Candidatus Hodgkinia cicadicola strain MAGTDC chromosome variant14, whole genome shotgun sequence.
type: Entry
definition: Candidatus Hodgkinia cicadicola strain MAGTDC chromosome variant14, whole genome shotgun sequence.
sequence version: NZ_CM008774.1
sequence date: 2023-04-10
sequence: sequence
division: CON
label: NZ_CM008774.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN07255135
keyword: WGS
keyword: RefSeq
source: Candidatus Hodgkinia cicadicola
organism: Candidatus Hodgkinia cicadicola
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Candidatus Hodgkinia.
reference: 1
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCM008774.1.\nBacteria and source DNA available from McCutcheon Lab.\n\nThis endosymbiotic bacterium typically consists of a single, highly\npolyploid (a few hundred copies of the genome) chromosome. In this\ncase however, the single chromosome has split into several dozen\nlineages, each with a different reduced version of the ancestral\nsingle chromosome. The chromosomes were named variantX to\ndistinguish them from each other. Some of the chromosomes are\ncomplete circular molecules, while others are likely circular\nmolecules but they still have a run of N's at the end of the\ncomponent contig to close the gap.\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Genome-Assembly-Data-START##\nAssembly Method :: SPAdes v. 3.6.2\nExpected Final Version :: yes\nGenome Coverage :: 100.0x\nSequencing Technology :: Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/20/2023 16:42:59\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 964\nCDSs (total) :: 921\nGenes (coding) :: 887\nCDSs (with protein) :: 887\nGenes (RNA) :: 43\nrRNAs :: 16, 16 (16S, 23S)\ncomplete rRNAs :: 14, 14 (16S, 23S)\npartial rRNAs :: 2, 2 (16S, 23S)\ntRNAs :: 11\nncRNAs :: 0\nPseudo Genes (total) :: 34\nCDSs (without protein) :: 34\nPseudo Genes (ambiguous residues) :: 0 of 34\nPseudo Genes (frameshifted) :: 2 of 34\nPseudo Genes (incomplete) :: 32 of 34\nPseudo Genes (internal stop) :: 4 of 34\nPseudo Genes (multiple problems) :: 3 of 34\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000340
sequence length: 13840
topology: circular
so has quality: SO_0000988
location: 1..13840
location: region:1-13840:1
RO_0002162: 573658

NZ_CM008774
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN07255135
type: BioSample
SIO_000068: biosample

1
title: Direct Submission
author: Campbell, M.A.
author: Lukasik, P.
author: Simon, C.
author: McCutcheon, J.P.
journal: Submitted (25-SEP-2017) Division of Biological Sciences, University of Montana, 32 Campus Drive, HS104, Missoula, MT 59812, USA

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:13840:1
position: 13840
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-13840:1:source
so part of: sequence
organism: Candidatus Hodgkinia cicadicola
mol type: genomic DNA
strain: MAGTDC
isolation source: bacteriome tissue
host: Magicicada tredecula
chromosome: variant14
country: USA: Marshall County, Kentucky
lat lon: 37.0086 N 88.3308 W
collection date: 2015-06-04

573658
type: Taxonomy
SIO_000068: taxonomy

MAGTDC_RS05190
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS05190
so part of: sequence
location: 23..157
location: region:23-157:1
so has part: feature:23-157:1:exon
subclass of: SO_0000010

79948307
type: Gene
SIO_000068: ncbigene

position:23:1
position: 23
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:157:1
position: 157
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:23-157:1:exon

MAGTDC_RS05190
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS05190
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MFSVDRFLCAYDFLLLIPIRCERSQPRGSMLFVDWIEILNWMWE
SIO_010081: MAGTDC_RS05190
subclass of: SO_0000673
so part of: MAGTDC_RS05190
location: 23..157
location: region:23-157:1
so has part: feature:23-157:1:exon

WP_278046853.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:23-157:1:exon

MAGTDC_RS00520
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS00520
old locus tag: magtdc_114
so part of: sequence
location: 397..4065
location: region:397-4065:1
so has part: feature:397-4065:1:exon
subclass of: SO_0000010

79947550
type: Gene
SIO_000068: ncbigene

position:397:1
position: 397
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4065:1
position: 4065
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:397-4065:1:exon

