dataesr/scientific-paragraphs-categorization huggingface dataset:
Data analysis. Generalized linear mixed-effects models (GLMMs) were computed using RStudio (version 1. 2. 5033) to explore the effects of management type and vegetation characteristics on different response variables (arthropod abundance in pitfall and sticky traps) (package glmmTMB, nbinom2 family for zero-inflated matrix). Arthropod abundance in pitfall and sticky traps were modelled separately. Vineyard (and sampling period only for pitfall traps) was included as random factor. We modelled separately the effects of inter-row management and vegetation. These two approaches are complementary: models testing the effect of the inter-row management provide information on the effect of the soil management at the vineyard level whereas models testing the effect of vegetation variables provide information on biotic interactions between arthropods and vegetation at a local scale within vineyards.
We modelled the abundance of each arthropod group (beetles, spiders, hemipteran, harvestmen, bees, lacewings) in pitfall and sticky traps according to inter-row management (as a categorical variable) and vegetation variables separately using GLMMs with a negative binomial distribution since these count data were generally overdispersed. We then specifically modelled the abundance of beetles per diet and trap according to inter-row management and vegetation variables. Inter-row management was further tested using the Tukey's post-hoc test (lsmeans package). The following variables describing the vegetation structure and community were fitted to the model: (i) vegetation cover, (ii) species richness, (iii) cover of nectariferous flowering plants, (iv) cover of Poaceae species, (v) cover of Fabaceae, (vi) perennial to annual species ratio, and (vii) within vineyard beta diversity calculated using the Bray-Curtis dissimilarity index (R package vegdist) for all pairs of quadrats within vineyards.
All vegetation variables (except vii) were recorded at the quadrat level. A stepwise selection procedure using the dredge function was employed to select the most parsimonious model. We also performed a path analysis (PA) to evaluate the effect of soil management on vegetation parameters and biotic relationships in both ground and canopy components (R package lavaan  31  ). Path analysis is a specific structural equation modelling (SEM) tool to disentangle relationships between several observed variables  32. Based on prior knowledge, we developed a conceptual model based upon expected ecological interactions. We assessed the relationships between soil management, the seven vegetation variables (see above), canopy-dwelling arthropods (Hemiptera, wild bees, lacewings, predatory and phytophagous beetles) and ground-dwelling arthropods (spiders, harvestmen, Hemiptera, and phytophagous, detritivorous, omnivorous and predatory beetles).
Invertebrates are known to be sensitive to climatic conditions, that change their abundance from year to year  53. This is particularly true in years of extreme drought and heat that are often associated with lower arthropod abundances. In the short term, such variability may mask the effects of agricultural practices, but major changes such as year-round tillage 1 or pesticide use  54  , seem be more important in explaining long-term changes in arthropod abundance. Spring 2018 was relatively wet with a peak in temperature and dryness at the end of June when sampling was already completed. Therefore, although we recorded data for one year, the cascading effects of inter-row management we recorded are strong enough to suggest consistency over multiple years despite inter-annual climatic variations.
Statistical analyses The data were analysed using the MIXED procedure of the SAS 9. 4 software package (SAS Institute Inc. , Cary, NC). SCC was log10-transformed to achieve normal distribution. Individualscow or calf -were considered as statistical unit and used in the models as random factors. For milk yield, milk composition, cow BW and BCS, the model took into account the effects of practice (Control-group and two CCC groups in Trial 1; Control-group and one CCC group in Trial 2), week of lactation (repeated factor, for milk yield and milk composition only), breed (Ho or Mo), parity (primiparous or multiparous) and interactions group Â week, group Â breed and group Â parity as fixed factors. Date of calving and initial values at calving (milk yield index, fat content index, protein content index, and BCS) were used as covariates.
Financial support statement This study was part of the  EU  project  ProYoungStock  funded by  CORE organic. This research was supported by  French government IDEX-ISITE  initiative  16-IDEX-0001  ( CAP 20-25 ). Trial 1 was partly funded by the  PHASE Research Division of INRAE. A. Nicolao  received a doctoral fellowship from the  Fondazione Cariparo at University of Padova (Italy).
