DOI: 10.6084/m9.figshare.24994625
title: Gene/Enzyme molecular evolution rates across each major taxonomic group of photosynthetic organisms

description: Compressed raw data files including the extent of molecular evolution in Form I rubisco as well as all other genes/enzymes encoded by each taxonomic group of photosynthetic organisms.Data are included in compressed files in “tsv” format.<br>Compressed files containing nucleotide/amino acid molecular evolution rates across all genes in each major taxonomic group of photosynthetic organisms:Land_Plants__Enzyme__Evolution_Rate_Data.zipBacteria__Enzyme__Evolution_Rate_Data.zipRed_Algae__Enzyme__Evolution_Rate_Data.zipGreen_Algae__Enzyme__Evolution_Rate_Data.zipSAR__Enzyme__Evolution_Rate_Data.zip<br>Compressed files containing nucleotide/amino acid molecular evolution rates across all enzymes in each major taxonomic group of photosynthetic organisms:Bacteria__Evolution_Rate_Data.zipLand_Plants__Evolution_Rate_Data.zipSAR__Evolution_Rate_Data.zipGreen_Algae__Evolution_Rate_Data.zipRed_Algae__Evolution_Rate_Data.zip<br>##<b>For an in-depth description of the analyses performed and all methodological details pertaining to this dataset, please refer to:</b>Bouvier, J.W., Emms, D.M. and Kelly, S., 2022. Rubisco is evolving for improved catalytic efficiency and CO2 assimilation in plants. bioRxiv, doi: https://doi.org/10.1101/2022.07.06.498985Available at: [https://www.biorxiv.org/content/10.1101/2022.07.06.498985v2]<br>##<b>For a brief description of this dataset:</b>These raw data contain measurements of the extent of nucleotide/amino acid evolution in all genes/enzymes across different taxa.Species included in this analysis are those for which both an rbcL and rbcS sequence could be obtained from the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/) and for which a whole-genome gene assembly was publicly available (see table below).Genes included in this analysis have been subject to data filtering processes as described in the above published manuscript. Other than rbcL, only gene sequences encoded by the nuclear genomes of species in the land plant, green algae, red algae and SAR taxonomic groups are included. All organellar genes in the bacteria were included subject to data filtering. The set of genes within each species that encode enzymes was determined using the DeepEC deep learning-based classifier algorithm (Ryu, J.Y., Kim, H.U. and Lee, S.Y., 2019. <i>Proceedings of the National Academy of Sciences</i>, <i>116</i>(28), 13996-14001). Each row in the data file contains the extent of molecular evolution for a unique gene ortholog pair per species comparison. These gene ortholog comparisons have been calculated for rbcL/RbcL and rbcS/RbcS, as well as all other genes/protein pairs.To assess the extent of rubisco molecular evolution in context all other genes/enzymes as the basis of our analysis, the percentile rank rate of rubisco nucleotide or protein evolution was computed relative to the cohort of nucleotide/protein evolution in all other genes/enzymes for that unique species comparison. In our analysis, a minimum threshold of 100 measurements for orthologous genes and protein sequences was ensured per species pair. In cases where multiple percentiles are calculated for a rubisco subunit in a given species pair (due to gene duplications in the rbcS of some species, or due to a single species gene assembly matching multiple sub-species in the rubisco sequence dataset) the mean percentile was taken.<br>##<b>Information on Column Headers:</b>Taxa: Taxonomic group to which the species belongCDS.AA: Extent of nucleotide evolution or amino acid evolution being measuredSpecies_Comparison: Name of both species being comparedSpecies1: Name of Species 1 being comparedSpecies2: Name of Species 2 being comparedSpecies1_ortholog: Gene ID of Species 1 being comparedSpecies2_ortholog: Gene ID of Species 2 being comparedTaxa_Specific_Orthogroup_ID: Orthogroup to which the compared genes belong toTreeModel: Model of sequence evolution used for phylogenetic gene tree inferencePhylogenetic_Distance: Extent of molecular evolution separating compared genes<br>##<b>List of all species in each taxonomic group included in the present analysis:</b>BacteriaAcaryochloris marinaAcidithiobacillus ferrooxidansAllochromatium vinosumAnabaenopsis circularisArthrospira platensisAurantimonas manganoxydansCrocosphaera subtropicaGloeobacter kilaueensisGloeobacter violaceusGloeomargarita lithophoraHalomicronema hongdechlorisHydrogenophaga pseudoflavaMethylacidimicrobium cyclopophantesMethylacidimicrobium tartarophylaxMethylacidiphilum fumariolicumMethylacidiphilum infernorumMicrocystis aeruginosaMicrocystis viridisNocardia novaNocardia seriolaeNovimethylophilus kurashikiensisPhaeobacter gallaeciensisPhormidesmis priestleyiPlanktothrix agardhiiProchlorococcus marinusProchlorothrix hollandicaRaphidiopsis brookiiSynechococcus elongatusThermosynechococcus elongatusThermosynechococcus vulcanusThioflexothrix psekupsiiTrichormus variabilis<br>Land PlantsAegilops tauschiiAmaranthus hypochondriacusArabidopsis thalianaBrassica napusBrassica oleraceaBrassica rapaCamellia sinensisCapsicum annuumCucumis sativusDendrobium catenatumGlycine sojaGossypium hirsutumHevea brasiliensisHordeum vulgareLactuca sativaMucuna pruriensNicotiana attenuataOryza sativaPanicum virgatumPhaseolus vulgarisSalvia splendensSorghum bicolorSpinacia oleraceaTriticum aestivumTriticum turgidumTriticum urartuZea mays<br>Green AlgaeBotryococcus brauniiChromochloris zofingiensisDunaliella salinaVolvox carteri<br>Red AlgaeChondrus crispusCyanidiococcus yangmingshanensisGaldieria sulphurariaGracilariopsis chordaPorphyra umbilicalisPorphyridium purpureum<br>SARAureococcus anophagefferensEctocarpus siliculosusFistulifera solarisMicrochloropsis salinaNannochloropsis gaditanaPhaeodactylum tricornutumThalassiosira oceanicaThalassiosira pseudonana<br>