MAGTDC_RS00520
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS00520
old locus tag: magtdc_114
inference: COORDINATES: protein motif:HMM:NF012771.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MSSAWYNRLKINNSNKNPPNKLFLCNPQKLTYYYNLIGIKNNHGINISKLKLLLTNQFPYQNENRSLELTSITNKSFNTDFYIYFKFNNIKYETFNKIPYVSHCLVFNLPKLILPKLNTKFKPYSEEEQKVIISKLIKSTSIYYNINERDNKILFNTSNNGHIEITTNNQCTISCDDYHELFLITLLKLRTKHQHLWKSLLNTKTVSFVNRRWWKFNYIQNQNNTKWYGKRRSNRPIKKFNEIYQNVEVILLRNLEKHQDTNPTTSCESLTLNNWLALHQTSIAYISADFELIDKLTCDTKLQPSVTNDINILEDELKELWLTSSDRQRVNNLTHIKHAYNPDHITKQDWLMIWKNQVNNNKFILPEDVDVLTVWSIGDTIIKFICQDIDKLLCLNNPDTIINNLMKETSISIWKALQTKIYTALNKSSFNQTVEQTNSLCEISHEQRLTCMNGDPNTQTLSLTQRDVQRWHQGGICPIESPEGHNIGLMFTLTTYSSIDVNGNILTAYYKVHNGLISNQIIYLSYLERLNYTTIIPGSKQFGDRITCERNNKISLTKLTEAEICYCSDIQFFSPSTNLIPFLKHNDPTRCLMAVNMEKQAIPLLTPQSPLIGTGTERLVTENCHNNIISKSNGIVTKVDSTKIIIYTTSTNRYFVYKLPSNEHNNQNIYIRIRPIVLPSQLVSKGELIAECQSHYHGELSLGTNLLVAFMCWKGYNFEDSVLISSEIVSKGTFQSLHVIQLDIELRKDEVLTNNIKTIPTKHLIHLQNNGIVKTGCKLHANDVIVGKIKFTTKPNNDVNSTNRYSLVYKDSSIRLQNDIQSATVIDVQRPERDELDGIINDVITKLELLSKKYIKHIWHLSGTKTIILKSRHQSYGIFEFNSIDVELSNNLQLVYKSYILKFTALYERCFESLNLYLSSKCNTYDQPNLDRIVIKLLTKRSIKVGDKICGRHGNKGVISKIVPKEDMPFMADGTVIDVIFNPLSIPSRMNVGQILESHLGLISYKMGLEFKKLLQIYNISNNKQGIIDIVKSKLSEIHPNVDFKSIDNKTILELISELSNGVKTNVQDMEIEKDIKFLESRVDLRHNKYQCQLYDGITGLKFDRKTTVGIMYVYKLNHMVDDKIYARSTGPYSTITQQPTKGKMNKGGQRLGEMEVWALQSYGAAFIIQEMLTAKCDDLKARKTLSASITEKHSGFKISCGETLFILIKELCSLCIEFKIT
SIO_010081: MAGTDC_RS00520
subclass of: SO_0000673
so part of: MAGTDC_RS00520
location: 397..4065
location: region:397-4065:1
so has part: feature:397-4065:1:exon

WP_146656576.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:397-4065:1:exon

MAGTDC_RS00525
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS00525
old locus tag: magtdc_115
so part of: sequence
location: 4110..8084
location: region:4110-8084:1
so has part: feature:4110-8084:1:exon
subclass of: SO_0000010

79947551
type: Gene
SIO_000068: ncbigene

position:4110:1
position: 4110
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8084:1
position: 8084
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4110-8084:1:exon

