Global Journal of Science Frontier Research, G: Bio-Tech & Genetics, Volume 22 Issue 2

Name: MycRef Reference: Mycoplasma mycoides subsp. mycoides strain izsam_mm5713, complete genome Publication: Orsini, 2015 Length: 1192498 bp Access: https://www.ncbi.nlm.nih.gov/nuccore/CP010267.1?repo rt=genbank Name: JCVI-syn1.0 Reference: Synthetic Mycoplasma mycoides JCVI- syn1.0 clone sMmYCp235-1, complete sequence Publication: Gibson, 2010 Length: 1078809 bp Access: https://www.ncbi.nlm.nih.gov/nuccore/296455217 Name: Capritrans Reference: Mycoplasma mycoides subsp. capri str. GM12 transgenic clone tetM-lacZ, complete genome Publication: Direct Submission JOURNAL Submitted (14-MAY-2009) The J. Craig Venter Institute, 9702 Medical Center Drive, Rockville, MD 20850, USA Length: 1089202 bp Access: https://www.ncbi.nlm.nih.gov/nuccore/CP001621.1 Name: Capri real Reference: Mycoplasma mycoides subsp. mycoides SC str. PG1 Length: 1211703 bp Access: https://www.ncbi.nlm.nih.gov/nuccore/NC_005364.2 Name: JCVI-Syn3.0 Reference: Synthetic bacterium JCVI-Syn3.0, complete genome Publication: Hutchinson, 2016 Length: 531490 bp Access: https://www.ncbi.nlm.nih.gov/nuccore/CP014940.1 Name: JCVI-Syn3A Reference: Synthetic bacterium JCVI-Syn3A chromosome, complete genome Publication: Breuer, 2019 Length: 543379 bp Access: https://www.ncbi.nlm.nih.gov/nuccore/CP016816.2 Part II: Computing DNA Supra Code Resonances: Let us consider the 2 digital sequences : Fibonacci: 1 1 2 3 5 8 13 21 34 55 89 Lucas: 2 1 3 4 7 11 18 29 47 76 For any contiguous sequence of nucleotides, one will search for "resonance" or exact proportions of the TG / CA types then mainly TC / AG. For example, if 34 TCAG bases are subdivided exactly into 13 TC bases and 21 AG bases, we will consider having discovered a TC / AG resonance of length 34. We will do the same for the search for Lucas resonances. The whole genome is explored by taking each of the positions as successive exploration points. On the other hand, the genome being circular, the analysis from the last pivots at the end of the sequence is looped back to the positions of the start nucleotides. We will thus search for 2 symmetrical types of resonances: Main resonances (or forward): Exp. 34 TCAG ==> 13 TC, 21 AG. Inverse Resonances (or backward): Exp. 34 TCAG ==> 21 TC, 13 AG. For each length of Fibonacci (or Lucas) 3 5 8 13 21 34 55 89, we memorize the respective accumulations of the forward resonances on the one hand, and backward on the other hand. It appears then that these 2 values are very close in the case of REAL genomes, whereas they are very different in the case of SYNTHETIC genomes. We will therefore consider very significant: The forward / backward ratios. Forward-backward spreads. Since the lengths of real and synthetic genomes are generally very different, we will weight the forward- backward differences by the respective lengths of the real or synthetic genomes. III. R esults We analyse here, in one hand, Caulobacter crescentus NA1000 genome and synthetic genome Caulobacter ethensis-2.0 (C. eth-2.0), and, in other hand, Mycoplasma Mycoides JCVI-syn1.0, JCVI-syn3.0 and JCVI-syn3A. Part I: Caulobacter crescentus NA1000 genome and synthetic genome Caulobacter ethensis-2.0 (C. eth-2.0). The actual NA1000 genome being about 5 times longer than the synthetic genome C. eth-2.0, one might think that the comparison of these 2 genomes is skewed. However, in all the above results, we had already incorporated this difference by weighting the results by the length of the respective genomes. 1 Year 2022 37 © 2022 Global Journals Global Journal of Science Frontier Research Volume XXII Issue ersion I VII ( G ) Epigenetics Theoretical Limits of Synthetic Genomes: The Cases of Artificials Caulobacter ( C. eth-2.0), Mycoplasma Mycoides (JCVI-Syn 1.0, JCVI-Syn 3.0 and JCVI_3A), E-coli and YEAST chr XII TC/AG analysis: Nota: All tables in this article are identical: each box contains 4 numerical values: 1/The number "L" of Fibonacci or Lucas constituting the length of the sub- sequence analyzed. 2/The cumulated volume of the corresponding resonances (n x L) in regular exploration (forward). 3/The cumulative volume of the corresponding resonances (L x n) in reverse (backward) exploration. 4/The ratio of the 2 values below regular/ reverse.