DOI: 10.5061/dryad.wh70rxwrq
title: Primary data of thiotrophic free-living and ectosymbiotic genomes

description: Thiotrophic symbioses between sulfur-oxidizing bacteria and various
 unicellular and metazoan eukaryotes are widespread in reducing marine
 environments. The giant colonial ciliate Zoothamnium niveum and its
 vertically transmitted ectosymbiont Candidatus Thiobius zoothamnicola
 (short Thiobius), however, is the only thiotrophic mutualism that has been
 cultivated so far. Because theoretical predictions posit a smaller genome
 in vertically transmitted endosymbionts compared to free-living relatives,
 we investigated whether this is true also for an ectosymbiont. We used
 metagenomics to recover the high-quality draft genome of this bacterial
 symbiont. For comparison, we have also sequenced a closely related
 free-living cultured but not formally described strain Milos ODIII6 (short
 ODIII6). We then performed comparative genomics to assess the functional
 capabilities at the gene, metabolic pathway, and trait levels. 16S rRNA
 gene trees and average amino acid identity confirmed the close
 phylogenetic relationship of both bacteria. Indeed, Thiobius had about a
 third smaller genome than its free-living relative ODIII6, with reduced
 metabolic capabilities and fewer functional traits. The functional
 capabilities of Thiobius were mostly a subset of those of the more
 versatile ODIII6, which possessed additional genes in the context of
 oxygen, sulfur, and hydrogen utilization and for the acquisition of
 phosphorus illustrating the adaptations to instable environmental
 conditions at hydrothermal vents. In contrast, Thiobius possessed genes
 for heterotrophy potentially enabling it to utilize lactate and acetate,
 which may be provided as byproducts by the host. The present study
 illustrates the effect of strict host-dependence of a bacterial
 ectosymbiont on genome evolution and host adaptation.
description: The files 1 to 6 are phylogenetic trees in newick format obtained
 with R and MrBayes. File 7 puts together the support metrics of the
 phylogenetic internal nodes whenever this are shared between trees. File 8
 provides the nucleotide alignment of the 16S rRNA gene sequences in fasta
 format. File 10 reports the information of the 310 employed 16S rRNA gene
 sequences. Sample collection details are reported in file 11, and DNA
 extraction in file 12. Files 13 and 14 report the outcome of the manually
 curated genome functional annotations. File 15 summarizes genome features.
 Metabolic pathways inference outcomes are reported in files 16 and 17.
 Ultimately, files 18 and 19 make the R-Markdown Primary Data
 report.
description: # Primary Data of Thiotrophic free-living and ectosymbiotic genomes ***
 <br> 01.ML16S.redu.nwk md5=403c2de8a2ac17fdd55559414657b454 This
 file includes the maximum likelihood (ML) 16S rRNA gene tree in newick
 format after prunning all branches of organisms that do not have an
 available genome. 02.ML.16S.306seqs.100BS.nwk
 md5=5df2c88afae8c5ec8643cc430ef22cfd This file includes the maximum
 likelihood 16S rRNA gene tree as obtained from the R workflow (see code in
 the R-Markdown .Rmd file 18). 03.MP16S.redu.nwk
 md5=d809ed2d245816d80fb8e14fc685ca9f This file includes the maximum
 parsimony (MP) 16S rRNA gene tree in newick format after prunning all
 branches of organisms that do not have an available genome.
 04.MP.16S.306seqs.100BS.nwk md5=32fdefd95b5d0ebee1631b43d7a87ede This file
 includes the maximum likelihood 16S rRNA gene tree as obtained from the R
 workflow (see code in the R-Markdown .Rmd file 18). 05.BI16S.redu.nwk
 md5=d9ac087e04306794b329fefb64722aaa This file includes the bayesian
 inference (BI) 16S rRNA gene tree in newick format after prunning all
 branches of organisms that do not have an available genome.
