dataesr/scientific-paragraphs-categorization huggingface dataset:
Dendrobium huoshanense has long been used to treat various diseases in oriental medicine. In order to study its gene expression profile, transcripts involved in the biosynthesis of precursors of polysaccharides, as well as mechanisms underlining morphological differences between wild and cultivated plants, three organs of both wild type and cultivated D. huoshanense were collected and sequenced by Illumina HiSeq4000 platform, yielding 919,409,540 raw reads in FASTQ format. After Trinity de novo assembly and quality control, 241,242 nonredundant contigs with the average length of 967. 5 bp were generated. qRT-PCR experiment on the selected transcripts showed the transcriptomic data were reliable. BLASTx was conducted against NR, SwissProt, String, Pfam, and KEGG. Gene ontology annotation revealed more than 40,000 contigs assigned to catalytic activity and metabolic process, suggesting its dynamic physiological activities.
Main stream software for de novo assembly of the data resulted from sequencers include SOAPdenovo2  [19]  (Short Oligonucleotide Analysis Package 2), AbySS  [20]  (Assembly by Short Sequences), and Trinity  [21]  with numerous downstream applications to facilitate individual tasks. In this study, 919,409,540 raw reads in FASTQ format from six organs of D. huoshanense were obtained by Illumina HiSeq4000 sequencing platform. De novo assembly was fulfilled by Trinity software. Transcripts possibly involved in the biosynthesis of important secondary metabolites, polysaccharides, and dendrobine, were proposed by analyzing findings from KEGG  [22]  (Kyoto Encyclopedia of Genes and Genomes) pathway and Gene Ontology databases. Assembled contigs, annotation, as well as differently expressed genes between distinct samples were uploaded to Github (https:// github.
mRNA fragmentation, library preparation Fragmentation buffer from Truseq RNA Sample Prep Kit (Illumina, USA) helped to randomly break mRNA, which could be several thousand kilobases long, into 300-bp fragments. With the presence of reverse transcriptase and random primers, first strand cDNA was synthesized. After the formation of double-stranded cDNA, end repair mix was added to make blunt end followed by attachment of adaptors. High throughput sequencing and de novo assembly cDNA libraries were enriched through PCR amplification for 15 cycles and then certified low range ultra agarose was used for electrophoresis to recover target fragments. After quantification by TBS380 Picogreen (Invitrogen), samples were loaded to cBot for bridge PCR to form clusters. Finally, original data were generated from Illumina instrument through sequencing by synthesis approach.
Transcripts annotation and KEGG pathway analysis Prior to gene annotation, we used ORF prediction package provided by Trinity to do gene prediction for all the transcripts obtained. For eukaryotes, each sequence should contain UTR and then best ORF region is predicted according to Markov models  [24]. Pfam database serves the purpose of revising predicted results and only protein sequences which can be matched to this database will be retained. For BLASTx (Basic Local Alignment Search Tool), all the contigs were used to search NCBI NR (nonredundant), String, SwissProt  [25] , and KEGG databases for functional annotation with E-value set to 1e-5. NCBI NR contains nonredundant information from SwissProt, PIR (Protein Information Resource), PRF (Protein Research Foundation), and PDB (Protein Data Bank) databases and the translated protein data from GenBank as well as RefSeq.
By comparing D. huoshanense transcriptomic data with NR, information for homologous sequences and similarity between related species could be attained. By standardizing biological jargons across different databases, gene ontology  [26]  (GO) aims to categorize the results related to genetic research all over the world. We analyzed GO classification for D. huoshanense to study biological meanings and its distribution of all gene products. Currently, information from 66 unicellular organisms in COG (Clusters of Orthologous Groups of proteins) is generally divided into functional classifications  [27]. By extracting COG number when comparing D. huoshanense sequence information against String database, we studied the functional attributes of this medicinal plant. In living organisms, gene products do not exist or take effect in isolation.
Gene expression analysis RSEM  [29]  software calculates number of read counts for each transcript in a specific library and then FPKM (fragments per kilobase of exon per million mapped reads) values were obtained to show gene expression level. Three ingredients are essential: total exon fragments, mapped reads (millions), and exon length (Kb). To perform differential gene expression (GE) analysis, edgeR  [30]  was used based on RSEM results. For D. huoshanense, screening criteria for differential GE were FDR (false discovery rate) < 0. 05 and log 2 |FC (fold change)| ≥ 1. We also analyzed upregulated and downregulated information in terms of GO and be aware that for a single transcript, it may correspond to several GO entries and vice versa.
