Evolutionary
divergence has been characterized based on morphological and molecular features
using rationale based on Darwin’s theory of natural selection. However,
universal rules that govern genome evolution have not been identified. Here, a
simple, innovative approach has been developed to evaluate biological evolution
initiating the origin of life: whole genomes were divided into several
fragments, and then differences in normalized nucleotide content between
nucleotide pairs were compared. Intramolecular nucleotide differences in
complete mitochondrial genomes reflect evolutionary divergence. The values of
(G – C), (G – T), (G – A), (C – T), (C – A) and (T – A) reflect biological
evolution, and these values except for (G – C) and (T – A) change inversely to
positive from negative along biological evolution of bacterial genomes. More
highly evolved organisms, such as primates and birds, seem to have greater
levels of (C – T) in mitochondria. Based on nucleotide content structures, Monosiga brevicollis mitochondria may
be the most primitive extant ancestor of the species examined here. The two
normalized nucleotide contents are universally expressed by a linear regression
line, (X – Y)/(X + Y) = a(X – Y) + b, where X and Y are nucleotide contents and
(a) and (b) are constants. The value of (G + C), (G + A), (G + T), (C + A), (C
+ T) and (A + T) was ~0.5. Plotting (X – Y)/(X + Y) against X/Y showed a
logarithmic function (X – Y)/(X + Y) = a lnX/Y + b, where (a) and (b) are
constant. Nucleotide content changes are expressed by a definitive equation, (X
– Y) ≈ 0.25 ln(X/Y).
References
[1]
Tsuji, G., Fujii, S., Sunami, T. and Yomo, T. (2016) Sustainable Proliferation of Liposomes Compatible with Inner RNA Replication. Proceedings of National Academy of Sciences of United States of America, 113, 590-595.
https://doi.org/10.1073/pnas.1516893113
[2]
Schopf, J.W. and Barghoorn, E.S. (1967) Alga-Like Fossils from the Early Precambrian of South Africa. Science, 3774, 508-512. https://doi.org/10.1126/science.156.3774.508
[3]
Nagy, B., Zumberge, J.E. and Nagy, L.A. (1975) Abiotic, Graphitic Microstructures in Micaceous Metaquartzite about 3760 Million Years Old from Southwestern Greenland: Implications for Early Precambrian Microfossils. Proceedings of National Academy of Sciences of United States of America, 72, 1206-1209.
https://doi.org/10.1073/pnas.72.3.1206
[4]
Noffke, N., Christian, D., Wacey, D. and Hazen, R.M. (2013) Microbially Induced Sedimentary Structures Recording an Ancient Ecosystem in the ca. 3.48 Billion-Year-Old Dresser Formation, Pilbara, Western Australia. Astrobiology, 13, 1103-1124. https://doi.org/10.1089/ast.2013.1030
[5]
Schopf, J.W. (2006) Fossil Evidence of Archaean Life. Philosophical Transactions of the Royal Society B Biological Sciences, 361, 869-885. https://doi.org/10.1098/rstb.2006.1834
[6]
Gray, M.W. (1992) The Endosymbiont Hypothesis Revisited. International Review of Cytology, 141, 233-357.
https://doi.org/10.1016/S0074-7696(08)62068-9
[7]
Ku, C., Nelson-Sathi, S., Roettger, M., Sousa, F.L., Lockhart, P.J., Bryant, D., et al. (2015) Endosymbiotic Origin and Differential Loss of Eukaryotic Genes. Nature, 524, 427-432. https://doi.org/10.1038/nature14963
[8]
Andersson, S.G., Zomorodipour, A., Andersson, J.O., Sicheritz-Pontén, T., Alsmark, U.C., Podowski, R.M., et al. (1998) The Genome Sequence of Rickettsia prowazekii and the Origin of Mitochondria. Nature, 396, 133-140.
https://doi.org/10.1038/24094
[9]
Thrash, J.C., Boyd, A., Huggett, M.J., Grote, J., Carini, P., Yoder, R.J., et al. (2011) Phylogenomic Evidence for a Common Ancestor of Mitochondria and the SAR11 Clade. Scientific Reports, 1, 13.
https://doi.org/10.1038/srep00013
[10]
Sorimachi, K. and Okayasu, T. (2014) Classification of Non-Animals and Invertebrates Based on Amino Acid Composition of Complete Mitochondrial Genomes. International Journal of Biology, 6, 1-16.
[11]
Sorimachi, K. (2015) Origine of Life in the Ocean: Direct Derivation of Mitochondria from Primitive Organisms Based on Complete Genomes. Current Chemical Biology, 9, 23-35.
https://doi.org/10.2174/2212796809666150911201738
[12]
Sorimachi, K. (2010) Genome Data Provides Simple Evidence for a Single Origin of Life. Natural Science, 2, 519-525.
[13]
Sorimachi, K., Okayasu, T., Ohhira, S., Fukasawa, I. and Masawa, N. (2012) Evidence for the Independent Divergence of Vertebrate and High C/G Ratio Invertebrate Mitochondria from the Same Origin. Natural Science, 4, 479-483.
