,175,598 bp; Table  2 ). Some arrays of tandem repeats, including the rDNA (see below), were collapsed and chromosome termini were not fully assembled. Around 55% of the assembled genome was estimated to be repeat sequences (RepeatMasker; Table  2 ). The genome size was estimated as 563,295,571bp (highest 17-mer peak frequency), with slightly higher estimates made by findGSE software (588,939,614 bp). The genome size of E. glaucum is similar to that of the x=11 Musa species (see  [20] ) using sequencing methods, and to estimates of both genera by flow cytometry  [21]. The heterozygosity rate of E. glaucum was 0. 164% (Supplementary Fig.
5S and 45S rDNA and rRNA genes Tandem repeats of the rDNA were predominantly located within extended, complex, loci on chromosomes eg05 (5S rDNA) and eg06 (45S rDNA) (Figs The 5S rDNA monomer length of 1056bp was exceptionally long in comparison to any other plant species (typically 400-500 bp long). The first 400bp of the intergenic spacer had no significant BLAST hits in GenBank, while the second part showed only short regions with weak homology largely to chromosome assemblies of Musa species in GenBank. There were no motifs characteristic of retroelements in the 937bp intergenic spacer. It is unclear why the monomer length for the 5S rDNA in E. glaucum should be twice that typical in other species, including Musa, and was to be relatively homogeneous over all copies (Fig. 7E ). Furthermore, in contrast to the single locus on eg04 of E.
Sample collection and distribution The individual Ensete glaucum plant used for genome sequencing and analysis was collected from Puer city, Yunnan province, China and maintained in the South China Botanical Garden, Guangdong province, China (accession no. 19990288; Fig. 1A-E ). The distribution of Ensete and Musa species were identified in databases of Flora of China, South China Botanical Garden, iNaturalist, GBIF  [54]  (excluding cultivation sites) and regional distributions maps. Fig. 1F  was then made from POWO  [55]  (overlaid and color-adjusted in Adobe Photoshop CC2018).
Illumina sequencing A genomic DNA library with 400bp fragments was constructed using Truseq Nano DNA HT Sample preparation Kit (Illumina USA Preparation Kit (Illumina, USA), and 150bp paired ends were sequenced with Illumina Novaseq by Grandomics Research Services (previously known as Nextomics, Wuhan, PR China). After applying Trimmomatic v0. 36  [56]  to trim adaptors, filtering out low quality reads and further quality control with fastQC v0. 11. 9  [57] , 246 million paired reads and 36. 88Gb of data resulted (Table  1 ).
Oxford Nanopore (ONT) sequencing ONT (Oxford Nanopore, Oxford, UK) sequencing was performed by Grandomics Biosciences Co. , Ltd. (Wuhan, China): long fragments longer than 12 kb were selected with BluePippin (Sage Sciences), and the SQK-LSK109 kit (Oxford Nanopore) was used to build a library that was sequenced using PromethION. The base calling was performed with Guppy and reads mean_q score_template (Phred) > 7 (base call accuracy >80%) were selected. A total of 129 Gb ONT reads (~ 250X coverage) was generated. fastp v0. 19. 7  [58]  was used for quality control including adaptor-trimming, filtering reads with too many Ns or mean q score lower than 7 and resulted in remaining clean data of 109 Gb (Table  1 ). The mean read length was c. 20kb, with the longest >120kb (Supplementary Fig. S11 ).
Hi-C chromatin interaction data The Hi-C library was prepared followed by a procedure with an improved modification  [59]. Nuclear DNA from fresh leaves was first fixed and cross-linked in situ with formaldehyde  [60] , extracted, and digested by the restriction enzyme DpnII. The resulting sticky ends were biotinylated, diluted, and ligated. The biotinylated fragments which contained DNA of two physically interacting regions were used to make a paired-end library and sequenced with Illumina HiSeq platform (performed by Grandomix, loc. cit. ). Quality control of Hi-C raw data was performed using Hi-C-Pro v2. 8. 1 (HiC-Pro, RRID:SCR_017643): low-quality sequences (quality scores<20), adaptor sequences, and sequences shorter than 30 bp were filtered out using fastp v0. 19. 7  [58].