Gene expression verification using quantitative RT-PCR Total RNA was extracted from different samples by the same method described in section "Plant materials and mRNA purification". RNA quality was then evaluated by ScanDrop 200 (Jena, Germany). Corresponding cDNA was synthesized with Superscript III Reverse Transcriptase (Invitrogen). Primers for qRT-PCR were designed by using NCBI/Primer-BLAST and tubulin was adopted as the internal control gene (Tab. S1). Amplification was performed using Stepone Plus Real-Time PCR System (Applied Biosystems, USA) with the method described previously  [32].
Trinity de novo assembly After high-throughput sequencing, trimming as well as quality validation of the raw reads are indispensable because they may include adapters or data with poor quality. The software of Trimommatic was used to detect and discard adapters, subsequences of ambiguous nucleotides, and low-quality reads. The resultant clean reads were used for downstream de novo assembly. Clean reads from all 17 libraries were put together to be processed by Trinity and the output contigs longer than 200 bp were retrieved. To remove duplicates of contigs, CD-HIT-EST  [33]  was applied and its threshold of 0. 9 was set to reduce noise interference and computational time. Finally, 241,242 nonredundant contigs were obtained. Tab. 1 shows statistics of sequencing and assembly. Percent of GC in eukaryotes varies from 20% to 60%  [34].
Annotation of assembled transcripts The number of contigs predicted to contain ORF by using ORF prediction package was 142,224 and this equaled 58. 9% of the total assembled contigs, suggesting reliable results of our analysis. BLASTx is an algorithm to search a protein database with a translated nucleotide query. We adopted this strategy to do BLASTx against NCBI NR and other four public repositories. As a result, 32. 99% of the transcripts had hit(s) in Pfam, 28. 28% in KEGG, 38. 20% in Swis-sProt, 22. 09% in String, and 65. 15% in NR. A detailed breakdown is presented in Fig. 3. By analyzing the hits against NCBI NR, transcripts from D. huoshanense that had similar sequences with different species could be studied. To our surprise, 39,861 contigs showed significant homology with Phoenix dactylifera, commonly known as date palm from family Arecaceae.
And only 1,034 contigs were found closely similar to Arabidopsis thaliana (Fig. 4 ). Gene ontology classification provides overall insights into expression pattern of organisms under certain circumstances. We used Blast2GO online facility (http://www. blast2go. com/ b2ghome) to conduct GO annotation. Due to the nature of GO categories, one contig may correspond to several GO numbers from the three distinct classes: biological process, cellular component, and molecular function. From Fig. 5 , over 40,000 contigs were assigned to catalytic activity and metabolic process, suggesting dynamic physiological properties taking place in D. houshanense, which is responsible for its medicinal efficacy. Nevertheless, the implications by using such strategy to analyze GO have obvious limitations. KEGG database is mostly dedicated for human and animal models and thus GO terms related to animal diseases may not be relevant to the study on plants.
We turned to agriGO v2. 0  [35] , which focused on agricultural species, for more information and compared D. huoshanense GO data with that of A. thaliana. The result (Fig. S2 ) showed representative GO terms of the two species had similar distribution pattern. Percent of genes for A. thaliana was higher than that for D. huoshanense and this may attribute to its abundant short contigs that could not hit corresponding GO terms. We retrieved COG numbers for D. huoshanense transcripts by comparing sequence similarity against String database and subsequently acquired their COG function classification. Within   the 25 classes, 3,909 transcripts were assigned to the type of information storage and processing with the functional label as translation, ribosomal structure, and biogenesis. Of the 12,472 genes that are related to metabolism, 1,144 transcripts were linked to secondary metabolites biosynthesis, transport, and catabolism (Fig.