 06.BI16S.306seqs.nwk md5=5b7eeb57af90de2d989f6189dbfb2bb7 This file
 includes the bayesian inference 16S rRNA gene tree as obtained from
 MrBayes. 07.BI\_ML\_MP\_supports.16Sredu.csv
 md5=628ab33dced304b5ceb3a893dfa3a5e9 Column "Node" refers to the
 internal phylogenetic node identifier. Columns "BI support",
 "ML support" and "MP support" refer to the internal
 phylogenetic support metrics (bootstrap for ML and MP, and posterior
 probability for BI), all in percent. Several "NA" values (not
 available) ocurr in the root nodes due to the used techniques. Internal
 nodes supports indicated as "--" mean that the tree topology of
 the column technique did not include this internal node. The ML tree
 topology is used as the reference. 08.Phylogeny.16S.mafft.trimal.fna
 md5=05119c491f84ac6f56377f2c4ae56dfe Alignment used to generate the
 phylogenies, in fasta nucleotide file format. 09.TaxaSelection16S.csv
 md5=3615b834dfa2a0589105d0b3d61392f8 Details of the sequences, including
 the following columns: SequenceID, SpeciesID, YearOfTree, Accession,
 PublishedTree, TipLabel, Database, Length, Start16S, End16S, Contig16S,
 Notes. The column "SequenceID" shows a running number for
 sequences. The column "SpeciesID" shows a running number for
 species. The column "YearOfTree" indicates the year of
 publication of the phylogenetic tree from where the sequence accesion
 number was taken. "Accession" means the accession number of the
 sequence. "PublishedTree" shows the peer-reviewed publication
 reference where the tree that includes the sequence was publicly released.
 "TipLabel" states the organism name. "Database" shows
 the name of the database that hosts the accession number instance of the
 sequence. "Length" states the sequence length in number of
 nucleotides. "Start16S" and "End16S" shows the
 coordinates of the sequence. "Contig16S" state the numeral of
 the contig where the 16S rRNA gene is taken from. The column
 "Notes" contain empty cells, in those instances where there was
 nothing to be noted. 10.Metagenomes.csv
 md5=8230850cbd1f1b3e03d8460ec294d18b Details of the metagenomes and their
 pair-end Illumina generated read pairs. The column "GenomeID"
 expresses the identifier of the genome, in the first three instances of
 Candidatus Thiobius zoothamnicola. "MD5" is the hashtag
 signature of the bam file from where the fastq files pairs originate.
 "FileSize" is the file size in bytes of the bam file from where
 the fastq files pairs originate. "ReadPairs" is the number of
 read pairs included in the files before any post-processing or filtering.
 11.SampleCollection.csv md5=aff4657109165b398aead88b5d1f7b73 Sample
 collection details, including geographical location, year and sampling
 collector person. "SalmplingSite" is the identifier of the place
 where samples were collected. "SovereignState" is the country of
 sampling. "LatitudeDMS" and "LongitudeDMS" are the
 sampling geographical coordinates in Degrees(d), Minutes(m) and
 Seconds(s), where "N" means Northern hemisphere and
 "W" means Western hemisphere. "LongitudeNumerical" and
 "LatitudeNumerical" are the sampling geographical coordinates in
 Degrees with decimals, with negative longitude values referring to those
 western of Greenwich meridian. "SamplingTime" shows the year of
 collection. "SamplingPerson" refers to the person that collected
 the sample. 12.DNAextraction.csv md5=d80e13a9889bf5151d1e561c5bbd0fcb
 Details of the genome extractions, including the columns: GenomeID,
 VialID, Wood, Fixation, NanoConcEx, Na260to280, Na260to230, PicoGreenEx,
 PicoGreenLi. "GenomeID" is a running number for a broader set of
 metagenomes that was tried, for which the best ones in terms of assembly
 metrics are used in this study. "VialID" is a internal reference
 from our lab connecting it to our sampling documentation. "Wood"
 is a running number for the sunken wood sampled through the years by our
 research group. "Fixation" stands either for "Cryo"
 (cryofixation, by flash-freezing in liquid nitrogen), or for
 "EtOH" that stands for absolute ethanol fixation. The column
 named "NanoConcEx" refers to the Nanodrop measurement of DNA
 concentration in ng/µL. "Na260to280" and "Na260to230"
 are the absorvance ratios between the two expressed wave lengths, in order
 to assess sample purity. "PicoGreenEx" is the concentration of
 the DNA extract according to the Picogreen essay, in ng/µL.
 "PicoGreenLi" is the concentration of the DNA library according
 to the Picogreen essay, in ng/µL. 13.ThiobiusG43.curated.tsv
 md5=7d8c1750732f8ec6af0abac20dfb99f1 Curated outcome of gene prediction
 and annotation, including the columns: Local\_ID, Contig\_id, Feature\_id,
 Type, Start, Stop, TraitNumber, TraitShortName, TraitEvidence,
 Inferred\_function, Notes, Orthogroup, GeneSymbol, GeneEvidence,
 GeneClass, COGcat. Some columns (e.g. GeneSymbol, GeneEvidence, ...)
 contain empty cells, meaning that for that particular instance in that
 row, there is no information available from the analysis.
 "Local\_ID" is a running number. "Contig\_id" states
 the numeral of the contig where the indicated gene is taken from.
 "Feature\_id" is the RASTtk annotation label.