All rights reserved. No reuse allowed without permission. Ensete glaucum chromosome-scale genome assembly. Wang et al. Page 26 of 57. 1. 4, order min n res in trunk = 60, order min n res in shreds=60. Finally, placement and orientation errors exhibiting obvious discrete chromatin interaction patterns were manually adjusted. A Hi-C contact matrix plot (Supplementary Fig. S12 ) showed no discontinuities in the assembly. Validation of the assembly was performed using Benchmarking Universal Single-Copy Orthologs with (BUSCO, RRID:SCR_015008) v5  [18]  to assess the completeness and presence of 1614 genes in the embryophyta_odb10 database in "genome" mode (Supplementary Table  S3a ).
acuminata v2 were used as EST and protein evidence, respectively. We also utilized GeMoMa v2. 3 (GeMoMa, RRID:SCR_017646)  [79]  to perform homology-based gene prediction using Musa acuminata v2 [19] as reference annotated genome. EvidenceModeler (EvidenceModeler, RRID:SCR_014659)  [80]  was used to combine de novo and homology-based predictions and our transcriptome evidence to produce the final structural gene annotation. To annotate the function of predicted genes, we performed BLASTP (e-value = 1e-10) (BLASTP, RRID:SCR_001010) from the BLAST+ package  [81]  for each predicted coding sequence against the databases: UniProtKB/Swiss-Prot, UniProtKB/TrEMBL  [82]  and NR (non-redundant protein database at NCBI). These sequences are then processed to produce a non-identical (often referred to as pseudo non-redundant) prediction.
Transcription factors Protein coding gene sequences for E. glaucum and M. acuminata v2 were searched in PlantTFDB v5. 0 (PLANTTFDB, RRID:SCR_003362) and iTAK online v1. 6  [95]. Predicted transcription factors (TFs) were verified through a Hidden Markov Model (HMM) with PFAM searching tools using the cutoff E-value of 0. 01 (Fig. 3D  and Supplementary Table  S9 ). Genes were verified by PFAM (Pfam, RRID:SCR_004726), CDD (Conserved Domain Database, RRID:SCR_002077, and SMART (SMART, RRID:SCR_005026) databases.
Repetitive DNA identification and annotation For repetitive DNA analysis, publicly available programs (see below and  [36] ) as well as manual searches and sequence comparisons were applied. Geneious v. 10. 2. 6 (Geneious, RRID:SCR_010519) (Biomatters Ltd. , Auckland, New Zealand) was used to produce the dotplots of Figs 5A, B, 7E and 8B. In the assembly, repeated sequences were first searched with REPET v2. 5 pipeline  [100]. The top 100 repeated sequences were plotted on the four reference Musa genome assemblies (i. e. M. acuminata, M. balbisiana, M. schizocarpa and E. glaucum) using BlastAndDrawDensity. py script described in  [20]  and available on the Github repository  [101] , (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
Transposable Elements Transposable elements were annotated by EDTA pipeline  [102] , which integrates various software to discovers TE including: long terminal repeat (LTR) retrotransposons  [103] [104] [105] , terminal inverted repeat (TIR) transposons  [106] , short TIR transposons or miniature inverted transposable elements (MITEs)  [107] , and Helitrons  [108]. According to suggestions in  [109] , we also adopt RepeatModeler2 (RepeatModeler, RRID:SCR_015027) v2. 0. 1  [109]  to find remaining TEs. The TE-denovo procedure was used on masked assembly to produce a batch of 4229 TE consensus sequences. From these 2800 consensus sequences, only those with full length fragments present in the assembly were kept for further analysis, quantification and annotation with the TE-ANNOT procedure. A first annotation was performed using public Repbase (Repbase, RRID:SCR_021169) release 20.
05, followed by Gypsy/Copia retroelement family identification using Hidden Markov Models (hmmsearch version 3) to search consensus for corresponding retrotransposase PFAM domains PF04195 and PF14244 respectively. The above results were then combined and CD-HIT v4. 1. 8 (CD-HIT, RRID:SCR_007105)  [110]  was used to reduce redundancy. The LTR retrotransposons were sent to TEsorter  [111]  to classify into lineage level and RT domain amino acid sequences were extracted. Phylogenetic trees of Copia and Gypsy were inferred by RT domain alignment results (Supplementary Figure  S4 ). The proportions of transposons in the assembly are given in Table  2  (Supplementary Tables  S11  and S12 ) and chromosomal distributions in based on the divergence of of the 5' and 3' end LTRs, and these two LTRs of every LTR retrotransposons were extracted into separate files with a custom script.
