dataesr/scientific-paragraphs-categorization huggingface dataset:
The current version of Cyanorak v2. 1 encompasses representatives of most of the lineages (SC and clades) known to date in Cluster 5, with the exception of the newly described freshwater members of SC 5. 3 as well as members of the yet-uncultured SC 5. 1 clades EnvA and EnvB  (18, 21). Since all Cluster 5 members possess a similar morphology (spherical to rod shaped) and lifestyle (aquatic, non-diazotrophic oxyphototrophs;  (11) ) and form a monophyletic branch within the Cyanobacteria phylum, we assume that members of most CLOGs defined within this genetically homogeneous group exhibit the same function, though this may not be true when considering more distant organisms, notably cyanobacteria exhibiting different lifestyles. Here, we describe the construction of the Cyanorak v2. 1 database, the rich functional annotation available for each CLOG and the tools and plugins that were developed to explore the genomic diversity of this ecologically relevant group of organisms, which has recently become one of the main microbial models in marine ecology.
Clustering of likely orthologous sequences and CLOG curation Following the construction of a first series of CLOGs based on the 14 first sequenced picocyanobacterial genomes  (8) , Cyanorak v1 CLOG numbers have been cited in a number of publications from our group (see e. g. ,  (22) (23) (24) (25) (26) (27) (28) (29) (30) ). In order to preserve at best these preexisting CLOG numbers after the addition of 83 new genomes either retrieved from Genbank or newly sequenced at our initiative (Fig. 1 ; (9)), all genes from the 97 genomes were first clustered using all-against-all BLASTP+ comparison  (31)  and the OrthoMCL clustering algorithm  (32)  with an e-value threshold of 10 -5 and new CLOGs were then mapped to previously defined Cyanorak v1 CLOGs. New CLOGs containing all sequences from a v1 CLOG plus additional sequences from new genomes as well as manually curated CLOGs were assigned the previous v1 CLOG numbers.
Paralogs were moved into different CLOGs when they grouped together into different branches as the bona fide orthologs. In order to refine assessment of the core genome  (9) , more than 1,750 genes missed by gene prediction software tools, either because they were too short (e. g. petM, psbM) or partially overlapping with other genes notably in the case of long 3'-3' overlaps (e. g. for pyrB-ndbA or panB-hemN), were also manually added to different genomes. Furthermore, many overpredictions of ORFs (e. g. , short CDS of unknown function totally overlapping long annotated CDS) were eliminated, and this even from genomes retrieved from Genbank. Finally, many start positions were corrected from sequences obviously too short or too long, based on an alignment of all CLOG members and/or 5'-end extensions using TBLASTN searches.
Implementation of the Cyanorak v2. 1 information system The development of Cyanorak v2. 1 was done in two steps. The first version (v2. 0) of this information system included a history feature to keep track of every change and allowing to readily revert any change at a very granular level as well as enabling curators to check the journal of changes undergone by every gene or CLOG. This private version of the information system is still currently used for the manual curation of the database. However, in order to give the general public access to the curated data with the best possible response times, especially now that the number of genomes and MAG's in the database has risen to 97, a completely new version of the Cyanorak information system, devoid of the history feature (v2. 1), was recently developed and proved to be two to three times faster than v2.
0. Two instances of the Cyanorak information system therefore co-exist on our server: i) the restricted access, editable Cyanorak v2. 0 version allowing expert curators to edit most fields of the 'CLOG' and 'gene' pages, and ii) the publicly accessible, non-editable Cyanorak v2. 1 version, the latter corresponding to the state of the Cyanorak database at the time of publication of a comparative genomics study of the 81 non-redundant, high quality genomes of the database (9) and of an extensive transcriptomic analysis of the response of the Synechococcus sp. WH7803 strain to various environmental stresses  (34). This public version will be regularly updated in the future, with concomitant changes in version number, when new whole genome sequences (WGS), single amplified-and metagenome assembled-genomes (SAGs, MAGs) and/or transcriptomes either retrieved from public databases (e.
g. Genbank) or generated by our group will be added to the Cyanorak database and described in the frame of forthcoming publications. A restricted access, editable instance based on the v2. 1 implementation is currently being developed and should replace the current v2. 0 instance in the near future for expert curation purposes. On a technical level, the bulk of the Cyanorak v2. 1 has been implemented using the Java programming language, with an extensive use of the Spring framework. The data itself is stored in a relational database (PostgreSQL), and the link between the application and the database is done through an object relational mapper (Hibernate). A small set of Python auxiliary tools has also been developed, mostly to prepare the data for import, to postprocess exported data or to perform specific batch updates.