HIM-mediated integrations of polydnavirus DNA circles in multiple lepidopteran genomes This analysis together with that of  Wang et al. (2021)  on DsIV, that of  Wang et al. (2021)  on CvBV and our earlier study on CtBV  (Muller et al. 2021)  shows that PDV circles undergo massive HIM-mediated chromosomal integration in host tissues during parasitism. We thus sought to assess whether horizontal transfer of PDV circles occurred from wasp to lepidopterans through HIM-mediated chromosomal integration in the germline of lepidopteran hosts, followed by vertical transmission in host populations. For this, we used HIM-containing HdIV and CtBV circles to perform blastn similarity searches on 775 lepidopteran genomes available in Genbank as of December 2021. Our search yielded 4,648 and 49,079 lepidopteran sequences longer than 300 bp that showed similarity to HIM-containing HdIV and CtBV circles, respectively, with an e-value lower than 0.
Our blastn searches did not allow us to directly retrieve full length PDV circles bordered by J1 on one side and J2 on the other side. This may be because integrations are ancient and were followed by rearrangements and/or degradation of the circles. Another reason behind the fragmentary nature of the blastn hits may be that the donor wasp species was distantly related to H. didymator or C. typhae. While complete, circles from such distant species may be too divergent to align over their entire length with no interruption to those of H. didymator or C. typhae. Importantly, we manually curated several lepidopteran PDV sequences and were able to reconstruct several examples of full-length integrated circles bordered by J1 and J2 (Supplementary Dataset 1). In the following, we refer to fragments of IV or BV sequences as retrieved by our blastn search, i.
1% nucleotide identity between C. nemesis and C. virginiensis and the split between the two species has been dated at 4. 9 MYA (Table  2 , Supplementary Dataset 3)  (Cong et al. 2017). By contrast, all other cases involve species for which divergence time is unknown but is likely recent because the species are congeneric and/or nucleotide identity between orthologous fragments is high (from 90. 9 to 99. 3%; mean = 96. 6%). Regarding IV orthologous fragments, two are shared between four very closely related species of metalmark butterflies (genus Apodemia, Riodiniidae)  (Zhang et al. 2019) , one of them is shared between the green-veined white (Pieris napi, Pieridae) and its close relative P. macdunnoughi  (Chew and Watt 2006)  and another one is shared between the European corn borer (Ostrinia nubilalis, Crambidae) and the Asian corn borer (O.
furnacalis), which diverged recently (Table  2 ; Supplementary Dataset 3)  (Bourguet et al. 2014). In terms of BV orthologous fragments, three are shared between C. nemesis and C. perditalis metalmark butterflies, one is shared between two species of firetips (Oxynetra hopfferi and O. stangelandi) and one is shared between Emesis lupina and E. tegula (Table  2 ; Supplementary Dataset 4)  (Cong et al. 2017). In addition to orthologous fragments shared between species, we found several paralogous IV fragments sharing the same immediate flanking region genome (Supplementary Table  5 ; Supplementary Dataset 5). Numbers of such paralogous fragments vary from two in the Kamehameha butterfly Vanessa tameamea, (Nymphalidae) to 83 in the wainscot hooktip Y. scabrella (Ypsolophidae), with a maximum of three sequences in a given paralogous group (Supplementary Table  5 ).
Characterizing integrations of wasp ichnovirus DNA circles in somatic host genomes To identify integrations of HdIV DNA circles in the S. frugiperda somatic genomes, we searched for chimeric reads, i. e. , reads for which a portion aligns exclusively on HdIV and another portion aligns exclusively on the S. frugiperda genome. Reverse and forward raw fastq files were converted into fasta files. The resulting fasta files were aligned on the wasp genome with blastn version 2. 6. 0 (-task megablast -max_target_seqs 1 -outfmt 6). Reads aligning on the wasp genome were extracted from the fasta file using seqtk subseq (https://github. com/lh3/seqtk) and aligned with blastn (same options as above) on the S. frugiperda genome. To further find chimeric reads most likely to result from the integration of HdIV into S.
frugiperda genome, we used the approach described in  Muller et al. (2021). Briefly, we used the tabulated outputs of the two successive blastn searches as entries of an R pipeline initially written to identify artificial chimeras generated during deep sequencing library preparation  (Peccoud et al. 2018). This script identifies reads as chimeric reads if (i) at least 90 % of the read aligns on one or the other genome, (ii) at least 16 bp align only on one of the two genomes, (iii) with a maximal of 20 bp overlap between the two read portions aligning on a different genome and (iv) a maximal of random 5 bp insert at the chimeric junction. Then, we estimated the number of independent integration events (IEs) by counting as one event all reads with identical or nearly identical coordinates in the two genomes.
