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
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
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