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Staphylococcus pseudintermedius strain SPSE-22-VL-SD-NC-0024 isolate Canis lupus familiaris, whole genome shotgun sequencing project

GenBank: ABJSQW000000000.1

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

LOCUS       ABJSQW010000000           46 rc    DNA     linear   BCT 08-DEC-2022
DEFINITION  Staphylococcus pseudintermedius strain SPSE-22-VL-SD-NC-0024
            isolate Canis lupus familiaris, whole genome shotgun sequencing
            project.
ACCESSION   ABJSQW000000000
VERSION     ABJSQW000000000.1
DBLINK      BioProject: PRJNA318594
            BioSample: SAMN32112164
            Sequence Read Archive: SRR22575679
KEYWORDS    WGS.
SOURCE      Staphylococcus pseudintermedius
  ORGANISM  Staphylococcus pseudintermedius
            Bacteria; Bacillati; Bacillota; Bacilli; Bacillales;
            Staphylococcaceae; Staphylococcus; Staphylococcus intermedius
            group.
REFERENCE   1  (bases 1 to 46)
  CONSRTM   Veterinary Laboratory Investigation and Response Network
  TITLE     Direct Submission
  JOURNAL   Submitted (08-DEC-2022) Center for Veterinary Medicine, US Food and
            Drug Administration, 8401 Muirkirk Rd, Laurel, MD, USA
COMMENT     The Staphylococcus pseudintermedius whole genome shotgun (WGS)
            project has the project accession ABJSQW000000000.  This version of
            the project (01) has the accession number ABJSQW010000000, and
            consists of sequences ABJSQW010000001-ABJSQW010000046.
            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         :: 08-DEC-2022
            Assembly Method       :: SKESA v. 2.2
            Assembly Name         :: PDT001517158.1
            Long Assembly Name    :: NCBI Pathogen Detection Assembly
                                     PDT001517158.1
            Genome Coverage       :: 329x
            Sequencing Technology :: ILLUMINA
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Date                   :: 12/08/2022 21:10:58
            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)                     :: 2,430
            CDSs (total)                      :: 2,363
            Genes (coding)                    :: 2,315
            CDSs (with protein)               :: 2,315
            Genes (RNA)                       :: 67
            rRNAs                             :: 2, 2, 2 (5S, 16S, 23S)
            complete rRNAs                    :: 2 (5S)
            partial rRNAs                     :: 2, 2 (16S, 23S)
            tRNAs                             :: 56
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 48
            CDSs (without protein)            :: 48
            Pseudo Genes (ambiguous residues) :: 0 of 48
            Pseudo Genes (frameshifted)       :: 24 of 48
            Pseudo Genes (incomplete)         :: 22 of 48
            Pseudo Genes (internal stop)      :: 12 of 48
            Pseudo Genes (multiple problems)  :: 9 of 48
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..46
                     /organism="Staphylococcus pseudintermedius"
                     /mol_type="genomic DNA"
                     /strain="SPSE-22-VL-SD-NC-0024"
                     /isolate="Canis lupus familiaris"
                     /isolation_source="Urine (Canis lupus familiaris)"
                     /db_xref="taxon:283734"
                     /geo_loc_name="USA: NC"
                     /collection_date="2022-06-06"
                     /collected_by="NCSU"
WGS         ABJSQW010000001-ABJSQW010000046
//
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