Chaperonins are a diverse family of molecular chaperones present in the plastids, mitochondria, and cytoplasm of eukaryotes, bacteria and archaea. The family is divided into group I (CPN60, also known as Hsp60 or GroEL, found in bacteria, some archaea, mitochondria and plastids) and group II (CCT, TriC or thermosome, found in archaea and the eukaryotic cytoplasm). Group I chaperonin sequences have been employed as targets for detection and identification of organisms and microbiome studies since a 549-567 bp segment of the cpn60 coding region is a molecular barcode that can be amplified with universal PCR primers. Species level identification of bacteria can be achieved with as little as 150 bp of the cpn60 barcode (Vancuren & Hill, 2019). The goal of the cpnDB project is to provide a manually curated, taxonomically broad collection of chaperonin sequences.
This repository contains cpn60 barcode sequence data along with tables of metadata for use in your workflows.
Current release is v13 (18,520 cpn60 reference barcode sequences) https://github.com/HillLabSask/cpnDB/releases/tag/v13
Ren, Q. and Hill, J.E. 2023. Rapid and accurate taxonomic classification of cpn60 amplicon sequence variants. ISME Communications, 3:77 doi.org/10.1038/s43705-023-00283-z
Vancuren, S.J. and Hill, J.E. 2019. Update on cpnDB: a reference database of chaperonin sequences. Database, 2019, doi:10.1093/database/baz033
Hill, J.E., Penny, S.L., Crowell, K.G., Goh, S.H. and Hemmingsen, S.M. 2004. cpnDB: a chaperonin sequence database. Genome Research 14:1669-1675. doi:10.1101/gr.2649204
If your goal is taxonomic assignment of microbiome data, you may want to check out the cpn60 Classifier: https://github.com/HillLabSask/cpn60-Classifier (Ren & Hill, 2023)
Protocols for cpn60 barcode amplification can be found on the Hill Lab website: https://research-groups.usask.ca/hilllab/cpn60-barcode-sequencing.php