S3 ). KEGG pathway enrichment provides information regarding genes' interaction in a metabolic web. We listed 20 biosynthetic pathways in KEGG, which involved the most transcripts from D. huoshanense in Fig. S4  and 3 ,679 genes were assigned to ribosome biosynthesis. Dendrobium huoshanense is famous for its high contents of polysaccharides. By referring to KEGG database, the following is a possible biosynthetic pathway for D. huoshanense to produce mannose as the precursor of polysaccharides. After α-d-glucose is synthesized via photosynthesis, xylose isomerase catalyzes it to produce d-fructose, which is then turned into β-d-fructose-6P with the help of hexokinase or fructokinase. Subsequently, mannose-6-phosphate isomerase catalyzes β-d-fructose-6P to yield d-mannose-6P which is catalyzed by phosphomannomutase to form d-mannose-1P.
Fig. 8  demonstrates downregulated GO terms related to growth in cultivar despite its longer stem and internode. This suggests the underling mechanisms of D. huoshanense morphology are complicated. Despite the effort to tackle genetic information for the medicinal plants in genus Dendrobium, RNA-Seq analysis for D. huoshanense has not been conducted so far. To provide transcriptomic data for this plant will facilitate the study on the biosynthesis of its abundant polysaccharides and other important secondary metabolites. By collecting 17 samples of wild and cultivated plants, we used Illumina platform to sequence its flower, stem, and leaf. Through qRT-PCR verification, the resultant data were reliable. RNA-Seq analysis provides not only the overall expression profile of this plant, but also detailed information of sequences that are involved in various biosynthetic pathways.
Developmental basis of the hybrid teeth Genetic regulation of mammalian tooth development is highly conserved  [32] , and reiterative activation of signalling centres, called secondary enamel knots, directs cusp development in all studied mammals  [32]. Consequently, computational modelling of genetic interactions and tissue biomechanics, based on empirical data on mouse tooth development, has been used to model tooth development of rodent  [33, 34]  and seal species  [27]. As neither seal tooth development nor hybridization is amenable to experimentation, we examined whether the hybrid morphology could be produced by modelling development. First, we generated virtual ringed and grey seal tooth rows (using real population mean shapes, see Material and methods) using the ToothMaker software  [33, 34]  (see Material and methods).
Specimen preparation The permanent teeth of the newborn hybrid were erupting and partially mineralized. Many of the teeth had cracked into halves during storage. The specimen was microCT scanned using a custom-built Although the Z-scores vary between the individuals, all but one individual (N7-07) show significant introgression (electronic supplementary material, table S12 and see Material and methods). Whiskers denote one standard error. rsos. royalsocietypublishing. org R. Soc. open sci. 5: 180903 microtomography system (Nanotom 180 NF, General Electric, Wunstorf, Germany) at the Department of Physics, University of Helsinki, Finland. The voxel size was 32. 1 mm for the skull and 16. 6 mm for the teeth. Volume data were processed in Avizo 9. 0 (FEI Visualization Sciences Group) and teeth were segmented from the jaw using Artec Studio 9.
Seal genetic data Hybrid DNA was isolated from the pulp of a tooth that had fallen from the specimen in storage using the NucleoMag kit (Macherey-Nagel GmbH & Co. , Germany). The same method was used to isolate DNA from Baltic grey seal, Baltic ringed and Saimaa ringed seal muscle tissue samples. All libraries and sequencing were performed at the DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Finland. The hybrid seal genome was sequenced with two separate runs of Illumina HiScanSQ platform and 11 separate runs of Illumina MiSeq platform to approximately 100Â raw sequencing coverage (electronic supplementary material, table  S1 ). The base calls in the Illumina HiScanSQ platform were converted into text format (FASTA-format with individual base quality scores) using the CASAVA toolkit (bcl2fastq v.
1. 8. 3) provided by the manufacturer. The Illumina MiSeq platform employed a primary analysis software MiSeq Reporter post-run that produced the base calls in text format. For all the Illumina reads, base call accuracy and read length filtering (adapter cut-off ) were performed with cutadapt  [58]  using minimum accepted base call accuracy of 90% and minimum postfiltering read length of 75 bp. The Weddell seal (Leptonychotes weddellii) draft genome (Broad Institute) was used as a reference genome for the downstream genetic distance analysis.