MAGTDC_RS00525
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS00525
old locus tag: magtdc_115
inference: COORDINATES: protein motif:HMM:NF016859.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MNRQTNKSIRLAIASDQTILSWSYGEVVNSILFDDRTGKPTKDGLFCPKIFGPINKNECLCNKPMINSNKCCSNCGTDFNINWRKAKQRFGHIELSKPIVHTWFHKTNTEVLEVLLGLSGSVIKSLINCDLHVINKRISDDLYDGKIINSSVYNDLGQQRDYDKVVSGGSAINYLLSKTNLNKLKQDIQRKYERVDSVTTSNELSERMKIIDGFLNKNVDPTWLVLKVLPVLPASLRPIVADDDEKVPSSDLNELYSQVITANNDLRCCYNLFKFGWQLATNELIQNIKKLQKAVDMLYDNSSDLDNHPSYNNEALKSISEMLKGKNGRFRQTLLGKRVDYSGRTVIVPGPNLKLDECSIPRTMAFDLFKPIIYLKAMLKLGTKANNSIESTLENNPIITNQILNEVTNYYPIILNRAPTLHKLSMLVFMVKLNSDRVIKVHPLVCAGYNADFDGDQMAIHVPLTSEAKLEAMKYMLSSKNILHPANGNVVITPTKEMIMGLYYLSLVNNDKECLKFGSLPLLKKTIDLNLITVHTKIMYTITVNNKLIEVVTTPGRILITDIVPSECCFRYDAYHPELTKELIIDLIQEVNINCDRRKTVRFCEALMRLGFKYATQSGLSLGLSDLLISKHKQNSLKSVRNKVREMINYKQIIPCKLQRPVFCKLWSNVADEINKNIDLNDSDIHPSNSSSIRIMMASGARGTLSQLQQLTGLRGRIICFNDELSKIPILHSYTEGLSSIEMFVLSYSSRKGLIDSVIKTSKSGYFMRKLVEASRECIIDEIDCRTKLGLEIDLSLDDYDNTSSWLIGRFLLNDVTVNNVVVADSNVVLTREVIFDLIKVCKYKVHVRSPLMCQANSGICRKCYGLNIGTRKLVNLGDSVGVLAAQSIGEPGTQLTLRSFHGLEISNFKTSPKSYQCYAKAPCCGQIKVLNLACTYSYQGDLIVVNNKCLVVIYQQAKLVWKVAVPIGSRLFFNNNDFVGVGKVLWLCCVQNESYISLANGKSYYDNLCHNVNLHRRSRRGDLSPTEKWGYTDKFIAKIILKVTNINLAYLIKNNVLSHVIIQNNCDVKIFDCIMFKIIEDYQDTVPNKSGGLYKLEQLFDNSEWDSDVAIVSPCSGMLKIGNTKGFSSYVIDPSSRCKFPIVYHLYDQHLNTKVDKYVNTMEMLLHGEVDLSDYAINHGFHCFVKYFIKSVQQIYEQYGINVNSKHIEVMLKLMTSTAVIWNDNCFNLTKYSSNKWWVIDCINRVCQTFRQEKIEYSRQVVGISKLCTKHQISPLSSMSYQGSTKAIVNAIINGSEFELTGIKDRTMFGMLPFIGLGYLKRC
SIO_010081: MAGTDC_RS00525
subclass of: SO_0000673
so part of: MAGTDC_RS00525
location: 4110..8084
location: region:4110-8084:1
so has part: feature:4110-8084:1:exon

WP_146656577.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4110-8084:1:exon

MAGTDC_RS05195
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS05195
so part of: sequence
location: 11945..12280
location: region:11945-12280:1
so has part: feature:11945-12280:1:exon
subclass of: SO_0000010

79948308
type: Gene
SIO_000068: ncbigene

position:11945:1
position: 11945
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:12280:1
position: 12280
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:11945-12280:1:exon

MAGTDC_RS05195
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS05195
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MFNRLGIIWDTLLVLSALILVLNHDISFTIKRCTLHFCKFNRPNTLKLLFLTDLIKFDIKISVKHGHDAMMLFVLHVFRDRELLEGLKPPNVESVKSDVLKIIKPGRPMIR
SIO_010081: MAGTDC_RS05195
subclass of: SO_0000673
so part of: MAGTDC_RS05195
location: 11945..12280
location: region:11945-12280:1
so has part: feature:11945-12280:1:exon

WP_278046852.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:11945-12280:1:exon

MAGTDC_RS04145
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS04145
so part of: sequence
location: 12569..12754
location: region:12569-12754:1
so has part: feature:12569-12754:1:exon
subclass of: SO_0000010

79948120
type: Gene
SIO_000068: ncbigene

position:12569:1
position: 12569
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:12754:1
position: 12754
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:12569-12754:1:exon

MAGTDC_RS04145
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS04145
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MMWIINNVGLPYHFVVIDGFLSNQWMIWDVRIIGVLTTCQNHITTLCHTNVVIDGIVLTVE
SIO_010081: MAGTDC_RS04145
subclass of: SO_0000673
so part of: MAGTDC_RS04145
location: 12569..12754
location: region:12569-12754:1
so has part: feature:12569-12754:1:exon

WP_192572924.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:12569-12754:1:exon