dataesr/scientific-paragraphs-categorization huggingface dataset:
Full genome sequencing of a new Filamentovirus in the wasp L. heterotoma In the parasitic wasp L. heterotoma, a preliminary analysis of the metagenomic dataset revealed the presence of a set of 12 contigs related to the behaviour manipulating virus LbFV (25 to 48% identity at the protein level). Because LbFV is most likely the unique member of a new dsDNA viral family  [37] , and because of the originality of the phenotype affected by the virus (superparasitism behavior), we sought to obtain the complete genome sequence of this virus. To this end, we sequenced (without the WGA step), one of the samples positive for these 12 contigs (sample 43, Igé, Sept. 2012) using Illumina technology. The library construction and sequencing was done by MACROGEN company using the protocol for low-input material (Truseq Nano DNA library).
51 million of paired-end reads (150bp) of high quality (96. 5 had a Phred-like score above 20) were obtained. After deduplication using fastuniq, reads were mapped to a database containing the genomic sequence of L. heterotoma and other insects of the community (L. boulardi, D. melanogaster, D. simulans, D. subobscura, D. hydei, D. immmigrans, D. obscura and D. suzukii) using hisat2, keeping only unmapped reads for the next step. After quality trimming using trimmomatic (v. 0. 38, parameters: LEADING:10 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:36), one sixth of the filtered dataset (i. e. N=8555009 paired-end reads) were assembled using MEGAHIT v1. 2. 9 (default parameters), ensuring around 1000x coverage on LhFV genome.
Inferring viral presence in each sample and each library type (wga/wta) To quantify virus presence in each sample, a unique database on which reads could be mapped was required. To produce this database, we assembled the reads obtained from all WGA libraries on one side and all WTA librairies on the other side using MEGAHIT v1. 2. 9 (default parameters). During the preliminary analysis, we realized that WGA and WTA datasets were associated with large variation in coverage. Other experiments in the lab suggested that small quantities of DNA was sufficient to produce good quality Illumina sequences. Thus, we decided to directly construct a unique illumina library containing the pooled sample of all the purified nucleic acids obtained from all samples (except sample 43 used for LhFV sequencing) together with the product of their reverse transcription, without any amplification (neither WGA, nor WTA).
This metagenomic sample (DNA/RNA) library was sequenced by MACROGEN company on an HiC machine and produced 211M high quality reads (96% with Phred-like score >20). After deduplication, host decontamination (mapping reads on the insect database as done for LhFV), and quality trimming, 192M reads were assembled using MEGAHIT using default parameters. Finally, the four assemblies obtained from the different analysis (wga, wta, metagenomic, LhFV) were merged using flye (with the -subassemblies option) in order to obtain a comprehensive view of the virome. This raw database contained 19604 contigs. Taxonomic assignation was performed by using the first hit of a mmseqs analysis performed on a local version of the refseq protein virus database augmented with additional virus proteins available in ncbi by querying "(virus[Title]) AND Drosophila " (2764 sequences), proteins from a few insect genomes (Drosophila melanogaster, D.
simulans, D. subobscura, D. obscura, D suzukii, Apis mellifera, Nasonia vitripennis), and proteins from some bacteria and human (downloaded on the 12th may 2021, evalue threshold = 0. 001). The reads from each individual sample obtained after either whole transcriptome (with reverse transcription) or whole genome (without reverse transcription) amplification (WTA/WGA) were then mapped individually against this common database. Contig coverage and contig average sequencing depth were then calculated using samtools, and used to infer viral presence in each sample. 1358 and 281 contigs were respectively covered by the reads produced from at least one sample of, respectively, the wga and the wta datasets (a coverage threshold of 25% was used). After filtering out sequences assigned to non viral entities, or assigned to phages, transposons, polydnaviruses, to RNA viruses in the wga libraries or to DNA viruses in the wta libraries (since they are not expected there), while keeping unassigned contigs with high coding density (>50%, as expected for viral genomes), this led finally to 47 putative contigs for the WGA dataset and 192 for the WTA dataset.
Grouping contigs into putative viral genomes We have tried to group contigs into single putative viral genomes for several reasons. Firstly, many viruses have a segmented genomic structure, which obviously necessitates clustering. In addition, we expected that at least some of the viruses present in our dataset would be poorly covered due to their low prevalence and/or low density in insects. This could lead to fragmented assemblages. To reach this goal, we used both phylogenetic information (contigs assigned to similar viruses are more likely to correspond to the same virus) and contig co-occurrence in insect samples (contigs that are always associated in the same samples are more likely to be part of the same virus). This grouping was done by eye inspection of the contigs heatmaps obtained after clustering contigs based on their co-occurrence in samples (fig.
