Candidatus Hodgkinia cicadicola strain MAGTDC chromosome variant16, whole genome shotgun sequence.
type: Entry
definition: Candidatus Hodgkinia cicadicola strain MAGTDC chromosome variant16, whole genome shotgun sequence.
sequence version: NZ_CM008776.1
sequence date: 2023-04-10
sequence: sequence
division: CON
label: NZ_CM008776.1
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\nCM008776.1.\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: 8803
topology: circular
so has quality: SO_0000988
location: 1..8803
location: region:1-8803:1
RO_0002162: 573658

NZ_CM008776
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:8803:1
position: 8803
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8803:1:source
so part of: sequence
organism: Candidatus Hodgkinia cicadicola
mol type: genomic DNA
strain: MAGTDC
isolation source: bacteriome tissue
host: Magicicada tredecula
chromosome: variant16
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_RS05225
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS05225
so part of: sequence
location: complement(101..661)
location: region:101-661:-1
so has part: feature:101-661:-1:exon
subclass of: SO_0000010

79948314
type: Gene
SIO_000068: ncbigene

position:101:-1
position: 101
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:661:-1
position: 661
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:101-661:-1:exon

MAGTDC_RS05225
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS05225
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: MAWLGVIPNFVKFRGIWWLRDQLDGMFIFLLDRPDVRAWMLSVRFLIQDLNGGYGPRSWLGPWLLDQLLNRLADMLRFWYADIRLEMYGLFVRIKPQEGPLREVVVAIVIRSHWNNGDGNDFVVTWVTMCKISANNGVSDLVCYSFGEVPICYGWTWNWVGNYEVWSVIHDLDYYFGYIFPTWGRM
SIO_010081: MAGTDC_RS05225
subclass of: SO_0000673
so part of: MAGTDC_RS05225
location: complement(101..661)
location: region:101-661:-1
so has part: feature:101-661:-1:exon

WP_278046859.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:101-661:-1:exon

MAGTDC_RS04175
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS04175
so part of: sequence
location: complement(627..794)
location: region:627-794:-1
so has part: feature:627-794:-1:exon
subclass of: SO_0000010

79948125
type: Gene
SIO_000068: ncbigene

position:627:-1
position: 627
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:794:-1
position: 794
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:627-794:-1:exon

MAGTDC_RS04175
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS04175
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: MVVHGKVWIGRRNVKDLVLSKNDVMPTRRGIGISYRDVTTVQPVFGMAGCYTKFC
SIO_010081: MAGTDC_RS04175
subclass of: SO_0000673
so part of: MAGTDC_RS04175
location: complement(627..794)
location: region:627-794:-1
so has part: feature:627-794:-1:exon

WP_192572941.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:627-794:-1:exon

MAGTDC_RS04180
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS04180
so part of: sequence
location: complement(1386..1562)
location: region:1386-1562:-1
so has part: feature:1386-1562:-1:exon
subclass of: SO_0000010

79948126
type: Gene
SIO_000068: ncbigene

position:1386:-1
position: 1386
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1562:-1
position: 1562
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1386-1562:-1:exon

MAGTDC_RS04180
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS04180
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: MNVRCWGEKGWIGLIIHVCCCFMGSSATLLRRWINLGDNWCKVGIRVSMREGRGNVVV
SIO_010081: MAGTDC_RS04180
subclass of: SO_0000673
so part of: MAGTDC_RS04180
location: complement(1386..1562)
location: region:1386-1562:-1
so has part: feature:1386-1562:-1:exon

WP_192572942.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1386-1562:-1:exon

MAGTDC_RS00640
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS00640
so part of: sequence
location: complement(1949..2152)
location: region:1949-2152:-1
so has part: feature:1949-2152:-1:exon
subclass of: SO_0000010

79947566
type: Gene
SIO_000068: ncbigene

position:1949:-1
position: 1949
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2152:-1
position: 2152
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1949-2152:-1:exon

