Chloroplast Genomes Exhibit Eight-Cluster Structuredness and Mirror Symmetry

Abstract

Chloroplast genomes have eight-cluster structuredness, in triplet frequency space. Small fragments of a genome converted into a triplet frequency dictionaries are the elements to be clustered. Typical structure consists of eight clusters: six of them correspond to three different positions of a reading frame shifted for 0, 1 and 2 nucleotides (in two opposing strands), the seventh cluster corresponds to a junk regions of a genome, and the eighth cluster is comprised by the fragments with excessive GC-content bearing specific RNA genes. The structure exhibits a specific symmetry.