DNA viruses Seven DNA viruses were identified in this host-parasitoid community (Fig. 5 ). From our previous work, we expected the presence of the maternally inherited DNA virus LbFV in the wasp Leptopilina boulardi. This virus induces a behaviour manipulation on infected females by increasing their propensity to superparasitize, i. e. lay eggs in already parasitized larvae. Since superparasitism conditions permits the horizontal transmission of the virus between parasitoid lineages  [14] , the virus reaches high prevalence in wasp populations  [26]. As. expected, we found LbFV in all five L. boulardi samples encompassing the two sampling years, the two locations and the two seasons (fig. S2 ). Because our dataset is only composed of Illumina short-read sequences, the virus was split in 10 contigs due to the presence of repeated regions (hrs) in the genome of LbFV  [37].
The total length of the LbFV-contigs obtained from this study was 105096bp which is very close to the expected size of the genome (111. 5Kb). The percent identity with LbFV proteins was, as expected, close to 100%. This virus was exclusively found in L. boulardi, thus confirming its specificity  [17]. Interestingly, in two samples of the related parasitoid L. heterotoma, we found a set of 12 contigs related to LbFV (25 to 48% identity at the protein level, see fig. S2 ). Surprisingly, most of these contigs also had high nucleotidic similarity (97. 98%) with a virus recently discovered from a sample of pool-sequenced wild D. melanogaster, sampled in Spain (so-called Drosophila melanogaster Filamentous Virus,  [38] ). Our dataset revealed 1444 reads that mapped uniquely to these 12 contigs. Among them 1431 (99.
With this additional dataset, we obtained 12 contigs. Sequencing depth for the 9 large contigs was homogeneous and high (mean=1181x, min=1148x, max=1302x), whereas the three small contigs ("contig_19696" "contig_19153" "contig_21206") had lower sequencing depth (mean=143. 32x , min=45. 35x, max=230. 27x). In total the 12 contigs contained 107350bp, which is very similar to the genome size of its closest relative LbFV (111. 5Kb). Our automatic pipeline predicted 105 ORFs (see suppl. file S1) which is also close to the number of proteins encoded in LbFV (n=108). Altogether, these data suggest that the 12 contigs contained the whole genome sequence of a virus infecting L. heterotoma that we propose to name LhFV instead of DmFV. A detailed description of this virus and other LbFV-related viruses will be given elsewhere (  [29] ).
We found two related viruses belonging to the Parvoviridae family in two Drosophila species. One of them, here denominated Vesantovirus_D. mel, was found in a D. melanogaster sample and was almost identical to the Vesanto virus discovered by  [38]  in the same species (Fig. S2 ). It was composed of 11 segments, 10 of which had high sequence homology with the Vesanto virus previously detected by  [38]. Additionally, contig_8677 which showed strict association with the 10 other segments was most likely an additional segment of this Vesanto virus but without homology in public databases. This 1. 8kb segment had high coding density as is Another Parvoviridae, referred to here as Parvoviridae_Pachy, was also detected in two samples of Pachycrepoideux dubius (Fig. S2 ). The corresponding contig is 5kb long which fits well with the expected genome size of related densovirus  [40].
RNA viruses Because the dataset for RNA viruses was large, we choose to describe them by modules of viruses showing similar distribution among insect species. These modules were defined by the unsupervised clustering analysis and are indicated by a number in fig. 5. Eleven such modules were identified this way. The dynamics of a virus included in a module was mainly driven by a single insect species (that produced the great majority of reads), although other species may sill present signs of infection (fig. S4 ). Drosophilid viruses are discussed first, followed by parasitoid viruses. The viruses not included in any cluster are presented in the last part.
Module 5 : viruses mainly driven by D. suzukii Two RNA viruses composed this module. La Jolla virus was already described by  [44]  and  [20]. It is very prevalent in D. melanogaster, also found in D. simulans and D. suzukii  [20, 44]. In our dataset, signs of infection We obtained two contigs (8247bp and 1422bp) of a virus distantly related (appr. 40% amino acid identity) to the Saiwaicho virus, that we refer to as Hepe-Virga_L. b. Saiwaicho virus was detected in wild collected D. suzukii  [20]. Its expected size is around 10kb, suggesting that we obtained the complete or almost complete sequence, despite being split in two parts. Similarly to what they found, the polyprotein encoded by con-tig_22560 contains the following domains: methyltransferase, Ftsj-like methyl transferase, helicase and RdRp.
