31 research outputs found
switchgrass_upland_panel_up_cnv_list.txt
switchgrass_upland_panel_up_cnv_list.tx
SNIPE_all_plates_matrix_biallelic_only_nomissing.txt
SNIPE_all_plates_matrix_biallelic_only_nomissing.tx
Pvirgatum_v1.1_273_gene_exons_updated_ChrUn_representative.gff3
Pvirgatum_v1.1_273_gene_exons_updated_ChrUn_representative.gff
Pvirgatum_v1.1_273_hardmasked_ChrUn.fasta
Pvirgatum_v1.1_273_hardmasked_ChrUn.fast
SNIPE_all_plates_matrix_biallelic_only_nomissing.exonic_variant_function
SNIPE_all_plates_matrix_biallelic_only_nomissing.exonic_variant_functio
Draft genome sequence of <i>Actinotignum schaalii</i> DSM 15541<sup>T</sup>: Genetic insights into the lifestyle, cell fitness and virulence
<div><p>The permanent draft genome sequence of A<i>ctinotignum schaalii</i> DSM 15541<sup>T</sup> is presented. The annotated genome includes 2,130,987 bp, with 1777 protein-coding and 58 rRNA-coding genes. Genome sequence analysis revealed absence of genes encoding for: components of the PTS systems, enzymes of the TCA cycle, glyoxylate shunt and gluconeogensis. Genomic data revealed that <i>A</i>. <i>schaalii</i> is able to oxidize carbohydrates via glycolysis, the nonoxidative pentose phosphate and the Entner-Doudoroff pathways. Besides, the genome harbors genes encoding for enzymes involved in the conversion of pyruvate to lactate, acetate and ethanol, which are found to be the end products of carbohydrate fermentation. The genome contained the gene encoding Type I fatty acid synthase required for <i>de novo</i> FAS biosynthesis. The <i>plsY</i> and <i>plsX</i> genes encoding the acyltransferases necessary for phosphatidic acid biosynthesis were absent from the genome. The genome harbors genes encoding enzymes responsible for isoprene biosynthesis via the mevalonate (MVA) pathway. Genes encoding enzymes that confer resistance to reactive oxygen species (ROS) were identified. In addition, <i>A</i>. <i>schaalii</i> harbors genes that protect the genome against viral infections. These include restriction-modification (RM) systems, type II toxin-antitoxin (TA), CRISPR-Cas and abortive infection system. <i>A</i>. <i>schaalii</i> genome also encodes several virulence factors that contribute to adhesion and internalization of this pathogen such as the <i>tad</i> genes encoding proteins required for pili assembly, the <i>nanI</i> gene encoding exo-alpha-sialidase, genes encoding heat shock proteins and genes encoding type VII secretion system. These features are consistent with anaerobic and pathogenic lifestyles. Finally, resistance to ciprofloxacin occurs by mutation in chromosomal genes that encode the subunits of DNA-gyrase (GyrA) and topisomerase IV (ParC) enzymes, while resistant to metronidazole was due to the <i>frxA</i> gene, which encodes NADPH-flavin oxidoreductase.</p></div
SNIPE_all_plates_matrix_unfiltered.txt
SNIPE_all_plates_matrix_unfiltered.tx
Comparison of the amino acid sequences of the QRDRs of both GyrA and ParC in <i>A</i>. <i>schaalii</i> with the equivalent region of <i>E</i>. <i>coli</i>.
<p>Hotspots for mutation giving rise to fluoroquinolone resistance are at serine 83 and aspartate 87 of the GyrA and at serine 80 and aspartate 84 of ParC (according to <i>E</i>. <i>coli</i> numbering).</p
Toxin-antitoxin systems of <i>Actinotignum schaalii</i>.
<p>Toxin-antitoxin systems of <i>Actinotignum schaalii</i>.</p
General genome characteristics of <i>Actinotignum schaalii</i> DSM 15541<sup>T</sup>.
<p>General genome characteristics of <i>Actinotignum schaalii</i> DSM 15541<sup>T</sup>.</p