Gaplasmid 1 0.49 Megaplasmid 2 0.39 Megaplasmid 3 0.20 Plasmid 1 Plasmid 2 0.098 0.MIGSSequencing platformsunknown ATTJ01000004 circular circular ATTJ01000005 ATTJMIGS 31.2 MIGS 30 MIGSFold coverage Assemblers Gene calling methodA18 5 3 17 26 13 15 22 19Locus Tag Genbank ID GenBank Date of Release GOLD ID Luteolin 7-O-��-D-glucoside cost BIOPROJECT MIGS 13 Source Material Identifier Project relevanceD. ficus DSMATTJ00000000.1 07/09/2013 Gp0007971 PRJNA157079 EXB L-1957 DNA repair mechanisms, bioremediationscaffolds1 6 7 10 14 20 21 24 25 23 8 30 11 16 9 2 27 1 2 3 4were corrected with manual editing in Consed [25?7]. Gap closure was accomplished using repeat resolution software [Wei Gu, unpublished], and sequencing of bridging PCR fragments with Sanger and/or PacBio technologies [Cliff Han, unpublished]. A total of 21 PCR PacBio consensus sequences were completed to close gaps and to raise the quality of the final sequence.Genome annotationcontigsD. ficus KS0 20 percent similarity 80BNC_000959 plasmid CP1 NC_000958 plasmid M1 NC_001264 chromosomeThe genome sequence was annotated using the JGI Prokaryotic Automatic Annotation Pipeline [28] and further reviewed using the Integrated Microbial Genomes Expert Review platform [29]. Genes were predicted using Prodigal [30], followed by a round of manual curation using the JGI GenePRIMP pipeline [31]. The genome PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28298493 sequence was analyzed and released publicly through the Integrated Microbial Genomes platform [32]. BLASTClust was used to identify internal clusters with thresholds of 70 covered length and 30 sequence identity [33]. SignalP [34] and TMHMM [35] were used to predict signal peptides and transmembrane helices, respectively.D. radiodurans BAA-NC_001263 chromosome4contigsGenome properties The D. ficus KS 0460 genome consists of a 4,019,382 bp sequence which represents six genome partitions: 2.84, 0.49, 0.39, 0.20, 0.098 and 0.007 Mbp (Table 3), consistent with PFGE (Fig. 2d); note, the smallest partition (0.007 Mbp) was too small to resolve by PFGE. The final assembly was based on 4946 Mbp of Illumina draft data, which providedD. ficus KSFig. 3 Genomic alignment of D. ficus KS 0460 with D. ficus DSM 19119 or D. radiodurans BAA-816. a Strain KS 0460 versus strain DSM 19119. b Strain KS 0460 versus strain BAA-816. Six-frame translations of scaffolds were aligned with Mummer 3.23. Homologous regions are plotted as dots, colored according to the similarity of the aligned loci. Diagonal lines of dots represent syntenic regions. Only contigs longer than 20 kbp are shown. Axes are not drawn to scaleMatrosova et al. Standards in Genomic Sciences (2017) 12:Page 7 ofan average of 1237?coverage of the genome. The total genomic GC content was 69.7 and was similar across all but the smallest contig, which contained 62.5 GC. The genome contains 3827 predicted protein-coding genes and 67 RNA-coding genes (total 3894).Table 5 Number of genes associated with general COG functional categoriesCode J A K L B D V T M N U O C G E F H I P Q R S Value 226 0 166 97 0 43 71 228 146 25 23 125 152 179 280 90 149 116 138 58 217 145 1080 age 6 0 4 3 0 1 2 6 4 1 1 3 4 5 7 2 4 3 4 2 6 4 28 Description Translation, ribosomal structure and biogenesis RNA processing and modification Transcription Replication, recombination and repair Chromatin structure and dynamics Cell cycle control, Cell division, chromosome partitioning Defense mechanisms Signal transduction mechanisms Cell wall/membrane biogenesis Cell motility Intracellular.