Module 3 : viruses mainly driven by L. heterotoma This module contained six RNA viruses. Two contigs (respectively 1127 and 1142bp long) showing similarity (approx. 40%) with Formica exsecta virus were detected (here called Iflaviridae_L. h). Formica exsecta virus has a 9160bp genome encoding a polyprotein  [49]. The genome we got here is thus probably incomplete. In the absence of RdRp in our dataset, we built a phylogeny based on the capsid domain (Fig. S13 ) which further confirmed the phylogenetic proximity of this virus with Formica exsecta virus and other Iflaviridae, including Deformed wing virus and Varroa destructor virus 1. We detected a 1557bp contig showing similarities with Takaungu virus (32%). This virus was first detected in D. melanogaster samples  [45]. This virus is poorly known and belongs to unclassified Flaviviridae.
No phylogeny was built since our pipeline detected homology with only one sequence. We named Phasmaviridae_L. h a partial genomic sequence related to Ganda bee virus (protein identity of 44% posed by (((repleta+virilis)+grimshawi)+immigrans). In addition, the basal species Scaptodrosophila lebanoni is detected in both subclades in basal position as could be expected. Most of this gene tree topology may be the explained by an ancestral endogenization that would have occurred before the diversification of these species, followed by a single duplication event and losses in lineages that do not nowadays encode this gene. This host integration event was previously identified by Ballinger et al. [50]. Their detailed analysis suggested that this gene has been coopted in Drosophila genomes. Our analysis, based on a more recent database further extends the diversity of species concerned by this event as it now includes the basal species Scaptodrosophila lebanoni.
Clearly, this result deserves further investigation in order to clarify the evolutionary history of this virally-derived gene and test its potential phenotypic effect on Drosophila sp. A virus related to Wuhan insect virus 15 was part of this module (here called Qinviridae_L. h). A single 5. 5kb contig was found, where we expect a bisegmented genome (one 1601bp segment encoding an hypothetical protein and the other is 5889 bp long and encodes the RdRp). Nevertheless, it contains a full length RdRp protein from which we constructed a phylogeny (fig. S11 ) indicating that this virus probably belongs to the family Qinviridae  [6]. We found a 1894bp contig with 93% identify with the Hermitage virus (here called Hermitage_L. h). Hermitage virus was first described in  Webster et al. 2016. No phylogeny was built since our pipeline detected a single homologous sequence in the database.
A putative Kwi virus, here named Quenyavirus_L. h, composed of 11 contigs was also detected. Among them, 3 contigs have no homology with known sequence in public database but, it was considered that they belong to this genome because of their co-occurrence with the other contigs (see fig. S3 ) and that they do contain an ORF covering most of the contig. Kwi virus has been described by  [51]  by analyzing "dark matter" obtained from a previous study. Their genome is expected to be composed of 5 segments approximately 2kb each. We think that several variants are present in our dataset, as some of these contigs appear to be homologous (contig_8520 and contig_9238; contig_9023 and contig_13838; contig_10017 and contig_19523). Both variants appear to be present at Ige in June 2012, whereas only one was present at the same location in 2011; the other variant is the unique we found at Gotheron in 2012.
Circulifer tenelus virus and Spissistilus festinus virus were isolated from threecornered alfalfa hopper (Spissistilus festinus) and beet leafhopper (Circulifer tenellus), two plant-feeding hemipteran insect pests. The taxonomic assignment of these viruses is unclear but they show proximity with Chrysoviridae and Totiviridae. Ten contigs were considered as composing a new Reovirus genome totalizing 23900bp (named Reoviri-dae2 Tricho). Among them, seven showed clear signs of homology with reoviruses (30% protein identity) and four contigs without homology in our initial analysis did show a perfect association with them (see fig. S3 ). In a subsequent analysis using an updated nr databases, three of them revealed homology with reoviruses (blastx): contig_9440 shows very weak similarity with Zoersel tick virus (VP7, QYV43125.