This explains why only one junction (out of six) verified by PCR was also found in the large-scale bioinformatic search. PCR primers were designed on each side of each PDV-butterfly junction. DNA was extracted from all 24 butterfly and a standard PCR protocol was used to screen for the presence/absence of six junctions in these individuals. Junctions found in at least two individuals were Sanger-sequenced and are provided in Supplementary Dataset 2, together with the genomic coordinates of each junction in the genomes of P. napi and P. rapae.
Phylogenetic analyses Sequences homologous to PDV DNA circles and starting or ending within HIM were extracted from lepidopteran genomes using seqtk subseq (https://github. com/lh3/seqtk) and are provided in Supplementary Table  1  and 2. These sequences were then aligned, together with homologous DNA circles from various parasitoid wasps (D. semiclausum, H. didymator and H. fugitivus for IV and Cotesia sesamiae, C. vestalis and C. congregata for BV) using MUSCLE  (Edgar 2004 ). Given the large number of IV junctions found in some species, we clustered these sequences for all species in which more than five sequences were found for a given junction using Trimal (-maxidentity 0. 95)  (Capella-Gutierrez et al. 2009). Alignments were then trimmed with Trimal (-automated1) and submitted to Neighbor-joining analysis in MEGA 11 (Maximum Composite Likelihood model of substitution, uniform rates among sites and lineages, pairw ise deletion)  (Tamura et al.
of the junction. Below are pictures of electrophoresis gels showing presence or absence of PCR bands obtained with primers targeting five PDV-P. napi junctions and one PDV-P. rapae junction in twelve individuals of each species sampled in three different geographical locations (S1, S2, S3, see methods). Asterisks indicate PCR products that were Sanger-sequenced. The sequences are provided in Supplementary Dataset 2. For each verified junction, the type of PDV circle is indicated at the bottom right of the gel. HdIV: Hyposoter didymator ichnovirus. CcBV:.
Legeai et al. (2020)ymator was sequenced byLegeai et al. (2020)using the short-read Illumina HiSeq technology and assembled with Platanus. It is available in the NCBI database under accession number PRJNA589497. The genome is 226,9Mb, it has an N50 of 3,3 Mb and it is composed of 131,161 sequences. HdIV regions were annotated byLegeai et al. (2020)using the genome annotation editor Apollo browser. 57 viral segments localized in 66 viral loci were annotated in 32 scaffolds.
Data availability All data produced during this study are available in public repositories. Genbank accession numbers of raw reads produced from Spodoptera frugiperda larvae parasitized by Hyposoter didymator are provided in Table  1. Scripts are provided in GitHub: https://github. com/HeloiseMuller/Chimera/tree/master/scriptsArticles/Heisserer2022. All wasp PDV circles and all lepidopteran PDV fragments bordered by HIM are provided in Supplementary Datasets 6 and Supplementary Tables  1  and 2. Accession numbers of lepidopteran genomes surveyed in this study are provided in Supplementary Table  7.
of the junction. Below are pictures of electrophoresis gels showing presence or absence of PCR bands obtained with primers targeting five PDV-P. napi junctions and one PDV-P. rapae junction in twelve individuals of each species sampled in three different geographical locations (S1, S2, S3, see methods). Asterisks indicate PCR products that were Sanger-sequenced. The sequences are provided in Supplementary Dataset 2. For each verified junction, the type of PDV circle is indicated at the bottom right of the gel. HdIV: Hyposoter didymator ichnovirus. CcBV: Cotesia congregata bracovirus. The genomic coordinate of each junction is provided in Supplementary Dataset 2. Note that polymorphism was observed in P. napi for CcBV1 J1 containing PCR products (2 individuals having two bands) and in CcBV17 J1 (amplification was reproducibly not obtained from the DNA of three individuals) probably reflecting a still ongoing erosion of these regions.
CcBV1 insertions in P. napi and P. rapae have different flanking regions (See Supplementary Dataset 2). Sequencing of the PCR products confirmed that J1 and J2 constituted actually the extremities of the four insertions identified from P. rapae and P. napi genomes, which thus appear to be fixed in the population and not a particular feature of the individuals used for genome sequencing. All sequences are provided in Supplementary Dataset 2. The P. napi HdIV 12 J2 sequence corresponds to the blastn hit number 167 in Supplementary Table1. The other five verified junctions were not recovered in the bioinformatic search because this experimental study was performed independently by GP, JMD and KM in 2018. The study differed from the bioinformatic survey performed in 2022 in that it used CcBV as a query bracovirus instead of CtBV and it included two genomes of P.