[14]
Sorimachi, K. (1999) Evolutionary Changes Reflected by the Cellular Amino Acid Composition. Amino Acids, 17, 207-226. https://doi.org/10.1007/BF01361883
[15]
Sorimachi, K., Itoh, T., Kawarabaysi, Y., Okayasu, T., Akimoto, K. and Niwa, A. (2001) Conservation of the Basic Pattern of Cellular Amino Acid Composition during Biological Evolution and the Putative Amino Acid Composition of Primitive Life Forms. Amino Acids, 21, 393-399. https://doi.org/10.1007/s007260170004
[16]
Chargaff, E. (1950) Chemical Specificity of Nucleic Acids and Mechanism of Their Enzymatic Degradation. Experientia, 6, 201-209. https://doi.org/10.1007/BF02173653
[17]
Rundner, R., Karkas, J.D. and Chargaff, E. (1968) Separation of B. subtilis DNA into Complementary Strands. 3. Direct Analysis. Proceedings of the National Academy of Sciences, 60, 921-922.
https://doi.org/10.1073/pnas.60.3.921
[18]
Sorimachi, K. (2009) A Proposed Solution to the Historic Puzzle of Chargaff’s Second Parity Rule. The Open Genomics Journal, 2, 12-14. https://doi.org/10.2174/1875693X00902010012
[19]
Sorimachi, K., Okayasu, T. and Ohhira, S. (2015) Normalization of Complete Genome Characteristic: Application to Evolution from Primitive Organisms to Homo sapiens. Current Genomics, 16, 99-106.
https://doi.org/10.2174/1389202916666150119215716
[20]
Sorimachi, K. (2014) Indices of Whole Genome Characteristics Based on Amino Acid or Nucleotide Content Ratios: Evolution from Primitive Organisms to Homo sapiens. Journal of Chemical Engineering and Chemistry Research, 1, 302-312.
[21]
Mitchell, D. and Bridge, R. (2006) A Test of Chargaff’s Second Rule. Biochemical and Biophysical Research Communications, 340, 90-94. https://doi.org/10.1016/j.bbrc.2005.11.160
[22]
Sorimachi, K. and Okayasu, T. (2008) Codon Evolution Is Governed by Linear Formulas. Amino Acids, 34, 345-350. https://doi.org/10.1007/s00726-007-0024-3
[23]
Sorimachi, K. and Okayasu, T. (2008) Universal Rules Governing Genome Evolution Expressed by Linear Formulas. Open Current Genomics, 1, 33-43. https://doi.org/10.2174/1875693X00801010033
[24]
Nikolaou, C. and Almirantis, Y. (2006) Deviations from Chargaff’s Second Parity Rule in Organellar DNA Insights into the Evolution of Organellar Genomes. Gene, 381, 34-41. https://doi.org/10.1016/j.gene.2006.06.010
[25]
Bell, S.J. and Forsdyke, D.R. (1999) Deviations from Chargaff’s Second Parity Rule Correlate with Direction of Transcription. Journal of Theoretical Biology, 197, 63-76.
[26]
Sorimachi, K. and Okayasu, T. (2003) Gene Assembly Consisting of Small Units with Similar Amino Acid Composition in the Saccharomyces cerevisia. Mycoscience, 44, 415-417.
https://doi.org/10.1007/S10267-003-0131-2
[27]
Sorimachi, K. (2010) Evolution Based on Genome Structure: The “Diagonal Genome Universe”. Natural Science, 2, 1104-1112.
[28]
Lobry, J.R. (1996) Asymmetric Substitution Patterns in the Two DNA Strands of Bacteria. Molecular Biology and Evolution, 13, 660-665. https://doi.org/10.1093/oxfordjournals.molbev.a025626
[29]
Tillier, E.R. and Collins, R.A. (2000) The Contributions of Replication Orientation, Gene Direction, and Signal Sequences to Base-Composition Asymmetries in Bacterial Genomes. Journal of Molecular Evolution, 50, 249-257. https://doi.org/10.1007/s002399910029
[30]
Anderson, S., Bankier, A.T., Barrell, B.G., de Bruijn, M.H., Coulson, A.R., Drouin, J., et al. (1981) Sequence and Organization of the Human Mitochondrial Genome. Nature, 290, 457-465. https://doi.org/10.1038/290457a0
[31]
Fonceca, M.M., Harris, D.J. and Posada, D. (2014) The Inversion of the Control Region in Three Mitogenomes Provides Further Evidence for an Asymmetric Model of Vertebrate mtDNA Replication. PLoS ONE, 9, e106654.
https://doi.org/10.1371/journal.pone.0106654
[32]
Seligmann, H. (2012) Coding Constraints Modulate Chemically Spontaneous Mutational Replication Gradients in Mitochondrial Genomes. Current Genomics, 13, 37-54. https://doi.org/10.2174/138920212799034802
[33]
King, N., Westbrook, M.J., Young, S.L., Kuo, A., Abedin, M., Chapman, J., et al. (2008) The Genome of the Choanoflagellates Monosiga brevicollis and the Origin of Metazoans. Nature, 451, 783-788.