The 5' and 3' LTRs were aligned by MUSCLE v3. 8. 1551  [112]. The divergence distances under K2P evolutionary model were calculated by R package ape v5. 4-1 (ape, RRID:SCR_017343). The average base substitution rate was selected to be 11. 3E-8  [113]. The insertion time T was calculated as T = K/(2r), with r as the rate of nucleotide substitution and K as the divergence distance between LTR pairs. Our script to perform the analysis is on github (2021)  [114].
Graph based clustering of reads using RepeatExplorer A sample of 2Gb of the Illumina HiSeq raw reads were used for assembly-free analysis by RepeatExplorer2  [37]. Graph-based clusters of similar sequence fragments were generated under default parameters. Clusters were assigned to repeat classes and retroelement lineages using the automated Repeat Masker and Domain hits provided by the program (Supplementary Table  S11 ). Pat Heslop-Harrison pers communication) were also analyzed (Supplementary Figure  S3 ) and compared with RepeatExplorer2 following "comparative repeat analysis" protocol. The results were visualized by R script "plot_comparative_clustering_summary. R" (Fig,  4A ).
Acknowledgments This work was technically supported by the high-performance cluster of the  UMR AGAP -CIRAD  of the  South Green Bioinformatics Platform  (http://www. southgreen. fr). Assistance and discussion with  Celia Hansen  and  Paulina Tomaszewska ,  University of Leicester , are acknowledged. We thank  Ye Yushi  for the assistance with growing and maintaining the plants. We thank the  International Musa Germplasm Transit Centre  (https://www. bioversityinternational. org/banana-genebank/) for samples of M. balbisiana.
Availability of Supporting Data and Materials Raw sequence reads (RNA-seq, Illumina HiSeq, the Oxford Nanopore and Hi-C) were deposited in the NCBI under accession number: PRJNA736572. In specifically, the Oxford Nanopore raw reads: SRR15039768 and SRR15039769; RNA-sequencing raw reads, as follows: leaf: SRR15039767, root: SRR15039766; genomic Illumina short-read data: SRR15039770; raw reads of the Hi-C library: SRR15039764 and SRR15039765. The raw reads data were also deposited in Genome Sequence Archive (GSA) of the China National Center for Bioinformation (accession code: CRA004283). The assembled genome was also deposited to GenBank in NCBI under the accession number: JAHSUZ000000000. Genome Assembly, gene and TE annotation data, transcriptomic data are also available on the Banana Genome Hub (http://banana-genomehub.
which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Ensete glaucum chromosome-scale genome assembly. Wang et al. Page 18 of 57. rDNA arrays. Garcia et al. [49]show the rather unusual and highly complex structure of 5S rDNA in M. acuminata using graph-based clusters of reads with multiple IGS and retroelement components, supporting the complexity reported here in the E. glaucum assembly. The multiple hybridization sites evident from the in situ hybridization site on one 2, 5C, 7, and 8). The 45S rDNA pair of chromosomes (Fig. 7B,C), with several, non-continuous, signals visible in the monomer containing the 18S rRNA gene -ITS1 -5. 8S rRNA gene -ITS2 -26S rRNA gene -extended prometaphase chromosomes (Fig. 7C, insets) support the non-continuous nature of NTS (GenBank: OL310719) was 9984 bp long, typical but slightly longer than other plant the 5S rDNA array.
species. The NTS region includes in most cases 16 copies of a degenerate 180bp tandem The 5S rDNA (GenBank: OL310718) comprised the 5S rRNA gene (119bp long, typical for all plants) and intergenic spacer (937bp), representing 0. 078% of the genome or approximately 366 copies, with a complete motif length of 1056bp (Supplementary Table S12). The 5S rDNA locus lies in the middle of the short arm of chromosome eg05, in three parts around 34. 5M, 37. 5M and 45. 5M with multiple interruptions. An example of insertion of a 4. 7kb LTR retrotransposon-related sequences in the 5S rDNA array of tandem repeats is [21]at. Based on occurrence in the unassembled Illumina reads, there were 587 copies of the 45S rDNA monomer (1. 21% of the genome, Tables 2 and Supplementary TableS12). Although in the whole genome assembly the rDNA array was collapsed, the strength of the in situ hybridization signal using the rDNA sequence from wheat (Figs7A,B) is consistent with representing 1% of the genome.
