Naming and Annotation of Plasmids

Abstract

Genome sequences are being added to the public databases at phenomenal rates as sequencing becomes faster and cheaper. Plasmids are an important subset of extrachromosomal elements that often make significant contributions to the character of their hosts. Predicting these potential attributes depends on analyzing and cataloging the plethora of sequencing data in consistent and sensible ways. Currently, there is no consensus within the plasmid community on plasmid and gene names or how to handle the annotation of plasmids during the submission process to databases such as GenBank, but there are good models which can form the basis of a general naming system. It is also important to have clearer rules for the naming of plasmid core functions such as replication, partitioning, and conjugative transfer, among others. This entry explores these issues and makes some proposals for a more sustainable and rational system for plasmid naming, annotation, and analysis as consensus is achieved among plasmid biologists. Based on the system used for naming plasmids from the Rhizobiaceae, natural plasmids should be given a unique name that, wherever possible, indicates its natural host, the host used in plasmid capture experiments (exogenous isolation), or the source in metagenome sequencing projects. This unique designation will allow less ambiguous linkage to relevant experimental data.