Abstract
In our previous study, complete single DNA strands which were obtained from nuclei, chloroplasts and plant mitochondria obeyed Chargaff’s second parity rule, although those which were obtained from animal mitochondria deviated from the rule. On the other hand, plant mitochondria obeyed another different rule after their classification. Complete single DNA strand sequences obtained from chloroplasts, plant mitochondria, and animal mitochondria, were divided into the coding and non-coding regions. The non-coding region, which was the complementary coding region on the reverse strand, was incorporated as a coding region in the forward strand. When the nucleotide contents of the coding region or non-coding regions were plotted against the composition of the four nucleotides in the complete single DNA strand, it was determined that chloroplast and plant mitochondrial DNA obeyed Chargaff’s second parity rule in both the coding and non-coding regions. However, animal mitochondrial DNA deviated from this rule. In chloroplast and plant mitochondrial DNA, which obey Chargaff’s second parity rule, the lines of regression for G (purine) and C (pyrimidine) intersected with regression lines for A (purine) and T (pyrimidines), respectively, at around 0.250 in all cases. On the other hand, in animal mitochondrial DNA, which deviates from Chargaff’s second parity rule, only regression lines due to the content of homonucleotides or their analogs in the coding or non-coding region against those in the complete single DNA strand intersected at around 0.250 at the horizontal axis. Conversely, the intersection of the two lines of regression (G and A or C and T) against the contents of heteronucleotides or their analogs shifted from 0.25 in both coding and non-coding regions. Nucleotide alternations in chloroplasts and plant mitochondria are strictly regulated, not only by the proportion of homonucleotides and their analogs, but also by the heteronucleotides and their analogs. They are strictly regulated in animal mitochondria only by the content of homonucleotides and their analogs.
Highlights
In our previous study, complete single DNA strands which were obtained from nuclei, chloroplasts and plant mitochondria obeyed Chargaff’s second parity rule, those which were obtained from animal mitochondria deviated from the rule
The coding region in the reverse strand was incorporated into the forward strand as the complement, and the nucleotide content in the coding region was plotted against the complete single DNA strand to understand whole genome evolution [2]
Genome data were obtained from the National Center for Biotechnology Information (NCBI; http://www.ncbi.nlm. nih.gov/sites), and the list of organelles examined has been described in our previous paper [13]
Summary
“Chargaff’s second parity rule” [1], G ≈ C, A ≈ T and [(G + A) ≈ (T + C)] is retained in single DNA stranded that is formed from double-stranded DNA; it is difficult to imagine how the G and C or A and T base pairs are formed in the single DNA strand, or why G ≈ C and A ≈ T. Nikolaou and Almirantis reported that mitochondrial DNA might be classified into three groups based on GC and AT skews, and that their DNA deviated from Chargaff’s second parity rule [7]. They reported that chloroplasts shared the patterns of bacterial genomes [7]. These analyses included homonucleotides, and heteronucleotides, as Chargaff’s second parity rule is linked to the double-stranded DNA structure [2,8]. It would be interesting to determine whether Chargaff’s second parity rule is preserved, in the complete genome, and in the separated coding and non-coding regions, to understand biological evolution
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