878 1407 407 IV 24 Hd27_J1 Ostrinia furnacalis O. nubilalis 99. 142 1049 433 Pieris IV 25 H12_J2 macdunnoughi P. napi 98. 541 754 1745 BV 2 S10_J1 Calephelis nemesis C. perditalis 93. 57 1377 479 BV 3 S1_J1 Calephelis nemesis C. perditalis 92. 62 1628 629 BV 4 S1_J2 Calephelis nemesis C. perditalis 93. 14 1890 901 BV 6 S16_J2 Emesis lupina E. tegula 94. 18 969 429 BV 7 S7_J1 Oxynetra hopfferi O. stangelandi 99. 07 1288 487 *Orthologous J1-or J2-bordered PDV fragments are listed by pair of species, number refer to their number label in sequence alignments provided in Supplementary Datasets 3 and 4. Letters between brackets indicate pairs of species sharing the same orthologous fragment (e. g. , PDV fragments 1, 5 and 7 are shared at the same orthologous locus in Apodemia duryi, A. virgulti, A.
sequencing depth on Hyposoter didymator and Spodoptera frugiperda genomes Legeai et al. (2020)ymator was sequenced byLegeai et al. (2020)using the short-read Illumina HiSeq technology and assembled with Platanus. It is available in the NCBI database under accession number PRJNA589497. The genome is 226,9Mb, it has an N50 of 3,3 Mb and it is composed of 131,161 sequences. HdIV regions were annotated byLegeai et al. (2020)using the genome annotation editor Apollo browser. 57 viral segments localized in 66 viral loci were annotated in 32 scaffolds. using the long-read, PacBio RSII (Pacific Biosciences) technology and assembled with Platanus. It is available on the BIPAA platform (https://bipaa. genouest. org/is/; Rennes, France) and under accession number PRJNA662887 in NCBI. This genome is 384.
46Mb, it has an N50 (i. e. , minimum contig length that covers 50 percent of the genome) of 13. 15Mb and it is composed of 125 contigs. Measuring (Langmead and Salzberg 2012)a reads we obtained (two parasitized caterpillar tissues at two timepoints post-parasitism; SRA accession numbers provided in Table1) were quality-trimmed with Trimmomatic v. 0. 38 (LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36 options)(Bolger et al. 2014) and the quality was evaluated with FastQC v. 0. 11. 8(Wingett and Andrews 2018). To get statistics on sequencing depth, we aligned the four datasets of trimmed paired-end reads using Bowtie2 v. 2. 3. 4. 1(Langmead and Salzberg 2012)in end-toend mode on both S. frugiperda and H. didymator reference genomes. We converted the output.
Carnation (Dianthus caryophyllus) is one of the most popular ornamental flowers in the world. Although numerous studies on carnations exist, the underlying mechanisms of flower color, fragrance, and the formation of double flowers remain unknown. Here, we employed an integrated multi-omics approach to elucidate the genetic and biochemical pathways underlying the most important ornamental features of carnation flowers. First, we assembled a high-quality chromosome-scale genome (636 Mb with contig N50 as 14. 67 Mb) of D. caryophyllus, the 'Scarlet Queen'. Next, a series of metabolomic datasets was generated with a variety of instrumentation types from different parts of the flower at multiple stages of development to assess spatial and temporal differences in the accumulation of pigment and volatile compounds.
Finally, transcriptomic data were generated to link genomic, biochemical, and morphological patterns to propose a set of pathways by which ornamental traits such as petal coloration, double flowers, and fragrance production are formed. Among them, the transcription factors bHLHs, MYBs, and a WRKY44 homolog are proposed to be important in controlling petal color patterning and genes such as coniferyl alcohol acetyltransferase and eugenol synthase are involved in the synthesis of eugenol. The integrated dataset of genomics, transcriptomics, and metabolomics presented herein provides an important foundation for understanding the underlying pathways of flower development and coloration, which in turn can be used for selective breeding and gene editing for the development of novel carnation cultivars.
Here, we present an assembled and annotated high-quality reference genome for the D. caryophyllus cultivar, popularly referred to as the 'Scarlet Queen', based on sequence data generated from the PromethION platform from Oxford Nanopore Technologies (ONT), and constructing pseudo-chromosomes using high-throughput chromosome conformation capture (Hi-C) techniques. Based on this reference genome, genetic regulators of important ornamental traits for carnation, including coloration of petal limbs and margins (technically the margin of the apex; hereafter referred to as the 'margin' for simplicity), eugenol biosynthesis, and formation of petaloid stamens were identified by means of comprehensive homology search, gene family analyses, integration of metabolomic data, and coexpression analyses from RNA-seq datasets.
