Gene/Enzyme molecular evolution rates across each major taxonomic group of photosynthetic organisms

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.

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.zip
Bacteria__Enzyme__Evolution_Rate_Data.zip
Red_Algae__Enzyme__Evolution_Rate_Data.zip
Green_Algae__Enzyme__Evolution_Rate_Data.zip
SAR__Enzyme__Evolution_Rate_Data.zip

Compressed files containing nucleotide/amino acid molecular evolution rates across all enzymes in each major taxonomic group of photosynthetic organisms:
Bacteria__Evolution_Rate_Data.zip
Land_Plants__Evolution_Rate_Data.zip
SAR__Evolution_Rate_Data.zip
Green_Algae__Evolution_Rate_Data.zip
Red_Algae__Evolution_Rate_Data.zip

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For an in-depth description of the analyses performed and all methodological details pertaining to this dataset, please refer to:
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/10.1101/2022.07.06.498985
Available at: [https://www.biorxiv.org/content/10.1101/2022.07.06.498985v2]

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For a brief description of this dataset:
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. Proceedings of the National Academy of Sciences, 116(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.

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Information on Column Headers:
Taxa: Taxonomic group to which the species belong
CDS.AA: Extent of nucleotide evolution or amino acid evolution being measured
Species_Comparison: Name of both species being compared
Species1: Name of Species 1 being compared
Species2: Name of Species 2 being compared
Species1_ortholog: Gene ID of Species 1 being compared
Species2_ortholog: Gene ID of Species 2 being compared
Taxa_Specific_Orthogroup_ID: Orthogroup to which the compared genes belong to
TreeModel: Model of sequence evolution used for phylogenetic gene tree inference
Phylogenetic_Distance: Extent of molecular evolution separating compared genes

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List of all species in each taxonomic group included in the present analysis:
Bacteria
Acaryochloris marina
Acidithiobacillus ferrooxidans
Allochromatium vinosum
Anabaenopsis circularis
Arthrospira platensis
Aurantimonas manganoxydans
Crocosphaera subtropica
Gloeobacter kilaueensis
Gloeobacter violaceus
Gloeomargarita lithophora
Halomicronema hongdechloris
Hydrogenophaga pseudoflava
Methylacidimicrobium cyclopophantes
Methylacidimicrobium tartarophylax
Methylacidiphilum fumariolicum
Methylacidiphilum infernorum
Microcystis aeruginosa
Microcystis viridis
Nocardia nova
Nocardia seriolae
Novimethylophilus kurashikiensis
Phaeobacter gallaeciensis
Phormidesmis priestleyi
Planktothrix agardhii
Prochlorococcus marinus
Prochlorothrix hollandica
Raphidiopsis brookii
Synechococcus elongatus
Thermosynechococcus elongatus
Thermosynechococcus vulcanus
Thioflexothrix psekupsii
Trichormus variabilis

Land Plants
Aegilops tauschii
Amaranthus hypochondriacus
Arabidopsis thaliana
Brassica napus
Brassica oleracea
Brassica rapa
Camellia sinensis
Capsicum annuum
Cucumis sativus
Dendrobium catenatum
Glycine soja
Gossypium hirsutum
Hevea brasiliensis
Hordeum vulgare
Lactuca sativa
Mucuna pruriens
Nicotiana attenuata
Oryza sativa
Panicum virgatum
Phaseolus vulgaris
Salvia splendens
Sorghum bicolor
Spinacia oleracea
Triticum aestivum
Triticum turgidum
Triticum urartu
Zea mays

Green Algae
Botryococcus braunii
Chromochloris zofingiensis
Dunaliella salina
Volvox carteri

Red Algae
Chondrus crispus
Cyanidiococcus yangmingshanensis
Galdieria sulphuraria
Gracilariopsis chorda
Porphyra umbilicalis
Porphyridium purpureum

SAR
Aureococcus anophagefferens
Ectocarpus siliculosus
Fistulifera solaris
Microchloropsis salina
Nannochloropsis gaditana
Phaeodactylum tricornutum
Thalassiosira oceanica
Thalassiosira pseudonana