Admixture and introgression analyses Short read data from seals were mapped to the Weddell seal reference genome using bwa mem (v. 0. 7. 15), samtools rmdup (v. 1. 3. 1) and GATK IndelRealigner (v. 3. 7). The resulting bam files were analysed using ANGSD  [59]. The admixture analysis of the hybrid was carried using NgsAdmix  [60]  on a random sample of 3. 6 million markers (10% of the data). NgsAdmix was run 10 times with K ¼ 2 clusters and all the runs converged to identical clustering. Introgression was studied using Patterson's D-statistics  [8]  that, other than requiring the ancestral population to be randomly mating, is robust to variables such as variations in population size  [61]. The statistic was calculated with the ANGSD's abbababa2 module for the first 1000 scaffolds (over 50% of the genome) having the Saimaa and Baltic ringed seals as P1 and P2, and Baltic grey seals as P3.
Genetic distances We analysed fourfold degenerate (ffd) sites from a large number of single-copy orthologous genes. Human genes and their orthologues in cat, dog, horse and chimpanzee were fetched from Ensembl BioMart (v. 83)  [62] , resulting in 4826 complete gene sets with unambiguous orthology ('Homology Type' is 'ortholog_one2one'; 'Orthology confidence' is 'high'). Nucleotide and peptide sequences of transcripts were fetched using the Ensembl REST API  [63]. Using last (v. 658)  [64] , scaffold-level genome assemblies of tiger, Weddell seal and donkey were aligned against the genomes of cat, dog and horse, respectively. Lift-over chains were built using the Kent source utilities  [65]. Short read data for donkey and lion were mapped to the horse and tiger genomes using bwa mem (v. 0. 7.
15), samtools rmdup (v. 1. 3. 1) and GATK IndelRealigner (v. 3. 7)  [66, 67]. Locally generated short read data for Baltic grey-ringed seals were mapped to the Weddell seal genome. The data for the Neanderthal human individual were obtained as bam alignment files. Data sources are listed in electronic supplementary material, table  S2. The annotations were divided into individual coding exons, removing split codons where necessary, and the exon coordinates in reference species (human, cat, dog and horse) were transferred to related non-reference genomes using CrossMap (v. 0. 2. 4)  [68]. For each transcript, exons were extracted from the non-reference genomes using samtools (v. 1. 3. 1) and matched against the reference peptide using Pagan's (v. 0. 61) translated pileup alignment  [69]. The resulting back-translated nucleotide alignments were flattened and degapped, combining all successfully extracted exons into one sequence.
For rsos. royalsocietypublishing. org R. Soc. open sci. 5: 180903 species with bam alignment data (donkey, grey and ringed seal, Neanderthal), the regions surrounding the exons were reconstructed by placing observed sequence changes to the genome sequences of horse, Weddell seal and human. For each exon separately, variants were inferred with samtools mpileup and bcftools call (v. 1. 3. 1) and then placed to the genome sequences with vcfutils vcf2fq, requiring sequencing depth of 10 or higher. The exon regions were extracted and combined into one sequence. Resulting sequences were aligned and the longest transcripts were selected using Pagan's translated pileup alignment. Multiple sequence alignments were filtered and regions where two neighbouring codons contain more than one non-identical base among the species were masked.
For different species sets, gene sequence alignments of at least 100 columns in length after filtering and removal of sites with missing data were concatenated, and ffd sites were extracted using R package rphast (v. 1. 6. 5) [70]. Pairwise genetic distances were computed using R package ape (v. 4. 0)  [71]  and model T92, and phylogenetic trees inferred with RAxML (v. 8. 2. 9)  [72]  using model GTRGAMMA. In addition, we measured the distances using all the codon third sites, and the relative distances remained largely the same. The different species sets analysed are in electronic supplementary material, tables S3 -S5.
Dental material and analyses Baltic grey and ringed seal material was used in comparison to the hybrid as the parents were reported to be from the Baltic Sea (electronic supplementary material, dataset S1 and table  S6 ). The number of cusps and top-cusp angles were tabulated from images taken from lingual side using ImageJ (v. 1. 51). The angle captures the relative height of the tallest cusp and correlates with cusp number because cusp spacing and number are developmentally linked  [26, 27]. For teeth that had only one or two cusps, the line was drawn to the maximum anterior or distal ends at the crown base. Our tabulations included small incipient cusps (arrowheads in electronic supplementary material, figure  S2b ). All the measurements reported are from the right side. The pattern of results remains the same for the left side.
