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Supplemental Information

Ratio between the observed and the randomly expected frequency of HK genes located next to RR genes in the genome

Phylum abbreviations are explained in Table 1. The colored box represents the range of percentage values comprised between the 25% and the 75% quantiles, and the edges of the vertical bar denotes the upper and lower percentage values for each phylum.

DOI: 10.7287/peerj.preprints.1267v1/supp-1

List of the 7609 surveyed species, classified per phylum

DOI: 10.7287/peerj.preprints.1267v1/supp-2

Percentage of each TCS/PR protein type per phylum

Phylum abbreviations are given in Table 1.

DOI: 10.7287/peerj.preprints.1267v1/supp-3

Percentage of HK genes and RR genes that are neighbors in the genome to other TCS/PR genes

Phylum abbreviations are given in Table 1.

DOI: 10.7287/peerj.preprints.1267v1/supp-4

Odds ratios (ratio between the observed and the randomly expected frequency) of HK genes located next to RR and HK2 genes in the genome

Only species with HK and RR genes are taken into account in the percentages. Phylum abbreviations are given in Table 1.

DOI: 10.7287/peerj.preprints.1267v1/supp-5

Genomic distribution of all IST domain coding genes per phylum

Phylum abbreviations are given in Table 1. Here we list all combinations of HK, RR and HPt coding genes found in consecutive positions in the genome, sorted by the number of orphan genes (with no other IST domain coding genes).

DOI: 10.7287/peerj.preprints.1267v1/supp-6

Odds ratios (ratio between the observed and the randomly expected frequency) of HK genes located in the genome next to RR, HK2 and RR2 genes

Only species with HK and RR genes are taken into account in the percentages. Phylum abbreviations are given in Table 1.

DOI: 10.7287/peerj.preprints.1267v1/supp-7

Odds ratios (ratio between the observed and the randomly expected frequency) of HKRR genes located in the genome next to HK2 and RR2 genes

Only species with HKRR genes are taken into account in the percentages. Phyla without this type of protein (Aquificae, Tenericutes, Chlamydiae, Crenarchaeota, Korarchaeota, Nanoarchaeota, Nanohaloarchaeota, Alveolates, Euglenozoa, Microsporidians and Monocots) do not appear in the table. Phylum abbreviations are given in Table 1.

DOI: 10.7287/peerj.preprints.1267v1/supp-8

Odds ratios (ratio between the observed and the randomly expected frequency) of HKRRHPt genes located in the genome next to RR2 genes

Only species with HKRRHPt proteins are taken into account in the percentages. Prokaryotic phyla without this type of protein (Aquificae, Tenericutes, Deinococcus-Thermus, Fibrobacteres, Elusimicrobia, Armatimonadetes, Nitrospinae, Crenarchaeota, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Nanohaloarchaeota) do not appear in the table. Eukaryotes are not included in the table since we have not found any HKRRHPt protein in this domain. Phylum abbreviations are given in Table 1.

DOI: 10.7287/peerj.preprints.1267v1/supp-9

Odds ratios (ratio between the observed and the randomly expected frequency) of HKRRHK2 genes located in the genome next to RR2 genes

Only species with HKRRHK2 proteins are taken into account in the percentages. Phyla without this type of protein (Aquificae, Tenericutes, Hyperthermophilic bacteria, Chloroflexi, Gemmatimonadetes, Fibrobacteres, Chlamydiae, Lentisphaerae, Planctomycetes, Chlorobi, Fusobacteria, Chrysiogenetes, Elusimicrobia, Armatimonadetes, Epsilonproteobacteria, Zetaproteobacteria, Other Proteobacteria, Nitrospinae, Synergistetes, Crenarchaeota, Korarchaeota, Thaumarchaeota, Nanoarchaeota, Nanohaloarchaeota, Alveolates, Amoeboflagellate, Euglenozoa, Microsporidians and Monocots) do not appear in the table. Eukaryotic phyla are not included in this statistics because, although there are some eukaryotic species with HKRRHK2 proteins, none of those HKRRHK2 genes have been found neighboring an RR gene. Phylum abbreviations are given in Table 1.

DOI: 10.7287/peerj.preprints.1267v1/supp-10

Supplementary Appendix

File including all figures and tables redone to include hypothetical proteins. Results are similar to those obtained for the dataset where these proteins are excluded.

DOI: 10.7287/peerj.preprints.1267v1/supp-11

Additional Information

Competing Interests

The authors declare they have no competing interests.

Author Contributions

Baldiri Salvado conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Ester Vilaprinyo analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Albert Sorribas analyzed the data, wrote the paper, reviewed drafts of the paper.

Rui Alves conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Funding

This work was partially funded by Grant BFU2010-17704 from the Spanish MINECO and from small grants CMB and TR255 from University of Lleida to RA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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