About this Research Topic
Plasmids are extrachromosomal DNAs, some of which carry genes that confer various functions (metabolism, virulence, resistance, etc.) on their host microorganisms. Some plasmids can be transferred between different bacteria and may thus contribute to the spread of these genes among different bacteria in microbial communities in natural and man-made environments. Understanding the contribution of plasmids to horizontal gene transfer and the rapid evolution of bacteria will be useful for advancing ecological knowledge of gene flow, solving medical problems such as drug resistance, and genetic engineering applications such as vector development. In order to correctly identify plasmids and evaluate plasmid diversity in microbial genomes and metagenomes, a high-quality plasmid database is required.
High-throughput DNA sequencing has generated a large number of plasmid sequences, which are available in the International Nucleotide Sequence Database Collaboration (INSDC: DDBJ, EMBL-EBI, and NCBI). These primary databases cover all available plasmid sequence data, but are not always well organized and annotated. Recently, several secondary databases for plasmids have been developed.
Secondary databases of plasmids have been developed by adding plasmid metadata (e.g., host taxonomy, presence of genes related to replication and mobility functions) from the primary databases such as the NCBI RefSeq and GenBank database. Bioinformatics tools with proprietary databases have also been developed to identify and classify plasmids in microbial genomes and metagenomes. However, currently available plasmid databases and bioinformatics tools have problems such as missing or biased data and inaccurate annotation. Solving problems such as missing data, data bias, and inaccurate annotation requires expert knowledge of plasmids accumulated in previous publications, experimental evidence (incompatibility, host range, etc.), and manual curation of the database.
We are interested in the following types of manuscripts related to high-quality plasmid databases and high-precision bioinformatics tools: original articles and reviews that discuss problems of the current plasmid databases and propose solutions. For example, plasmid databases that are manually annotated by compiling experimental results (equivalent to reviewed UniProtKB/Swiss-Prot) are welcome, but plasmid databases with only automatically annotated computational results (equivalent to unreviewed UniProtKB/TrEMBL) are not eligible for publication. We also welcome original papers that provide experimental evidence (plasmid copy number, host range, incompatibility, etc.) that contribute to a manually curated, high-quality plasmid database, but simple genome reports will not be considered for publication. Papers on the following topics with a clear focus on improving the quality of plasmid databases are welcomed:
1.) Discussing problems of the current plasmid databases and tools
2.) Experimental evidence for (re)construction of plasmid database
3.) New databases, tools, and algorithms
4.) Plasmid classification
5.) Gene Ontology
Keywords: Plasmid, Database, Metadata, Experimental evidence, Computational tools
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