In our dataset, it is unclear whether the three contigs belong to the same virus or if only one of the two contigs encoding the "hypothetical protein" does. We built a phylogeny based on RdRP (fig. S24 ) that confirmed the proximity with Wuhan insect virus 22, Galbut virus and other Partitiviridae such as Vera virus. We refer to this virus as Partiti-like4_Tricho. Six contigs were considered to be part of a single incomplete Phasmaviridae related to Ganda bee virus (Phasmaviridae_Tricho). Four of the contigs encode parts of an RdRp suggesting either that several viruses are present or that the assembly is fragmented. After inspection of the blast results, it was clear that the assembly is incomplete leading to a fragmented Ganda-like RdRp. We artificially fused the 4 parts of the RdRp (order is : contig_10992, contig_10108, contig_10707 and contig_17877) which covered most of the the related RdRp protein (from positions 57 to 1958, out of 2087 amino acids for YP_009666981.
1, 1458aa long): contig_12726 covers amino acids from position 50 to 433, contig_18151 covers from position 407 to 781 and contig_8245 covers amino acids from position 870 to 1386. We merged these three parts of the RdRp to build a phylogeny which further suggests this is a reovirus related to Rice Gall Dwarf virus (fig. S18 ). A chuvirus, composed of 4 contigs, was identified (Chuviridae4_Tricho). The majority of the RdRp of the closest relative (Hubei chuvirus-like virus 1, 2172 aa long, YP_009337904. 1) is covered, but is split between two contigs : contig_22765 covers protein from 201 to 1698 and contig_13828_62_1273_-covers from 1791 to 2158. Hubei chuvirus-like virus 1 is composed of two segments 6873bp and 3958bp. The P-protein seems to be lacking in our dataset, indicating that this is a partial genome.
The phylogeny built on RdRp shows that this virus together with Wuhan cricket virus 2, Wuhan millipede virus 4 and Wuhan tetragnatha maxillosa virus 8 do form a monophyletic clade, related to Partitiviridae (fig. S24 ). Viruses not included in modules Four putative viruses, three of them being RNA viruses, were not included in any module since they had a more diffuse distribution among insects. A 1044bp contig (contig_20830) without homology with public databases in our initial analysis, was considered as a viral candidate (here denominated Dark1). This was motivated by the fact it encodes a large ORF (suppl. file S1). This interpretation was validated by a less stringent analysis revealing a low sequence similarity with an hypothetical protein from a Diaphorina citri cimodo-like virus (QXG83187.
Discussion Using a protocol designed to identify both RNA and DNA viruses, our analysis uncovered a rich community of heritable viruses in this interacting community of insects. As most studies generally focus on (or enrich for) viruses of one of the two types (RNA or DNA), neglecting the other, we believe this dataset is quite unique, giving an unbiased view of the virome in this insect community. Of the 53 viruses detected, the vast majority (45) had a genome composed of RNA. This result is in line with the diversity deposited in the public databases  [11, 56] , reinforcing the conventional wisdom that RNA viruses dominate the eukaryotic virus community  [56]. Current knowledge about what factors shape viral communities in animals is still very limited, despite its importance in the context of sanitary vigilance required by certain systems.
Acknowledgements We are indebted to  Ms Weistroffer  ( Igé ) and the  INRAE station of Gotheron  for allowing us to collect the insects in their garden/orchards. The bioinformatic work was performed using the computing facilities of the CC LBBE/PRABI. The sequencing has been performed on the ProfileExpert platform of the  University Lyon  1. This work is dedicated to  Roland Allemand , who left us too soon.
RNA viruses found in the Drosophila/parasitoid community. Numbers indicated next to each virus name (n) indicates the number of contigs assigned to the virus. The percentage indicates the average percentage of identity with the closest proteins available in public databases. Total contig size is indicated next to % identity. season year location Figure 2. LbTV_Lb n=1 100% 7844bp species Hepe-Virga_L. b n=2 44% 9669bp Galbut_virus_D. mel n=13 97% 19384bp Galbut_virus_D. sim n=5 92% 6825bp Muthill_virus_D. im n=1 99% 10490bp Dark1 n=1 NaN% 1044bp Virga_Tricho n=1 24% 10210bp Partiti-like4_Tricho n=3 42% 5707bp Chuviridae4_Tricho n=4 37% 9737bp Rhabdoviridae1_Tricho n=5 60% 10009bp dsRNA_virus1_Tricho n=1 36% 7315bp contig coverage season season Reoviridae2_Tricho n=10 30% 23900bp 1 1 June June Reoviridae5_Tricho n=22 29% 34344bp 0.
