Database Authors
Diego Santos-Garcia1, Francisco J. Silva1
1Cavanilles Institute of Biodiversity and Evolutionary Biology
Summary Candidatus Cardinium hertigii is a facultative endosymbiont of the sweet potato whitefly Bemisia tabaci MED (strain QHC-VLC). Its genome is enriched in Insertion Elements that have recently inactivated different genes. Some recent pseudogenes are related to the biosynthesis of some cofactors and can be the result of its settlement in Bemisia. The organism also possesses several genes that are probably involved in gliding motility and insecticidal toxins.

The PGDB was created from the sequenced genome [SantosGarcia14] by a team from the Cavanilles Institute of Biodiversity and Evolutionary Biology in Paterna, Spain, using the PathoLogic component of the Pathway Tools software [Karp11, Karp19] and the MetaCyc reference database [Caspi20]. The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation.

Genome
Replicon/ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
CBQZ01000000162144932140611,945
CBQZ010000002885023680,396
CBQZ010000003876212477,603
CBQZ010000004734322873,784
CBQZ010000005714612466,860
pCHV38300852,050RefSeq:HG422566
CBQZ010000006412451241,415
CBQZ01000000729212630,333
CBQZ01000000825611813,514
CBQZ0100000091330107,466
CBQZ01000001084045,158
CBQZ01000001191084,114
Total:1,103739463181,064,638
Ortholog data available?Yes
Database Contents
Genes1,103
Pathways70
Enzymatic Reactions514
Transport Reactions20
Polypeptides739
Protein Complexes25
Enzymes229
Transporters54
Compounds308
Transcription Units899
tRNAs35
Protein Features1,039
Database Version29.0
Sequence SourceCavanilles Institute
Synonyms Procaryotae
Prokaryota
Prokaryota
Prokaryotae
Prokaryotae
bacteria
eubacteria
not Bacteria Haeckel 1894
prokaryote
prokaryote
prokaryotes
prokaryotes
Cardinium endosymbiont of Bemisia tabaci cBtQ1Cavanilles Institute
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
FCB group
Bacteroidota/Chlorobiota group
Bacteroidota
Cytophagia
Cytophagales
Amoebophilaceae
Candidatus Cardinium
Candidatus Cardinium hertigii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI-Taxonomy247481

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp19: Karp PD, Midford PE, Billington R, Kothari A, Krummenacker M, Latendresse M, Ong WK, Subhraveti P, Caspi R, Fulcher C, Keseler IM, Paley SM (2019). "Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform. PMID: 31813964

SantosGarcia14: Santos-Garcia D, Rollat-Farnier PA, Beitia F, Zchori-Fein E, Vavre F, Mouton L, Moya A, Latorre A, Silva FJ (2014). "The genome of Cardinium cBtQ1 provides insights into genome reduction, symbiont motility, and its settlement in Bemisia tabaci." Genome Biol Evol 6(4);1013-30. PMID: 24723729

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