MAGTDC_RS00640
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS00640
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: MYRSETVVTGCQRSKLACWLWGDRRLRDRSLEMITMKGGDGSNDDRSMPNTNDNCRSIDLWSLLTFY
SIO_010081: MAGTDC_RS00640
subclass of: SO_0000673
so part of: MAGTDC_RS00640
location: complement(1949..2152)
location: region:1949-2152:-1
so has part: feature:1949-2152:-1:exon

WP_146656597.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1949-2152:-1:exon

MAGTDC_RS04185
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS04185
so part of: sequence
location: complement(2235..2372)
location: region:2235-2372:-1
so has part: feature:2235-2372:-1:exon
subclass of: SO_0000010

79948127
type: Gene
SIO_000068: ncbigene

position:2235:-1
position: 2235
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2372:-1
position: 2372
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2235-2372:-1:exon

MAGTDC_RS04185
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS04185
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: MVEINQLTGMPTMSWALACVYLLVSMDGKIGLEANRGSVMLIDIE
SIO_010081: MAGTDC_RS04185
subclass of: SO_0000673
so part of: MAGTDC_RS04185
location: complement(2235..2372)
location: region:2235-2372:-1
so has part: feature:2235-2372:-1:exon

WP_192572943.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2235-2372:-1:exon

MAGTDC_RS00645
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS00645
so part of: sequence
location: complement(2458..2826)
location: region:2458-2826:-1
so has part: feature:2458-2826:-1:exon
subclass of: SO_0000010

79947567
type: Gene
SIO_000068: ncbigene

position:2458:-1
position: 2458
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2826:-1
position: 2826
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2458-2826:-1:exon

MAGTDC_RS00645
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS00645
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: MKGTIEVGTLDREIWSLVMPRIVGGRRLVYSHDRCWVGWDHQVESLIWCTLRWGWSSGFGLFIPLLNGRGDMIMFDPSDLDLDEWLCGGSAPWRGASEHEDQIKVWLKVNDQQQQQKVWGWD
SIO_010081: MAGTDC_RS00645
subclass of: SO_0000673
so part of: MAGTDC_RS00645
location: complement(2458..2826)
location: region:2458-2826:-1
so has part: feature:2458-2826:-1:exon

WP_146656598.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2458-2826:-1:exon

MAGTDC_RS00650
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS00650
so part of: sequence
location: complement(2850..3065)
location: region:2850-3065:-1
so has part: feature:2850-3065:-1:exon
subclass of: SO_0000010

79947568
type: Gene
SIO_000068: ncbigene

position:2850:-1
position: 2850
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3065:-1
position: 3065
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2850-3065:-1:exon

MAGTDC_RS00650
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS00650
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: MIGCSQWIKITMGCYRIGWCNVPKKENFKCSYYPSSDGGNTDRAVDGRRMADGKPTFEGWIRYFSTNVVIK
SIO_010081: MAGTDC_RS00650
subclass of: SO_0000673
so part of: MAGTDC_RS00650
location: complement(2850..3065)
location: region:2850-3065:-1
so has part: feature:2850-3065:-1:exon

WP_146656599.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2850-3065:-1:exon

MAGTDC_RS00655
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS00655
old locus tag: magtdc_122
so part of: sequence
location: 3503..5027
location: region:3503-5027:1
so has part: feature:3503-5027:1:exon
subclass of: SO_0000573

79947569
type: Gene
SIO_000068: ncbigene

position:3503:1
position: 3503
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5027:1
position: 5027
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3503-5027:1:exon

MAGTDC_RS00655
type: Ribosomal RNA
subclass of: SO_0000252
RO_0002162: 573658
locus tag: MAGTDC_RS00655
old locus tag: magtdc_122
product: 16S ribosomal RNA
inference: COORDINATES: nucleotide motif:Rfam:14.4:RF00177
inference: COORDINATES: profile:INFERNAL:1.1.4
note: Derived by automated computational analysis using gene prediction method: cmsearch.
SIO_010081: MAGTDC_RS00655
subclass of: SO_0000673
so part of: MAGTDC_RS00655
location: 3503..5027
location: region:3503-5027:1
so has part: feature:3503-5027:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:3503-5027:1:exon

