Additional file 1: Figure S1. of Nitrous oxide emission by the non-denitrifying, nitrate ammonifier Bacillus licheniformis
Creators: name: Yihua Sun
name: Vos, Paul De
name: Heylen, Kim
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: Phylogenetic tree of full-length NarG. Sequences were taken from genomes included in the manuscript as well as all from publically available B. licheniformis genomes (dd June 2014) and genomes from other Bacillus species, protein ID or locus tag is given between brackets. The evolutionary history was inferred using the Neighbor-Joining method. The optimal tree with the sum of branch length = 1,68972248 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated. There were a total of 1094 positions in the final dataset. Evolutionary analyses were conducted in MEGA6. Figure S2. Phylogenetic tree of full-length NarK. Sequences were taken from several Bacillus species, as well as reference genomes, locus tag is given between brackets. The evolutionary history was inferred using the Neighbor-Joining method. The optimal tree with the sum of branch length = 6,03046656 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. All positions containing gaps and missing data were eliminated. There were a total of 358 positions in the final dataset. Evolutionary analyses were conducted in MEGA6. Figure S3. Whole genome clustering based on a similarity matrix using the peptidome content, in which amino acid sequences of a genome are converted to tryptic peptides, i.e. the tryptic peptidome. All publically available B. licheniformis genomes (dd June 2014) were included and are designated by their strain number: 9945A (accession number NC_021362), ATCC 14580 (accession number NC_006270), DSM 13 (=ATCC 14580; accession number NC_006322), 5-2-D (accession number NZ_AJLW01000000), F1-1 (accession number NZ_AZSL01000000), 3F-3 (accession number NZ_JFYM01000000), F2-1 (accession number NZ_AZSM01000000), WX-02 (accession number NZ_JH636050), 10-1-A (accession number NZ_AJLV01000001), CGMCC 3963 (accession number NZ_AMWQ01000000), CG-B52 (accession number NZ_AVEZ01000000). Analyses were performed using the Peptidome tool (http://unipept.ugent.be/). (DOCX 29Â kb)