General characteristics of the database Built from 97 picocyanobacterial genomes, including 43 Prochlorococcus and 54 Synechococcus/Cyanobium, which are representative of the wide genetic and pigment diversity existing within these genera (Fig. 1 ), Cyanorak v2. 1 encompasses 252,176 genes that were split into 25,834 CLOGs. A plot of the distribution of the number of sequences per CLOG expectedly shows that the most frequent categories are CLOGs with one sequence, i. e. unique genes (15,283 CLOGs), and CLOGs with few (2 to 5) members (Fig. S1 ). Although most of these CLOGs (e. g. 91% of unique genes) are annotated as "hypothetical" or "conserved hypothetical" proteins, a number of them display a more precise functional annotation, since they share some similarities to genes or domains of known function, with among the most abundant: glycosyltransferases, restriction-modification system proteins, integrases, transposases, methyltransferases, NAD-dependent epimerases/dehydratases and tetratricopeptide repeat (TPR) family proteins.
The next most abundant CLOG category (611 CLOGs) is the one containing 97 sequences, which corresponds to the picocyanobacterial core genome sensu stricto. As expected, this number is significantly lower than the picocyanobacterial strict core gene set (911 genes) estimated by Doré et al. (9)  using the 81 non-redundant, high-quality genomes of the Cyanorak database. Yet, given that some of the 97 genomes or MAG's, especially those not included in this 81-genome set, are incomplete and/or contain frameshifted genes (in this case, the two or more gene fragments resulting from a frameshift have been put into the same CLOG), many CLOGs contain a number of genes that is close but not exactly equal to 97. So, the picocyanobacterial core genome sensu lato is likely much larger than 611 genes, and we estimated it using a relaxed definition of core genes (CLOG is considered as core of a taxonomic group if it is present in ≥ 90% of the strains within this group) to be 1271 genes.
Cyanorak web interface and tools The homepage of the Cyanorak v2. 1 information system shortly describes the origin of the genomes used to build the CLOGs database, the history of its construction and the main references that used it. The top banner available from all pages encompasses several clickable menus, including the 'organisms page' that lists the different genomes of the database and their characteristics, a 'search page' with different options to access the CLOG or gene pages of interest, a 'BLAST scroll down menu', a JBrowse menu giving access to direct links to the viewer of each genome, as well as several other menus providing useful information about the database (Previous Versions, References, Links, About us).
Organisms page The 'organisms page' consists of two tables, the first one listing Prochlorococcus genomes and the other one Synechococcus and Cyanobium genomes. They provide taxonomy, pigment type, sequencing center as well as various genomic characteristics (size, GC%, status, accession numbers, number of CDS, etc. ) for each genome included in the database. Next to each strain name is a clickable 'J' logo that gives access to the JBrowse page of the corresponding genome (see below). A distribution map of all of the strains drawn with OpenStreetMap® (https://www. openstreetmap. org/) is also available in this section (Fig. 2 ), offering a flexible set of options to focus on individual strains or to select all or a subset of Prochlorococcus and Synechococcus/Cyanobium strains. Strains collected in nearby locations can also be shown with a single marker to enhance readability.
In this section, each strain name in the Table can be clicked to get more detailed information (e. g. , isolation site, isolator, environment ontology (ENVO) code, etc. ) and also allows the user to export gene and protein sequences in FASTA format as well as whole genomes in Genbank format. In each of these files, the annotation of every gene corresponds to that found on CLOG pages (see below), which was given priority over the initial gene annotation, even if the genome was retrieved from Genbank.