Because seals have laterally compressed teeth, lateral biases (Lbi and Bbi) were kept constant  [27]. All the used parameter values are listed in the electronic supplementary material, table  S7. We modelled tooth rows by making constant parameter changes from tooth to tooth to mimic gradual shape changes along the jaw. All the simulations were run for the same number of iterations. Hybridization was simulated by averaging parameter values between the species in different combinations (electronic supplementary material, figure  S4b  and table  S8 ). ToothMaker is available at https://github. com/jernvall-lab/ToothMaker.
Analysis of the crania Forty-six three-dimensional landmarks obtained from ventral and dorsal views were acquired from newborn to adult skulls of grey and ringed seals from the collections of Finnish Museum of Natural History (Helsinki, Finland) using a Microscribe G2X (Immersion) (electronic supplementary material, figure  S5 ), with digitizing error also assessed (electronic supplementary material, table  S11 ). A generalized Procrustes analysis was used to simultaneously superimpose all symmetrized configurations and extract shape data by removing the effects of scale, orientation and position  [39]. Permutation tests were used for testing differences in mean shapes using function 'permudist' from 'Morpho' R package  [76]. A principal component analysis (PCA) was used to show the main patterns of morphological variation between the two species (electronic supplementary material, dataset S2).
All analyses were performed with MorphoJ 1. 06d  [79] , custom R  [80]  and Python scripts. Ethics. The Baltic seal tissue samples were obtained from the collections of the Saimaa Ringed Seal Genome Project, University of Helsinki and Natural Resources Institute Finland, whereas the Saimaa samples originated from the collections of the University of Eastern Finland, which has got permission from Finnish environmental authorities for taking possession of and storing tissues of the Saimaa ringed seal ( permission number: Dnro VARELY/3480/2016).
Acknowledgements. We thank  S. Mallick  and  S. Martin  for discussions and advice on genome-related analyses,  J. Laakkonen ,  M. Kunnasranta  and  M. Olsen  on seal biology and  W. Morita  on hominin dentitions. For collection access and specimen loans, we thank  I. K. Hanski  and  E. -S. Hyytia  ¨inen from the  Finnish Museum of Natural History (Helsinki, Finland)  and  D. Kalthoff  from the  Museum of Natural History (Stockholm, Sweden) , who also helped to locate the hybrid. We thank  H. Suhonen ,  A. Kallonen ,  M. Christensen  and  J. Muszynski  for tomography and three-dimensional data processing, and  P. Timonen  and  S. Oksanen  for their help with Baltic seal samples. We thank  CSC-IT Center for Science, Espoo, Finland , for computing facilities. The personnel at  DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki  are acknowledged for their excellent technical work and  Saimaa Ringed Seal Genome Project  for discussions.
Data accessibility. The aligned sequences are available through the European Nucleotide Archive under accession number PRJEB25679 (https://www. ebi. ac. uk/ena/data/view/PRJEB25679) with additional analysis data at http:// wasabiapp. org/download/data/bastard/. Software is available from https://github. com/jernvall-lab/ToothMaker. All other data used in the analyses are available in the electronic supplementary material. The cranial and dental specimens are archived in the Finnish Museum of Natural History (Helsinki) and Swedish Museum of Natural History (Stockholm).
Functional genome annotation of amphioxus We generated an exhaustive resource of genomic, epigenomic and transcriptomic data for the Mediterranean amphioxus (B. lanceolatum), comprising a total of 52 sample types (Fig. 1a  and Supplementary Data 2, datasets 1-5). These datasets were mapped to a B. lanceolatum genome that was sequenced and assembled de novo, with 150× coverage, a total size of 495. 4 Mbp, a scaffold N50 of 1. 29 Mbp and 4% gaps (Extended Data Fig. 1a-c ). To facilitate access by the research community, we integrated these resources into a UCSC Genome Browser track hub (Fig. 1b ; available at http://amphiencode. github. io/Data/), together with an intra-cephalochordate sequence conservation track and a comprehensive annotation of repetitive elements (Extended Data Fig. 1d-f ) and long non-coding RNAs (Extended Data Fig.