= --- To calculate this margin, we made the following choices: 1) We assumed that for all the viticultural systems, the yield fixed by the AOP 1 label was obtained; the performance of a viticultural system is assessed for "normal" climate conditions and "normal" biotic pressures: the aim was to compare the practices of the systems and not the profitability of the vineyards. 2) Given that the yield is fixed, we took into account a database reference of six fixed total revenue per hectare. The revenue amount depends on the practices carried out on the vine, like pruning or the removal of suckers from vinewood and of the cover crop in the inter-row. According to different information provided by winegrowers, the total revenue can range from 5400 euros/ha for basic systems to 8000 euros/ha for organic systems (Appendix 1).
Discussion Several multicriteria methods for decision aiding (MCDA) were explored, including the MASC and DEXiPM methods which could not be applied in this study. DEXiPM models (DEXi® software)  [25]  perform a qualitative hierarchical aggregation of the criteria based on decision trees. All the components of the hierarchical structure (called "attributes") are defined by qualitatively grouping the values (e. g. , high, medium and low). The aggregations are performed for each attribute with "utility functions" specified in tables completed with 'IF-THEN' aggregation rules  [25]. The DEXiPM model has been applied to viticulture and it proposes a range of criteria for the three dimensions of sustainability (environmental, economic and social)  [40]. This method could not be applied here as some criteria and indicators were difficult to evaluate in our study; for example, the criteria which are calculated from the description of the environment (soil and climate), and which must be estimated on a field scale.
In addition, the application of low doses of copper within short intervals can improve pest control and reduce yield losses; this would require the winegrower to monitor the growth and health of the vine in order to regulate the copper dosage. Given that the yield is fixed, we used a database reference of six fixed total revenues per hectare. Each viticultural system was linked to one total revenue reference when the crop practices were the same in all systems, or to more than one total revenue reference weighted by the treated surface when the crop practices were heterogeneous. A significant increase in organic production in the future could entail a reduction in gross product per ha; however, because organic wine producers often market their own wine themselves, such a drop would be mitigated as a result of higher supply.
Acknowledgements We warmly acknowledge all the partners in this study: the winery of Tutiac, the wine trade union of the independent winegrowers, all the winegrowers,  Delphine & Benoit Vinet  of the  Domaine Emile Grelier  for imparting their experience in agroecology, the  Interprofessional Council of Bordeaux Wines (CIVB) , the  Gironde Chamber of Agriculture , the  French Institute for Vine and Wine (IFV) , the local authorities along the Gironde estuary, and the  Val-de-Livenne local authority. We would like to thank  Adeline Ugaglia  ( Bordeaux Sciences Agro ) for her valuable and helpful comments, and  Kevin Petit  ( INRAE ) for his help in the field surveys. We are also grateful to  Stephanie Hayes  ( Hayes4Com ) for copyediting the text.
Material and methods The material has been preserved in 75% ethanol. A Nexius-Z stereo microscope (Euromex) was used for the dissection of the appendages. The sexual appendages, pereopods, pleopods and antennae, have been temporarily mounted in glycerine for microscopic study and, later, preserved in microvials with ethanol. The mouthparts and tergites have been treated with Amman's lactophenol and mounted using Faure's liquor. The drawings were made using a camera lucida attached on an Olympus CH30 biological microscope. Photographs of the complete animals were taken using a digital microscope (Dino-Lite) and the main measurements have been taken with the associated software (Dino-capture 2. 0). Some of the photographs have been stacked using the free software Combine ZP. The final drawings were also prepared using the GIMP2 software  (Montesanto, 2015)  and the additional use of an Intuos drawing tablet (Wacom).
Genome assembly and annotation The read quality was checked with FastQC (Andrews 2010) and adapters were removed using Trimmomatic  (Bolger et al. 2014). The trimmed reads were mapped against the reference mitogenome of H. quadripunctatus (accession number KU739489) using BWA software and its bwa-mem algorithm  (Li and Durbin 2009). This allowed us to assemble ~85% of H. sicardi mitogenome (accession number: MW759025) used in the downstream analyses. The assembled mitogenome was annotated in Geneious using the reference mitogenome of H. quadripunctatus  (Olivier, 1789).
Molecular dataset The ingroup consisted of 44 operational taxonomic units (OTUs) belonging to ~30 species of Helictopleurus; two H. sicardi OTUs were used, the new one and the one from previous phylogenetic study  (Wirta et al. , 2008). The outgroup included nine species from various Afrotropical and Oriental lineages of Oniticellini. The dataset comprised 13 protein-coding and two rRNA genes (16S and 12S) from mitogenome, and two nuclear rRNA genes (18S and 28S). Thus, our molecular dataset included novel sequences for H. sicardi, as well as GenBank data for Helictopleurus and Oniticellini from mitogenomic  (Breeschoten et al. 2016 ) and individual genes  (Wirta et al. 2008; Monaghan et al. 2009 ; see Suppl. material 1) phylogenetic studies. The dataset was compiled using phylotaR  (Bennett et al.