Genomic Search tools The main entry to the Cyanorak v. 2. 1 database content is through the 'genomic search' menu, with three possible options. The first one is a 'quick search' of any term mainly through 'cluster number', 'gene names' and 'product descriptions' fields, a term that can be searched either as an exact match or as a pattern in a more complex sentence. For instance, a search for 'dna' in 'pattern' configuration will provide a list of CDS clusters whose gene name annotation includes 'dna' (e. g. dnaA, dnaB, etc. ) as well as a list of products whose description includes DNA (e. g. DNA gyrase, formamidopyrimidine-DNA glycolase, etc. ). Search results are organized in three distinct tabs. The first one lists the matching clusters, the second one lists the matching CDS and the third one lists the matching RNA entries.
CLOG page By clicking on a Cyanorak CLOG number (format: CK_XXXXXXXX) in the result list of any search (see above), the user is sent to a cluster page providing a full description of the function and phyletic pattern of the corresponding CLOG. An indication in the upper right corner of the CLOG page specifies whether the CLOG has been manually annotated, i. e. whether an expert has edited and validated its sequence content and functional annotation. The cluster page contains several fields, including from top to bottom: i) the corresponding gene identifier in the Cyanorak v1 database (if any), generally corresponding to the last digits of the Cyanorak v2. 1 CLOG number, ii) a gene name and its synonyms (if any) as well as the product description, iii) functional categories including COG  (5)  and EggNOG  (6)  identifiers and their description, CyOG number (as reported in  (35) ), Enzyme Commission (EC) and K numbers referring to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (www.
Gene page By clicking on any gene in the cluster page or the relevant search result tab, the user accesses the 'gene page', which includes most fields previously described for the CLOG page. Specificities compared to the latter include i) the source and location of the gene, namely the strain name, contig and gene location (position and strand) on the contig, generally consisting of the whole chromosome, ii) a series of identifiers in Cyanorak and, if relevant, in other databases (Genbank, RefSeq, etc. ) and iii) the gene sequence in nucleotides and (for CDS) in amino acids. It must be stressed that this page contains the initial annotation of the gene (e. g. if the genome was retrieved from Genbank), and the latter often differs from the CLOG annotation which is typically much more extensive, especially if the cluster was manually curated.
All genes included in Cyanorak (even when retrieved from public databases) were given, in addition to their initial ORF_ID, a unique Cyanorak ORF_ID with the standardized format CK_Genus_Strain_XXXXX (e. g. CK_Syn_PROS-U-1_00601) in order to normalize gene names and ease the identification of the genome source. Also noteworthy is that the genomes included in Cyanorak, even those that have been sequenced by other groups, have all been manually curated to some extent, including predictions of missing genes or removal of wrong predictions, and thus differ from their counterparts in other public databases (Genbank, RefSeq, etc. ) not only regarding their annotation (made at CLOG level) but also their gene content.
BLAST An indispensable complement to the Cyanorak database is the possibility for users to search any sequence in all genomes or proteomes of the database using two BLAST options available from a BLAST scroll down menu. This includes an implementation of the BLAST algorithm using the SequenceServer graphical interface  (38)  allowing to blast one or several nucleotide or protein sequence(s) against a selection of up to 97 genomes ('Blast a selection') or all genomes ('Blast all'). Results of a Blast search returns the Cyanorak ORF_ID, the strain taxonomy (at the SC, clades and/or subclade level) and pigment type, the CLOG number as well as the CLOG gene name and product (e. g. CK_Syn_A15-24_00652_III_IIIa_3c CK_00001060!rpoC1!DNA-directed RNA polymerase complex, gamma subunit).
JBrowse page Clicking on the 'J' logo next to each strain name in the JBrowse page (or 'Organisms' page) gives access to a JBrowse viewer  (39)  allowing the user to visualize the whole annotated genome and to zoom in to see the local context and detailed annotation of any gene, as derived from the 'CLOG page' (see above). Right clicking on a gene gives access to the detailed functional annotation of the corresponding gene, as derived from the cluster page in Cyanorak, with hyperlinks to Cyanorak and external functional databases. The genes can be searched by annotation or Cyanorak ORF_ID. A 'select tracks' menu gives access to additional data associated with each genome, when available. These include strict and large core and accessory genomes, gained genes as well as genomic islands, as determined in a recent comparative genomic study of 81 non-redundant picocyanobacteria genomes  (9).