https://doi.org/10.1038/nature06617
[34]
Groseth, A., Stroher, U., Theriault, S. and Feldmann, H. (2002) Molecular Characterization of an Isolate from the 1989/90 Epizootic of Ebola Virus Reston among Macaques Imported into the United States. Virus Research, 87, 155-163. https://doi.org/10.1016/S0168-1702(02)00087-4
[35]
Sanchez, A. and Rollin, P.E. (2005) Complete Genome Sequence of an Ebola Virus (Sudan Species) Responsible for a 2000 Outbreak of Human Disease in Uganda. Virus Research, 113, 16-25.
https://doi.org/10.1016/j.virusres.2005.03.028
[36]
Volchkov, V.E., Volchkova, V.A., Chepurnov, A.A., Blinov, V.M., Dolnik, O., Netesov, S.V., et al. (1999) Characterization of the L Gene and 5’ Trailer Region of Ebola Virus. Journal of General Virology, 80, 355-362.
https://doi.org/10.1099/0022-1317-80-2-355
Jenkins, P.D., Kilpatorick, C.W., Robinson, M.F. and Timmins, R.J. (2004) Morphological and Molecular Investigations of a New Family, Genus and Species of Rodent (Mammalia: Rodentia: Hystricognatha) from Lao PDR. Systematics and Biodiversity, 2, 419-454. https://doi.org/10.1017/S1477200004001549
[39]
Dawson, M.R., Marivaux, L., Li, C.K., Beard, K.C. and Métais, G. (2006) Laonastes and the “Lazarus Effect” in Recent Mammals. Science, 311, 1456-1458. https://doi.org/10.1126/science.1124187
[40]
Gaudin, T.J., Emry, R.J. and Wible, J.R. (2009) The Phylogeny of Living and Extinct Pangolins (Mammalia, Pholidota) and Associated Taxa: A Morphology Based Analysis. Journal of Mammalian Evolution, 16, 235-305.
https://doi.org/10.1007/s10914-009-9119-9
[41]
Gatesy, J., Hayashi, C., Cronin, M.A. and Arctander, P. (1996) Evidence from Milk Casein Genes That Cetaceans Are Close Relatives of Hippopotamid Artiodactyls. Molecular Biology and Evolution, 13, 954-963.
https://doi.org/10.1093/oxfordjournals.molbev.a025663
[42]
Ursing, B.M. and Arnason, U. (1998) Analyses of Mitochondrial Genomes Strongly Support a Hippopotamus-Whale Clade. Proceedings of the Royal Society B: Biological Sciences, 265, 2251-2255.
https://doi.org/10.1098/rspb.1998.0567
[43]
Sorimachi, K. and Okayasu, T. (2013) Phylogenetic Tree Construction Based on Amino Acid Composition and Nucleotide Content of Complete Vertebrate Mitochondrial Genomes. IOSR Journal of Pharmacy, 3, 51-60.
[44]
Session, A.M., Uno, Y., Kwon, T., Chapman, J.A., Toyoda, A., Takahashi, S., et al. (2016) Genome Evolution in the Allotetraploid Frog Xenopus laevis. Nature, 538, 336-343. https://doi.org/10.1038/nature19840
[45]
Hellsten, U., Simakov, O., Chapman, J., Fahey, B., Gauthier, M.E., Mitros, T., et al. (2010) The Genome of the Western Clawed Frog Xenopus tropicalis. Science, 328, 633-636. https://doi.org/10.1126/science.1183670
[46]
Pollet, N. and Mazabraud, A. (2006) Insights from Xenopus Genomes. Genome Dynamics, 2, 138-153.
https://doi.org/10.1159/000095101
[47]
Tymowska, J. (1973) Karyotype Analysis of Xenopus tropicalis Gray, Pipidae. Cytogenetics and Cell Genetics, 12, 297-304. https://doi.org/10.1159/000130468
[48]
Sakaguchi, D.S., Murphey, R.K., Hunt, R.K. and Tompkins, R. (1984) The Development of Retinal Ganglion Cells in a Tetraploid Strain of Xenopus laevis: A Morphological Study Utilizing Intracellular Dye Injection. Journal of Comparative Neurology, 224, 231-251. https://doi.org/10.1002/cne.902240205
[49]
Ohno, S. (1970) Evolution by Gene Duplication. Springer, Berlin. https://doi.org/10.1007/978-3-642-86659-3
[50]
Janvier, P. (2010) Micro RNAs Revive Old Views about Jawless Vertebrate Divergence and Evolution. Proceedings of the National Academy of Sciences, 107, 19137-19138. https://doi.org/10.1073/pnas.1014583107
[51]
Van Rheede, T., Bastiaans, T., Boone, D.N., Hedges, S.B., de Jong, W.W. and Madsen, O. (2006) The Platypus Is in Its Place: Nuclear Genes and Indels Confirm the Sister Group Relation of Monotremes and Therians. Molecular Biology and Evolution, 23, 587-597. https://doi.org/10.1093/molbev/msj064