Acknowledgements We are thankful to  Gunilla Ståhls-Mäkelä  for DNA extraction of H. sicardi, and to  Alexey Solodovnikov  ( Natural History Museum of Denmark ) and  Victoria Twort  ( Finnish Museum of Natural History, LUOMUS ) for their valuable advices. Tiana Vololontiana  (Antananarivo, Madagascar) facilitated Madagascar fieldwork ( 249/18/ MEEF/SG/DGF/DSAP/SCB ) resulting in discovery of the horned male of Helictopleurus sicardi. Open access funded by  Helsinki University Library. This study was supported by the  Pentti Tuomikoski Fund  and the  Academy of Finland  Grant (# 331631 ), awarded to ST.
Acknowledgements The experimentation was funded by the  CLD National III , research program  INSSICCA PITE  and the  MESRI (Ministère de l'Enseignement supérieur, de la Recherche et de l'Innovation, France). The authors thank  Claire Collas ,  Matthieu Delannoy ,  Frédéric Desor ,  Hervé Toussaint ,  Stefan Jurjanz ,  Marion Huguet ,  Claire Soligot ,  Julie Peiffer ,  Damien Banas  and  Christine Grandclaudon  ( UR AFPA ) for their contribution. They warmely thank  Pamela Hartmeyer  ( UR AFPA ) for her support during the experiments and  Catherine Adam  ( LEAE-CART ) for serum analysis.
One particularly interesting extension of the DEB theory, the Dynamic Isotope Budget (DIB) model  (Pecquerie et al. , 2010)  was developed to study the fluxes of C, N, H and O isotopes within organisms. DIB models are used to analyse the composition in stable isotopes (13C and 15N), which reflects species trophic position in food webs. The approach, which was applied to 13C and 15N in the pacific oyster Crassosteas gigas only  (Emmery et al. , 2011) , might be highly useful to predict 14C transfer in aquatic organisms. The approach requires adequate experimental data which are too scarce in the literature. In this context, the present study aims to investigate direct and trophic 14C transfer in the common carp Cyprinus carpio, as a representative species inhabiting French rivers. Furthermore, accumulation and elimination kinetics might vary depending on the biochemical form of 14C and this hypothesis is tested using various 14C sources, including arginine (an essential amino acid for carps) and glucose (an important source of energy in a majority of animal species)  (Bouche & Vellas, 1975; Murai et al.
Mortality might also be considered when C turnover was addressed at the population level. In practice, authors acknowledged that a precise quantification of ingestion, digestion, assimilation and turnover rates were not easy for wild fish and was complicated by the diversity of their trophic positions in natural food webs. As a consequence, model parameterization relied most often on indirect estimation methods. In  Smith, (2006) , a generic value of assimilation efficiency was estimated for stable carbon using data on growth rates in Brown trout Salmo trutta  (Elliott, 1975) , assuming that equilibrium among biotic compartments was reached. Long term turnover rates were addressed in a natural lake, by analysing changes in 14C activities over several years  (Stephenson et al. , 1994) , showing that specific activity in fish was much higher than that measured in their food items at the time of sampling.
Identification of the crayfish innate immunity genes and taxonomical distribution of transcripts We retrieved a dataset of innate immunity related genes identified in Malacostraca by  Lai and Aboobaker [35]. This dataset was expanded with the selected differentially expressed genes (DEGs) identified in the Hap B challenged noble crayfish. Furthermore, we included the genes specifically related to the proPO cascade. The complete list of used innate immunity genes and their respective sequences are available in the Table  S1  and File S1. Transcriptome assemblies were queried against the subset of innate immunity related genes with BLASTn and BLASTx 2. 10. 1+. Hits were then inspected, their function was confirmed based on their e-value (lower than 1e-10), and the presence of the functionally important gene domains identified with a Pfam search.
The taxonomical distribution of the reads was reconstructed by conducting a DIAMOND 2. 0. 4  [36]  search against the NCBI non-redundant protein database which contains sequences form GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSeq (sensitive mode, e-value≤1e-25). A single best BLAST hit was considered. The hierarchical distribution of BLASTx hit counts was further explored using interactive Krona 2. 7. 1  [37].