DISCUSSION As the most ancient photosynthetic organisms, cyanobacteria had a key role in the oxidation of the primitive Earth atmosphere  (41)  but also in the primary endosymbiosis, an event that led to the advent of green and red algae and ultimately to all eukaryotic oxygenic phototrophs  (42). Besides their relevance in evolutionary biology, cyanobacteria are also of great interest in ecology, given their ubiquity and abundance in many ecosystems, including oceans and deserts  (43)  and the noxious impacts of their bloom-forming toxic representatives in freshwater environments  (44). For all these reasons, but also thanks to their fairly small genomes sizes, ranging from 1. 4 to 11. 6 Mbp, these microorganisms have been the subject of many sequencing projects  (8, 12, 45) , which in turn triggered the generation of a number of dedicated genome databases.
The oldest of these databases is Cyanobase (http://genome. microbedb. jp/CyanoBase), initially created to provide access to the first sequenced cyanobacterial genome, the model freshwater strain Synechocystis sp. PCC6803  (46, 47). This database has since then been extended to host many more recently sequenced freshwater and marine cyanobacterial genomes (376 entries, including 86 complete genomes in April 2019), but has been 'under maintenance' since summer 2019. Although this database provides much useful genomic information, this is not a CLOG database and is therefore not designed to make extensive genomic comparisons. Also worth noting, CyanoClust (http://gclust. c. u-tokyo. ac. jp/CyanoClust/) is a database of homologous groups initially limited to cyanobacteria and plastids and which was more recently extended to a heterotrophic bacteria and Archaea  (48).
It provides lists of orthologs generated by the program Gclust, but functional annotation is limited to the original product description and fasta sequence of individual members of each CLOG. The database that was most similar to Cyanorak v2. 1, was the 'Prochlorococcus portal' a. k. a. 'Proportal'  (49). It was also based on CLOGs computed from a number of Prochlorococcus and marine Synechococcus genomes, with a strong focus on the former genus. Since 2018, this database has however been merged to the Joint Genome Institute Integrated Microbial Genomes and Microbiomes (JGI-IMG) and renamed 'IMG-Proportal' (http://img. jgi. doe. gov/cgi-bin/proportal/main. cgi). The latter site lists all publicly available genomic, transcriptomic, metagenomic and population data on Prochlorococcus, Synechococcus and their cyanophages, which can be analyzed using the IMG's data warehouse and comparative analysis tools  (50) , but the initial CLOG-centered organization of Proportal has been lost.
Compared to these databases, Cyanorak is more function-oriented and aims to provide rich and up-to-date functional annotations of CLOGs, with a preference for those derived from genes or proteins that were characterized in cyanobacteria. In contrast to most large CLOG databases currently available, such as COG  (5)  or EggNOG (6) that encompass very distantly related organisms, Cyanorak is focused on Prochlorococcus and marine Synechococcus/Cyanobium, i. e. a monophyletic and homogenous group of microorganisms sharing a similar morphology and lifestyle, making more reliable the assumption that reciprocal best hits in different genomes truly correspond to orthologs. Thanks to this CLOGbased approach, the continuous expert curation efforts employed since the mid-2000's have allowed us to improve the annotation of all genomes of the Cyanorak database, even those initially retrieved from Genbank.
Furthermore, a number of genes that were missing in these often automatically annotated genomes have been added, while many over-predictions have been suppressed, so that both gene content and annotations differ between genomes in Cyanorak and their counterparts in large public databases. Another important asset of Cyanorak is the variety of tools for exploring and exporting genomes from the database. For instance, one can search for CLOGs common or specific to a particular phylogenetic group of interest, an approach that can provide clues to identify genes coding for a specific function. For instance, searching Cyanorak for homologs of MpeZ, an enzyme involved in type IV chromatic acclimation (CA4), i. e. a reversible pigmentation change occurring in some Synechococcus strains when shifted from blue to green light  (44) , allowed us to identify a second type of chromatic acclimation, so-called CA4-B, which possess MpeW, a MpeZ homolog.