MAGTDC_RS00660
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS00660
old locus tag: magtdc_121
so part of: sequence
location: 5184..7881
location: region:5184-7881:1
so has part: feature:5184-7881:1:exon
subclass of: SO_0000573

79947570
type: Gene
SIO_000068: ncbigene

position:5184:1
position: 5184
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7881:1
position: 7881
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5184-7881:1:exon

MAGTDC_RS00660
type: Ribosomal RNA
subclass of: SO_0000252
RO_0002162: 573658
locus tag: MAGTDC_RS00660
old locus tag: magtdc_121
product: 23S ribosomal RNA
inference: COORDINATES: nucleotide motif:Rfam:14.4:RF02541
inference: COORDINATES: profile:INFERNAL:1.1.4
note: Derived by automated computational analysis using gene prediction method: cmsearch.
SIO_010081: MAGTDC_RS00660
subclass of: SO_0000673
so part of: MAGTDC_RS00660
location: 5184..7881
location: region:5184-7881:1
so has part: feature:5184-7881:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:5184-7881:1:exon

MAGTDC_RS00665
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS00665
so part of: sequence
location: complement(7878..8123)
location: region:7878-8123:-1
so has part: feature:7878-8123:-1:exon
subclass of: SO_0000010

79947571
type: Gene
SIO_000068: ncbigene

position:7878:-1
position: 7878
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:8123:-1
position: 8123
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7878-8123:-1:exon

MAGTDC_RS00665
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS00665
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: MRWNHVLGLGDLRLLGHEMGLVSSCVHLVGSDDGIRCWFDYSDGIWWYWVLLSGDRRLDNCKVYTYTLLDGGCLQFRLTFC
SIO_010081: MAGTDC_RS00665
subclass of: SO_0000673
so part of: MAGTDC_RS00665
location: complement(7878..8123)
location: region:7878-8123:-1
so has part: feature:7878-8123:-1:exon

WP_146656600.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7878-8123:-1:exon

MAGTDC_RS04190
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS04190
so part of: sequence
location: complement(8247..8399)
location: region:8247-8399:-1
so has part: feature:8247-8399:-1:exon
subclass of: SO_0000010

79948128
type: Gene
SIO_000068: ncbigene

position:8247:-1
position: 8247
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:8399:-1
position: 8399
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8247-8399:-1:exon

MAGTDC_RS04190
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS04190
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: MRLLSCRSDGSWWWLDVVVAVSNSLCSNRTDVWSELVSLMEAEFNWLIDG
SIO_010081: MAGTDC_RS04190
subclass of: SO_0000673
so part of: MAGTDC_RS04190
location: complement(8247..8399)
location: region:8247-8399:-1
so has part: feature:8247-8399:-1:exon

WP_192572938.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8247-8399:-1:exon

MAGTDC_RS00670
type: Gene
subclass of: SO_0000704
RO_0002162: 573658
locus tag: MAGTDC_RS00670
so part of: sequence
location: complement(8401..8772)
location: region:8401-8772:-1
so has part: feature:8401-8772:-1:exon
subclass of: SO_0000010

79947572
type: Gene
SIO_000068: ncbigene

position:8401:-1
position: 8401
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:8772:-1
position: 8772
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8401-8772:-1:exon

MAGTDC_RS00670
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 573658
locus tag: MAGTDC_RS00670
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: MYIWLLEFDRTLADSQSKVVLVLLMATCSKATKMLELSGRGWSESRMAWAFSIAWETGDCVKPRFRLVKYLICSFNNRDSNQTLRFGWVSIGKETSVLVLYELVWSSSETGGWFIIWIVNVVL
SIO_010081: MAGTDC_RS00670
subclass of: SO_0000673
so part of: MAGTDC_RS00670
location: complement(8401..8772)
location: region:8401-8772:-1
so has part: feature:8401-8772:-1:exon

WP_192572939.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8401-8772:-1:exon