| utogig {JMDplots} | R Documentation |
Plots from the paper by Dick et al. (2023).
utogig1(pdf = FALSE)
utogig2(pdf = FALSE, logact = -3)
utogig3(pdf = FALSE)
utogig4(pdf = FALSE)
utogigS1(pdf = FALSE)
utogigS2(pdf = FALSE)
utogigS4(pdf = FALSE)
calc_logaH2_intermediate(class = NULL, logact = -3)
pdf |
logical, make a PDF file? |
logact |
numeric, logarithm of activity of organic species |
class |
character, organic compound class |
This table gives a brief description of each plotting function.
utogig1 | Chemical analysis of reference proteomes of methanogens reveals adaptation to redox conditions |
utogig2 | Relative stabilities of organic compounds depend on redox conditions |
utogig3 | Thermodynamic model for methanogen niche partitioning |
utogig4 | Chemical and thermodynamic analysis of evolutionary divergence along redox gradients |
utogigS1 | Comparison of ZC of proteomes predicted by Glimmer and downloaded from NCBI |
utogigS2 | Association between redox gradients and ZC of proteins and lipids in alkaline Yellowstone hot springs |
utogigS4 | logaH2-T plots for different organic compound classes |
utogig3(logact = -6) is used to make Figure S3.
utogig3() and utogig3(logact -6) print p-values that are used to make Table S5.
utogig4() returns an invisible data frame of p-values that is used to make Table S6 and prints values of logaH2 retrieved from the thermodynamic analysis in Figure 4b.
calc_logaH2_intermediate is used to find intermediate logaH2, where affinity vs Zc has a slope of 0, for a group of organic compounds.
class gives the class of compounds to consider , or NULL to consider compounds in all classes at once.
The output is saved in files named ‘H2_intermediate_*.csv’ (see description below), which are used for making some of the plots.
Optimal growth temperatures (°C) of methanogens compiled from the literature.
Amino acid compositions of reference proteomes of methanogens. See ‘R/utogig.R’ for the code used to make this file.
H2 concentrations measured in methanogenic and non-methanogenic sediments, from Lovley and Goodwin (1988).
Intermediate logaH2 (where the slope of affinity vs ZC is zero) for organic compounds, calculated using calc_logaH2_intermediate with logact set to -3 or -6.
Intermediate logaH2 for different classes of organic compounds (‘C1andC2’, ‘Acid’, ‘Aminoacid’, ‘Sugar’, ‘Nucleobase’, ‘TCA’), all with logact set to -3.
Hierarchical clustering tree for functional genes of Class I and Class I methanogens. Tree was digitized and modified from Fig. 1 of Lyu and Lu (2018) and is provided in Newick format.
Amino acid compositions for predicted proteomes of basal, terrestrial, and shallow-water groups of Thaumarchaeota (habitats are listed in the ‘protein’ column). Proteins were predicted using Glimmer version 3.02b (Delcher et al., 1999) from the genomes downloaded from NCBI (accession numbers in the ‘organisms’ column).
Amino acid compositions for proteomes of basal, terrestrial, shallow- and deep-water groups of Thaumarchaeota obtained from IMG (numeric TaxonID in the ‘organisms’ column) or NCBI (alphanumeric accession number in the ‘organisms’ column). Taxon IDs and accession numbers were taken from Table S1 of Ren et al. (2019)
.
Nif_homolog_genomes.R, Nif_homolog_genomes.csv, Nif_homolog_AA.csvThe R script reads Supplemental Table 1A of Poudel et al. (2018) and adds the columns ‘Refseq.name’ and ‘taxid’, which contain the closest matching genome name in the RefSeq database (see chem16S-package) and corresponding taxonomic ID.
Output file #1: Names of genomes (organisms) containing different nitrogenase (Nif) homologs.
Output file #2: Amino acid compositions of RefSeq proteomes for each matched genome.
Delcher AL, Harmon D, Kasif S, White O and Salzberg SL (1999) Improved microbial gene identification with Glimmer. Nucleic Acids Res. 27, 4636–4641. doi:10.1093/nar/27.23.4636
Dick JM, Boyer GM, Canovas PA III and Shock EL (2023) Using thermodynamics to obtain geochemical information from genomes. Geobiology 21, 262–273. doi:10.1111/gbi.12532
Lovley DR and Goodwin S (1988) Hydrogen concentrations as an indicator of the predominant terminal electron-accepting reactions in aquatic sediments. Geochim. Cosmochim. Acta 52, 2993–3003. doi:10.1016/0016-7037(88)90163-9
Lyu Z and Lu Y (2018) Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments. ISME J. 12, 411–423. doi:10.1038/ismej.2017.173
Ren M, Feng X et al. (2019) Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. ISME J. 13, 2150–2161. doi:10.1038/s41396-019-0418-8
utogigS1()