PGG Core Genes - Tables F1000.xlsx

This is a collection of Excel spreadsheet tables in support of the article "A pan-genome method to determine core regions of the <i>Bacillus subtilis </i>and <i>Escherichia coli</i> genomes" DOI (10.12688/f1000research.51873.1). The tables show characteristics of pan-genome graph (PGG) determined core genes for <i>Bacillus subtilis </i>and <i>Escherichia coli.</i><i><br></i><b>Table 1</b>. Pan-genome graph statistics for<i> B. subtilis </i>and <i>E. coli</i>.<b>Table 2. </b>The number of deleted genes from <i>B. subtilis</i> reduced strains which are noncore versus core.<b></b><b>Table 3. </b>Large noncore regions which have not been deleted from any of the strains delta 6, IIG-Bs27-47-24, or PG10, PS38.<b>Supplementary Table 1</b>. All <i>B. subtilis </i>genes compared to the PGG based annotation of core regions for the type strain genome used by Kobayashi et al and Koo et al. (strain 168, GenBank sequence AL009126.3, BioSample SAMEA3138188, Assembly ASM904v1<b>/</b>GCF_000009045.1). Columns 1-5 are the start, stop, strand, OGC, and OGC size for the PGG annotation. Columns 6-11 are the gene type, start, stop, strand, locus tag, and gene symbol/name for the GenBank annotation. Column 12 is a list of synonyms for <i>B. subtilis</i> genes associated with the Koo and Kobayashi genes. Column 13 is the Koo et al. gene symbol/name. Columns 14-15 are the Kobayashi et al. gene symbol/name and evidence type (from Supporting Table 4 “RB, reference to study with <i>Bacillus subtilis</i>; RO, reference to study with other bacteria; TW, this work; TW*, inactivation failed but IPTG mutant could not be made”). Columns 16-17 are the GenBank protein product accession and name. Column 18 is the PGG core or non-core region the gene is contained in. Column 19 indicates if the gene is in <i>MiniBacillus</i>. Columns 20-23 show genes deleted for strains delta 6, IIG-Bs27-47-24, PG10, and PS38 respectively. <b>Supplementary Table 2. </b>The 305 <i>B. subtilis</i> genes deemed essential by either Kobayashi et al. or Koo et al. These genes are compared to the PGG based annotation of core regions for the type strain genome used by Kobayashi et al. and Koo et al. (strain 168, GenBank sequence AL009126.3, BioSample SAMEA3138188, Assembly ASM904v1<b>/</b>GCF_000009045.1). Columns 1-5 are the start, stop, strand, OGC, and OGC size for the PGG annotation. Columns 6-11 are the gene type, start, stop, strand, locus tag, and gene symbol/name for the GenBank annotation. Column 12 is a list of synonyms for <i>B. subtilis</i> genes associated with the Koo and Kobayashi genes. Column 13 is the Koo et al. gene symbol/name. Columns 14-15 are the Kobayashi et al. gene symbol/name and evidence type (from Supporting Table 4 “RB, reference to study with <i>Bacillus subtilis</i>; RO, reference to study with other bacteria; TW, this work; TW*, inactivation failed but IPTG mutant could not be made”). Columns 16-17 are the GenBank protein product accession and name. Column 18 is the PGG core or non-core region the gene is contained in. <b>Supplementary Table 3</b>. The 258 <i>B. subtilis</i> core regions identified through the pan-genome graph.<b> </b><b>Supplementary Table 4</b>. All <i>B. subtilis </i>tRNA and rRNA genes for the type strain genome (strain 168, GenBank sequence AL009126.3, BioSample SAMEA3138188, Assembly ASM904v1<b>/</b>GCF_000009045.1) compared to the refined PGG. Columns 1-5 are the start, stop, strand, OGC, and OGC size for the PGG annotation. Columns 6-11 are the gene type, start, stop, strand, locus tag, and gene symbol/name for the GenBank annotation. <b>Supplementary Table 5</b>. The 108 <i>B. subtilis</i> genomes used in the study. Data is from GenBank RefSeq: BioSample ID, Assembly ID, GenBank Species, GenBank Strain, Genome SIaze, and whether the genome is a type strain.<b> </b><b>Supplementary Table 6. </b>The 414 <i>E. coli</i> genes deemed essential by Goodall et al., Baba et al., or Yamazaki et al. These genes are compared to the PGG based annotation of core regions for the K-12 BW25113 strain used by Goodall (GenBank sequence CP009273.1, Assembly ASM75055v1/GCA_000750555.1, BioSample SAMN03013572). Columns 1-5 are the start, stop, strand, OGC, and OGC size for the PGG annotation. Columns 6-11 are the gene type, start, stop, strand, locus tag, and gene symbol/name for the GenBank annotation. Column 12 is a list of gene synonyms for the gene from GenBank. Columns 13-21 are from Goodall et al.: 13-15 from Table S1 (normal essentiality), 16-18 from Table S4 (essentiality after outgrowth), 19-20 from Table S3 (outlier discrepancies), and 21 from Table S2 (comparison of data sets). Column 22 is the PGG core or non-core region the gene is contained in.<b>Supplementary Table 7</b>. The 521<i> E. coli </i>core regions identified through the pan-genome graph.<b>Supplementary Table 8</b>. All <i>E. coli </i>genes compared to the PGG based annotation of core regions for the K-12 BW25113 strain used by Goodall (GenBank sequence CP009273.1, Assembly ASM75055v1/GCA_000750555.1, BioSample SAMN03013572). Columns 1-5 are the start, stop, strand, OGC, and OGC size for the PGG annotation. Columns 6-11 are the gene type, start, stop, strand, locus tag, and gene symbol/name for the GenBank annotation. Column 12 is a list of gene synonyms for the gene from GenBank. Columns 13-21 are from Goodall et al.: 13-15 from Table S1 (normal essentiality), 16-18 from Table S4 (essentiality after outgrowth), 19-20 from Table S3 (outlier discrepancies), and 21 from Table S2 (comparison of data sets). Column 22 is the PGG core or non-core region the gene is contained in. <b>Supplementary Table 9</b>. The 971 <i>E. coli</i> genomes used in the study. Data is from GenBank RefSeq: BioSample ID, Assembly ID, GenBank Species, GenBank Strain, Genome SIaze, and whether the genome is a type strain.<i></i>