Both the mpeZ and mpeW genes are located in a specific genomic island, but gene content, organization and genomic context differ between the CA4-A and CA4-B islands  (26). Another interesting example concerns the chlorophyll (Chl) biosynthesis pathway. It is well known that Prochlorococcus lacks monovinyl-Chl a, which is replaced by divinyl-Chl a, even in reaction centers  (51, 52). Comparing the genomic context of the core malQ gene (encoding a glucanotransferase) between all genomes of the Cyanorak database shows that in marine Synechococcus this gene is always preceded by an enzyme that reduces divinyl-Chl a into mononyl-Chl a, but surprisingly there are two possible mutually exclusive reductase genes depending on strains, either dvr  (53)  in strains from clades I-IV, VII, CRD1, WPC1 XX and UC-A or cvrA  (54)  in all other Synechococcus/Cyanobium lineages (Fig.
S3 ). Dvr and CvrA possess the same enzymatic function but share no sequence identity, and are thus analogs. In Prochlorococcus genomes, neither dvr nor cvrA are found upstream of malQ, and none of these genes is found elsewhere in the genome, explaining why these strains are all incapable of producing monovinyl-Chl a. Cyanorak v2. 1 is also a repository for a variety of transcriptomic data, the interpretation of which relies heavily on the quality of genome annotation. In Cyanorak, these data are connected to the genome database through a JBrowse interface, which also gives access to genomic features such as predicted operons, gained genes or the core or accessory nature of genes, which can be used to further refine the interpretation of gene expression data (see e. g. (  34 )).
FUTURE DEVELOPMENTS The current version of the database includes rRNAs, tRNAs and tmRNAs, but still no small RNAs (sRNAs), so we plan to add such information in a forthcoming release, at least for the most conserved sRNAs. Another planned improvement of the database concerns the curation of gene starts. Although many gene starts have been corrected manually, amino acid alignments readily made from exports of CLOG pages show that a large number of those starts are still mis-predicted, leading to seemingly too short or too long sequences in a number of genomes. We will thus develop an application that allows to automatically correct likely wrong starts, at least when N-termini are not too variable. Finally, new fields will be added on the CLOG page, including for instance orthologs of each CLOG in relevant biological models, such as the freshwater cyanobacteria Synechocystis sp.
PCC 6803 and Synechococcus sp. PCC 7942, the heterotrophic bacteria Escherichia coli and Bacillus subtilis or the higher plant Arabidopsis thaliana. Future versions of the Cyanorak database will include a number of transcriptomes for several Synechococcus strains recently generated by our team but that are still unpublished as well as genomes newly released from public databases. It must be stressed that the aim of Cyanorak is not to host all of the rapidly-growing number of incomplete SAGs and MAGs, apart from a few representative uncultivated lineages (e. g. , Synechococcus EnvA/B, Prochlorococcus HLIII-VI). Thus, a pipeline is currently being developed to easily transfer the rich functional annotation of the Cyanorak genomes to these new partial genomic sequences and, more generally, to any picocyanobacterial environmental reads retrieved from metagenomes and metatranscriptomes.
A few previous studies, where annotations made in Cyanorak were used to analyze omic data, have notably allowed us to i) compare the nitrogen assimilation capacities of Prochlorococcus populations from inside and outside the Agulhas rings in the South Atlantic Ocean (55), ii) highlight differences between Prochlorococcus and Synechococcus populations in their adaptation and acclimation responses to iron deficiency in the vicinity of the Marquesas island (56) and iii) demonstrate through the global oceanic distribution of desaturase genes the key role of these enzymes involved in the modulation of membrane fluidity for the colonization of different thermal niches by distinct Synechococcus lineages  (28). We envision that Cyanorak will become a reference genome database for the taxonomic and functional annotation of not only newly released genomes and transcriptomes of marine picocyanobacteria, but also the everincreasing marine meta-omes, which given the natural abundance and ubiquity of these microorganisms in the marine environment constitute a significant part of all reads retrieved from the upper lit layer of marine waters.