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Cronobacter sakazakii strain CFSAN135062, whole genome shotgun sequencing project

GenBank: ABPDNR000000000.1

  • This entry is the master record for a whole genome shotgun sequencing project and contains no sequence data.

LOCUS       ABPDNR010000000           37 rc    DNA     linear   BCT 25-JAN-2024
DEFINITION  Cronobacter sakazakii strain CFSAN135062, whole genome shotgun
            sequencing project.
ACCESSION   ABPDNR000000000
VERSION     ABPDNR000000000.1
DBLINK      BioProject: PRJNA258403
            BioSample: SAMN38370670
            Sequence Read Archive: SRR26919271
KEYWORDS    WGS.
SOURCE      Cronobacter sakazakii
  ORGANISM  Cronobacter sakazakii
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Cronobacter.
REFERENCE   1  (bases 1 to 37)
  CONSRTM   GenomeTrakr network: Whole genome sequencing for foodborne pathogen
            traceback
  TITLE     Direct Submission
  JOURNAL   Submitted (22-NOV-2023) Center for Food Safety and Applied
            Nutrition, US Food and Drug Administration, 5100 Paint Branch Pkwy,
            College Park, MD, USA
COMMENT     The Cronobacter sakazakii whole genome shotgun (WGS) project has
            the project accession ABPDNR000000000.  This version of the project
            (01) has the accession number ABPDNR010000000, and consists of
            sequences ABPDNR010000001-ABPDNR010000037.
            The annotation was added by the assembly submitters using the NCBI
            Prokaryotic Genome Annotation Pipeline (PGAP). Information about
            stand-alone PGAP can be found here: https://github.com/ncbi/pgap/
            This draft WGS assembly was generated by running SKESA to generate
            a de-novo assembly. The de-novo assembly was then concatenated with
            contigs generated using a guided assembler using antimicrobial
            resistance genes as baits to comprehensively catalog the set of
            resistance genes in the isolate. Note, some parts of the contigs
            derived from the guided assembler may overlap de-novo contigs, and
            other guided assembler contigs. De-novo contigs can be
            differentiated from guided assembler contigs by their names , which
            include either 'denovo' or 'guided'.
            
            ##Genome-Assembly-Data-START##
            Assembly Date         :: 22-NOV-2023
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT001996205.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT001996205.1
            Genome Coverage       :: 92x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 11/23/2023 02:25:15
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Provider               :: NCBI
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA;
                                                 repeat_region
            Annotation Software revision      :: 2021-01-11.build5132
            Genes (total)                     :: 4,298
            CDSs (total)                      :: 4,209
            Genes (coding)                    :: 4,123
            CDSs (with protein)               :: 4,123
            Genes (RNA)                       :: 89
            rRNAs                             :: 5, 2, 4 (5S, 16S, 23S)
            complete rRNAs                    :: 5 (5S)
            partial rRNAs                     :: 2, 4 (16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 86
            CDSs (without protein)            :: 86
            Pseudo Genes (ambiguous residues) :: 0 of 86
            Pseudo Genes (frameshifted)       :: 22 of 86
            Pseudo Genes (incomplete)         :: 56 of 86
            Pseudo Genes (internal stop)      :: 12 of 86
            Pseudo Genes (multiple problems)  :: 4 of 86
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..37
                     /organism="Cronobacter sakazakii"
                     /mol_type="genomic DNA"
                     /strain="CFSAN135062"
                     /isolation_source="grain"
                     /db_xref="taxon:28141"
                     /geo_loc_name="USA"
                     /collection_date="2023-03-01"
                     /collected_by="FDA Contracted Laboratory"
WGS         ABPDNR010000001-ABPDNR010000037
//
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