ORF prediction for Reoviridae3_L. sp. Contig_17745 did not show sequence homology with public databases, but was associated with the other contigs, suggesting it is part of this virus genome. Phylogeny of two new Phasmaviridae detected in L. heterotoma and Trichopria sp. and evidence for horizontal transfers to various insects, including numerous Drosophila species. The nucleoprotein was used to build this phylogeny. Phylogeny of virus closely related to Motts Mill virus (Motts_Mill_virus_D. sub) detected in D. subobscura and possibly D. obscura based on putative viral coat protein. Phylogeny of the Reoviridae detected in this study based on RdRp. 0. 91 0. 4 0. 85 0. 86 0. 88 0. 89 0. 92 1. 00 1. 00 0. 87 0. 98 contig_2320_1853_2266_+Parvoviridae_Pachy 0. 98 1. 00 1. 00 1. 00 0. 85 1. 00 0.
ACKNOWLEDGEMENTS This work is supported by a grant from  INRAE (Animal Health Division)  and the  French Region Pays de la Loire. We are grateful to the  INRAE MIGALE bioinformatics facility  (MIGALE, INRAE, 2020. Migale bioinformatics Facility, DOI: 10. 15454/1. 5572390655343293E12 ) for providing computing resources.
Acknowledgements We are grateful to all the members of the RIMEL network whose shared thinking made the design of this study possible. We thank the staff of the poultry alternative breeding experimental unit (EASM, INRAE, 17700 Surgères, France, DOI:  10. 15454/1. 5572418326133655E12 )for the development of the experimental set-up and the conduct of the experimentation. We are very grateful to the staff of the  MOQA team (INRAE, 37380 Nouzilly, France)  for their help during the experimentation. The manuscript has been professionally proofread.
Clusters present in less than 4 samples, and having a minimum abundance of 0. 005% are removed. After this step, 261 clusters have remained with 6716271 sequences. The PhiX database was used to removed contaminants such as chloroplasmic or mitochondrial sequences  (Mukherjee et al. , 2015). Then, taxonomic affiliations are carried out for each OTUs (Operational Taxonomic Unit), using the silva138. 1 pintail100 16S reference database ("https://www. arb-silva. de/documentation/release-138/," n. d. ). However, some multi-affiliations can be generated when a cluster is composed by several amplicons with not the exact same nucleotide sequence.
Statistical analysis Zootechnical parameters, including initial and final body weight, specific growth rate, feed intake, feed efficiency, and protein retention efficiency were calculated per tank (n=3). The hepatosomatic index (liver weight*100/fish weight) were obtained during the final sampling of the trial experimentation (n=12). All data were presented as mean ± SEM. All statistical analysis were performed with R software (version 4. 0. 3). Data were tested for normally distribution using the Shapiro-Wilk test and homogeneity of variance using the Bartlett's test. All Data were analyzed using the one-way ANOVA. These statistical tests were followed by Tukey's HSD as post hos test when the normal distribution is respected, otherwise a Wilcoxon non-parametric test is carried out. Results with a P-value ˂ 0.
05 were considered statistically significant. In the figures: *, P < 0. 05; **, P < 0. 01; ***, P < 0. 001. The microbial composition was analyzed using the phyloseq package. For alpha and beta diversity, data samples were rarified. Beta-diversity was analyzed with the Bray-Curtis distance using permutational multivariate analysis of variance (PERMANOVA). The mixOmics package was used to perform a Partial Least Square Discriminant Analysis (PLS-DA) to determine the most discriminant OTUs. The rCCA (regularized canonical correlation analysis) function of the same package was used to understand the correlations between the bacterial OTUs and different host parameters. The core microbiota visualization was made using the phyloseq package on R and the Venn diagram using a website.
, 2023; Rasmussen et al. , 2021). In the last version of silva database (n°138. 1) used in this study ("https://www. arbsilva. de/documentation/release-138/," n. d. ), Mycoplasma is now part of the Bacilli class explaining the high abundance of Firmicutes in mucosa associated microbiota. The mucosa associated microbiota in salmonids is well known to be dominated by Mycoplasma, a potential intracellular bacterium  (Cheaib et al. , 2021). Previous studies have shown a lack of pathogenicity genes in Mycoplasma strains identified in salmon suggesting a symbiotic relationship by enhancing host defense  (Bozzi et al. , 2021; Lian et al. , 2020)  and providing biotin in a nutrient poor environment  (Lian et al. , 2020). Ralstonia is already described in high abundance in the gut of marine fish  (Huang et al.