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Nomenclature conventions for plastome-encoded genes

According to already existing conventions, chloroplast-encoded genes are named using three lowercase letters defining the protein or protein complex followed by an uppercase letter defining the subunit encoded by the specific gene e.g. 'psbA'. This convention is generally applied to protein coding genes in all GenBank entries of chloroplast and mitochondrial genomes. However, in the case of non-protein-coding tRNA and rRNA genes, these conventions are not generally obeyed. We have found several different and informative formats to name these non-protein-coding genes, e.g., "tRNA-Trp (UGG)" or "anticodon: UGG" or "codon recognized: UGG" just to name a few. To unify the naming of chloroplast genes and to provide the shortest possible description we propose (and apply) the following format :

trnAMINOACID ONE-LETTER-CODE-ANTICODON e.g. trnA-GCC.

Similarly, we propose to use the nomenclature

rrnSIZE IN SVEDBERG UNITS without the 'S'

to describe ribosomal RNA genes. Many of the deposited chloroplast genomes already follow these guidelines. In all other cases, the software will try to reformat the names to match the above format if the 'tidy-up' option is activated.