 "Feature" is the type of feature, in this case for all
 "peg". "Start" and "Stop" are the cordinates
 of the feature in the indicated contig. "TraitNumber" is a
 running number of the trait. "TraitShortName" is a short name
 for the trait. "TraitEvidence" is the evidence backing the trait
 call. "Inferred\_function" is the functional annotation.
 "Notes" are free text comments whenever needed.
 "Orthogroup" is the label of the orthology analysis.
 "GeneSymbol" is a short name for the gene.
 "GeneEvidence" is the evidence backing the gene call.
 "GeneClass" is the attribution whenever possible to the core
 genome or to the shell or to the cloud. "COGcat" is the
 attribution to a functional COG category. 14.ODIII6.curated.tsv
 md5=25f4a9fa34e36eb1c16d5dbafd0bd73e Curated outcome of gene prediction
 and annotation, including the columns: Local\_ID, Contig\_id, Feature\_id,
 Type, Start, Stop, TraitNumber, TraitShortName, TraitEvidence,
 Inferred\_function, Notes, Orthogroup, GeneSymbol, GeneEvidence,
 GeneClass, COGcat. Some columns (e.g. GeneSymbol, GeneEvidence, ...)
 contain empty cells, meaning that for that particular instance in that
 row, there is no information available from the analysis.
 "Local\_ID" is a running number. "Contig\_id" states
 the numeral of the contig where the indicated gene is taken from.
 "Feature\_id" is the RASTtk annotation label.
 "Feature" is the type of feature, in this case for all
 "peg". "Start" and "Stop" are the cordinates
 of the feature in the indicated contig. "TraitNumber" is a
 running number of the trait. "TraitShortName" is a short name
 for the trait. "TraitEvidence" is the evidence backing the trait
 call. "Inferred\_function" is the functional annotation.
 "Notes" are free text comments whenever needed.
 "Orthogroup" is the label of the orthology analysis.
 "GeneSymbol" is a short name for the gene.
 "GeneEvidence" is the evidence backing the gene call.
 "GeneClass" is the attribution whenever possible to the core
 genome or to the shell or to the cloud. "COGcat" is the
 attribution to a functional COG category. 15.ThiobiusMAGandODIII6.csv
 md5=d28becd25f63777c699c8b61040f36ca Sumary of genome metrics, including
 the following columns: GenomeID, MD5, FileSize, ContigsNumber,
 Nucleotides, N50, BUSCO\_Completeness, CheckM\_Completeness,
 CheckM\_Contamination, CheckM\_Heterogeneity, GCcontentPerCent, tRNAs,
 AAtRNAs, MissingAAtRNA. "GenomeID" is a running number for a
 broader set of metagenomes that was tried, for which the best ones in
 terms of assembly metrics are used in this study. "MD5" is the
 hashtag signature of the bam file from where the fastq files pairs
 originate. "FileSize" is the file size in bytes of the bam file
 from where the fastq files pairs originate. "ContigsNumber" is
 the number of contigs the assembly includes. "Nucleotides" is
 the assembly size in number of nucleotides. "N50" is the metric
 of contiguity in nucleotides. "BUSCO\_Completeness",
 "CheckM\_Completeness", "CheckM\_Contamination",
 "CheckM\_Heterogeneity" are metrics of assembly quality.
 "tRNAs" is the number of encoded tRNAs. "AAtRNAs" is
 the number or amino acid transcriptions covered by the encoded tRNAs.
 "MissingAAtRNA" specifies what amino acid is not having tRNA, as
 a indication of incompleteness in the assembly. This file is
 semicolon-delimited with comma used as the decimal, instead of a period.
 16.MetaCycOUTCOME.csv md5=7a557d8c45186e0decaae663268eba90 Outcome of the
 MetaCyc pathways assessment including the following columns: LocalID,
 Pathway, MetaCycID, css, mso, tzb, tta, tbm, svs, tes, tea, epe, sti, avm,
 tdi, mpm, lpa, tms, toi, ts0, hhs, hcs, hki, hms, tcs, tca, tae, bss, bas,
 sup, taa, rma, voi, tss, TraitShortName, CoreTouched, KEEGm.
 "LocalID" is a running number. "Pathway" states the
 name of the metabolic pathway. "MetaCycID" is the label from
 MetaCyc database. "TraitShortName" is a short name for the
 trait. "CoreTouched" is wether the genes employed for the core
 genome phylogeny are touched by the pathway, where blank cells mean
 "no". "KEGGm" is the correspondent KEGG module.