41 Gb ~62. 609 coverage, after filtering) were used to further polish ONT data (Table  S1  and Figure S1 ). Because of its 1. 2% heterozygosity rate  (Figures S2 and S3  and Table  S2 ), redundant sequences were removed from the initially assembled genome to obtain a de-redundant genome. The final 636. 30 Mb genome assembly (D. caryophyllus v1. 0) contained only 75 contigs with a contig N50 of 14. 67 Mb, which is close to the estimated genome size of ~640 Mb obtained by K-mer survey and flow cytometry (Table  S2  and Figure  S4 ). The paired-end reads from Hi-C were used to cluster, order, and orient (Table  S3 ), then 580. 05 Mb (91. 16%) was anchored onto 15 pseudochromosomes (2n = 30) using the LACHESIS package with manual adjustments. The final assembly was achieved to N50 with 38. 55 Mb and the pseudochromosome lengths ranged from 30.
Finally, 91. 82% of the predicted genes were annotated using different databases (Table  S10 ). The number of genes annotated from the carnation genome was significantly larger than that in Spinacia oleracea, Suaeda aralocaspica, and Beta vulgaris (Figure  1d ). In addition, 1453 transfer RNA, 594 ribosomal RNA (rRNA), 2433 small nuclear RNA, and 95 microRNA (mRNA) genes were predicted using Infernal (Table  S11 ). BUSCO analysis of the newly assembled genome was 95% complete, whereas the D. caryophyllus_r1 draft genome  (Yagi et al. , 2014)  was only 82. 1% complete using the same pipeline (Embryophyta_odb10 database) (Table  1 ), which implied that our genome had higher integrity. In our carnation genome, the repeat sequences accounted for 70. 62%, with LTR retrotransposons accounting for 36.
Characterization of pigment synthesis pathway genes involved with petal color To gain further insights into pigment biosynthesis, especially the anthocyanin biogenesis pathway, seven different stages (S1-S3 samples exhibit colorless petals, and S4-S7 petals exhibit red margins, and among them, 'Lorca' petals form red margins gradually during S4) were sampled to extract and sequence gene transcripts. Based on homology search and genome functional annotation, we identified several genes involved in pigment biosynthesis, including PAL, C4H, 4CL, CHS, CHI, F3H, FLS, DFR, ANS, and AT/ GT. We outlined the putative pigment biosynthetic pathway (Figure  3 ) based on the Kyoto Encyclopedia of Genes and Genomes database and those previously published for other higher plants  (Belwal et al. , 2020; Falcone Ferreyra et al.
Plant material and tissue collection The carnation (D. caryophyllus L. ) cultivars, 'Scarlet Queen' and 'Lorca' (well-known cultivars possessing petals with marginal coloration), were grown in a greenhouse at the experimental growth facility of Huazhong Agricultural University (located at 30°28 0 36. 5 N and 114°21 0 59. 4 E) in Wuhan, Hubei Province, China. Young leaves of 'Scarlet Queen' were collected to extract high-quality DNA for Illumina and ONT sequencing. RNA-seq data from stems, leaves, and roots of 'Scarlet Queen' and published data from the NCBI Sequence Read Archive database (BioProject: PRJDB5916) were used for genome annotation.
Raw sequencing data were processed using FastQ (v0. 20. 0) (Chen et al. , 2018) and FastQC (Brown et al. , 2017)  to filter and detect poor-quality reads and over-represented sequences. The Hi-C library (PE 150bp) was constructed by chromatin extraction and digestion using a standard procedure. Details of the Hi-C library procedure, including DNA ligation, purification, and fragmentation, are described in Supplementary Notes. The HiC library was sequenced on an Illumina NovaSeq platform and resulting data were used to construct the chromosome-level genome assembly.
Genome assembly and pseudochromosome scaffolding Illumina clean reads were analysed using kmerfreq to generate the k-mer depth distribution with a k-mer size of 17 bp. These data were then used to estimate the genome size. Correction of ONT long reads and de novo assembly were performed using NextDenovo (reads_cutoff: 1k and seed_cutoff: 32k). For genome polishing, ONT reads and Illumina sequencing reads were separately subjected to three and four rounds of genome correction, respectively, using NextPolish v1. 2. 4 (https://github. com/Nextomics/NextPolish. git). A subprogram of Purge_Haplotigs  (Roach et al. , 2018)  was used to generate the final contig assembly to retain only one copy of each contig from the heterozygous regions. For Hi-C sequence data, we also initially filtered out low-quality reads using fastp and validated paired-end reads using Bowtie2 v2.