 Organisms: avm,Allochromatium vinosum; bss,Bathymodiolus sp. SMAR
 symbiont; bas,Bathymodiolus azoricus symbiont; epe,Candidatus Endoriftia
 persephone; rma,Candidatus Ruthia magnifica; tzb,Candidatus Thiobios
 zoothamnieoli str. BelizeG43; tes,Candidatus Thiodiazotropha endoloripes;
 tea,Candidatus Thiodiazotropha endolucinida; taa,Candidatus Thioglobus
 autotrophica; tss,Candidatus Thioglobus singularis; toi,Candidatus
 Thiosymbion oneisti; voi,Candidatus Vesicomyosocius okutanii;
 css,Chrysomallon squamiferum symbiont; hcs,Hydrogenovibrio crunogenus;
 hhs,Hydrogenovibrio halophilus; hki,Hydrogenovibrio kuenenii;
 hms,Hydrogenovibrio marinus; lpa,Lamprocystis purpurea; mpm,Marichromatium
 purpuratum; mso,Milos strain ODIII6; sti,Sedimenticola thiotaurini;
 svs,Solemya velum symbiont; tms,Thioflavicoccus mobilis; tbm,Thiolapillus
 brandeum; tcs,Thiomicrorhabdus chilensis; tae,Thiomicrospira aerophila;
 tca,Thiomicrospira cyclica; tdi,Thiorhodococcus drewsii;
 ts0,Thiorhodovibrio sp. 970; tta,Thiosocius teredinicola; sup,uncultured
 SUP05 cluster bacterium. "1" stands for presence, and
 "0" for absence. Some columns (TraitShortName, KEGGm) contain
 empty cells, meaning that for that particular instance in that row, there
 is no information available from the analysis. This file is
 semicolon-delimited. 17.KEGGmOUTCOME.csv
 md5=00162551d1e98e5e7ba128cce9ecd4ad Outcome of the KEGG modules
 assessment including the following columns: LocalID, ModuleName, ModuleM,
 css, mso, tzb, tta, tbm, svs, tes, tea, epe, sti, avm, tdi, mpm, lpa, tms,
 toi, ts0, hhs, hcs, hki, hms, tcs, tca, tae, bss, bas, sup, taa, rma, voi,
 tss, TraitNumber, TraitShortName, CoreTouched. "LocalID" is a
 running number. "ModuleName" states the name of the KEGG module.
 "ModuleM" is the short KEGG identifier.
 "TraitShortName" is a short name for the trait.
 "CoreTouched" is wether the genes employed for the core genome
 phylogeny are touched by the module, where blank cells mean
 "no". Organisms: avm,Allochromatium vinosum; bss,Bathymodiolus
 sp. SMAR symbiont; bas,Bathymodiolus azoricus symbiont; epe,Candidatus
 Endoriftia persephone; rma,Candidatus Ruthia magnifica; tzb,Candidatus
 Thiobios zoothamnicoli str. BelizeG43; tes,Candidatus Thiodiazotropha
 endoloripes; tea,Candidatus Thiodiazotropha endolucinida; taa,Candidatus
 Thioglobus autotrophica; tss,Candidatus Thioglobus singularis;
 toi,Candidatus Thiosymbion oneisti; voi,Candidatus Vesicomyosocius
 okutanii; css,Chrysomallon squamiferum symbiont; hcs,Hydrogenovibrio
 crunogenus; hhs,Hydrogenovibrio halophilus; hki,Hydrogenovibrio kuenenii;
 hms,Hydrogenovibrio marinus; lpa,Lamprocystis purpurea; mpm,Marichromatium
 purpuratum; mso,Milos strain ODIII6; sti,Sedimenticola thiotaurini;
 svs,Solemya velum symbiont; tms,Thioflavicoccus mobilis; tbm,Thiolapillus
 brandeum; tcs,Thiomicrorhabdus chilensis; tae,Thiomicrospira aerophila;
 tca,Thiomicrospira cyclica; tdi,Thiorhodococcus drewsii;
 ts0,Thiorhodovibrio sp. 970; tta,Thiosocius teredinicola; sup,uncultured
 SUP05 cluster bacterium. “co”, complete; “1m”, one module missing; “2m”,
 two modules missing; “in”, incomplete, and "0" stands for
 absence. Some columns (e.g. GeneSymbol, GeneEvidence, ...) contain empty
 cells, meaning that for that particular instance in that row, there is no
 information available from the analysis. This file is semicolon-delimited.
 18.Espada-Hinojosa\_et\_al\_2022\_PrimaryData.Rmd
 md5=b7297234dc067b1dd587f91482ce7f62 R-Markdown Primary Data report code.
 This file is made available under CC0 license waiver.
 19.Espada-Hinojosa\_et\_al\_2022\_PrimaryData.html
 md5=88fb0354828aae82d00eee5c25a96eb2 R-Markdown Primary Data html report.
 This file is made available under CC0 license waiver.