Genome size and GC‐percent were determined by means of a special method of DNA flow cytometry in 154 vertebrate species. For the total dataset, a highly significant positive correlation was found between both parameters. The overall distribution of points is not linear but triangular: a wide range of GC‐percent values is observed at the lower end of genome size range, whereas with an increase in genome size the lower limit for GC‐percent is elevated, gradually approaching the upper limit (about 46%). In teleost fishes, which occupy the lower part of genome size range, the negative relationship between both parameters was observed. Two positive linear relationships were found between mean genome size and GC‐percent of the main vertebrate groups (one includes fishes, amphibians, and mammals, the other consists of reptiles and birds, which show the higher GC‐percent for their genome sizes). Distribution of variance between taxonomic levels indicates that GC‐percent is more evolutionarily conservative than genome size in anamniotes. Anuran amphibians show the greatest part of genome size variability at the lower taxonomic levels as compared to other vertebrates (with no additional variance already above the genus level). The data obtained with different methods are compared. It is shown that the proposed method can provide useful data for studies on genome evolution and biodiversity. Cytometry 31:100–109, 1998. © 1998 Wiley‐Liss, Inc.

A new explanation for the emergence of heavy (GC-rich) isochores is proposed, based on the study of thermostability, bendability, ability to B-Z transition and curvature of the DNA helix. The absolute values of thermostability, bendability and ability to B-Z transition correlated positively with GC content, whereas curvature correlated negatively. The relative values of these parameters were determined as compared to randomized sequences. In genes and intergenic spacers of warm-blooded animals, both the relative bendability and ability to B-Z transition increased with elevation of GC content, whereas the relative thermostability and curvature decreased. The usage of synonymous codons in GC-rich genes was also found to augment bendability and ability to B-Z transition and to reduce thermostability of DNA (as compared to synonymous codons with the same GC content). The analysis of transposable elements (Alu and B2 repeats in the human and mouse) showed that the level of their divergence from the consensus sequence positively correlated with relative bendability and ability to B-Z transition and negatively with relative thermostability. The bendability and ability to B-Z transition are known to relate to open chromatin and active transcription, whereas curvature facilitates chromatin condensation. Because heavy isochores are known to be gene-rich and show a high level of transcription, it is suggested here that isochores arose not as an adaptation to elevated temperature but because of a certain grade of general organization and correspondingly advanced level of genomic organization, reflected in genome structuring, with physical properties of DNA in the gene-rich regions being optimized for active transcription and in the gene-poor regions for chromatin condensation ('transcription/grade' concept).

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The resting metabolic rate of passerines is shown to be negatively correlated with genome size when body mass is held constant (r = -0.75, P < 0.01). This finding extends previous conclusion for mammals to this bird order. The result holds when higher taxonomic levels are used instead of the species (for genera, r = -0.76, P < 0.03; for families, r = -0.991, P < 0.01) as well as when the independent contrasts derived from the resolved phylogeny are used instead of the taxa (r = -0.73, P < 0.02), with the evolutionarily older contrasts being more strongly correlated (for the contrasts older than 30 million yr, r = -0.998, P < 0.002). The concept of evolutionary characters consolidation (ECC), previously formulated for mammals, is tested with special reference to the error fraction in the total character variance. In this test, the ECC for the nucleotypic effect cannot be proven for mammals as a whole class, but it holds for the two separate orders tested, rodents and passerine birds. An upper taxonomic limit for the ECC is suggested.

The housekeeping (ubiquitously expressed) genes in the mammal genome were shown here to be on average slightly GC-richer than tissue-specific genes. Both housekeeping and tissue-specific genes occupy similar ranges of GC content, but the former tend to concentrate in the upper part of the range. In the human genome, tissue-specific genes show two maxima, GC-poor and GC-rich. The strictly tissue-specific human genes tend to concentrate in the GC-poor region; their distribution is left-skewed and thus reciprocal to the distribution of housekeeping genes. The intermediately tissue-specific genes show an intermediate GC content and the right-skewed distribution. Both in the human and mouse, genes specific for some tissues (e.g., parts of the central nervous system) have a higher average GC content than housekeeping genes. Since they are not transcribed in the germ line (in contrast to housekeeping genes), and therefore have a lower probability of inheritable gene conversion, this finding contradicts the biased gene conversion (BGC) explanation for elevated GC content in the heavy isochores of mammal genome. Genes specific for germ-line tissues (ovary, testes) show a low average GC content, which is also in contradiction to the BGC explanation. Both for the total data set and for the most part of tissues taken separately, a weak positive correlation was found between gene GC content and expression level. The fraction of ubiquitously expressed genes is nearly 1.5-fold higher in the mouse than in the human. This suggests that mouse tissues are comparatively less differentiated (on the molecular level), which can be related to a less pronounced isochoric structure of the mouse genome. In each separate tissue (in both species), tissue-specific genes do not form a clear-cut frequency peak (in contrast to housekeeping genes), but constitute a continuum with a gradually increasing degree of tissue-specificity, which probably reflects the path of cell differentiation and/or an independent use of the same protein in several unrelated tissues.

The intron-genome size relationship was studied across a wide evolutionary range (from slime mold and yeast to human and maize), as well as the relationship between genome size and the ratio of intervening/coding sequence size. The average intron size is scaled to genome size with a slope of about one-fourth for the log-transformed values; i.e., on the global scale its increase in evolution is lower than the increase in genome size by four orders of magnitude. There are exceptions to the general trend. In baker's yeast introns are extraordinarily long for its genome size. Tetrapods also have longer introns than expected for their genome sizes. In teleost fish the mean intron size does not differ significantly, notwithstanding the differences in genome size. In contrast to previous reports, avian introns were not found to be significantly shorter than introns of mammals, although avian genomes are smaller than genomes of mammals on average by about a factor of 2.5. The extra-/intragenic ratio of noncoding DNA can be higher in fungi than in animals, notwithstanding the smaller fungal genomes. In vertebrates and invertebrates taken separately, this ratio is increasing as the increase in genome size. Two hypotheses are proposed to explain the variation in the extra-/intragenic ratio of noncoding DNA in organisms with similar numbers of genes: transition (dynamic) and equilibrium (static). According to the transition model, this variation arises with the rapid shift of genome size because the bulk of extragenic DNA can be changed more rapidly than the finely interspersed intron sequences. The equilibrium model assumes that this variation is a result of selective adjustment of genome size with constraints imposed on the intron size due to its putative link to chromatin structure (and constraints of the splicing machinery).

To elucidate the functional significance of genome multiplication in somatic tissues, we performed a large-scale analysis of ploidy-associated changes in expression of non-tissue-specific (i.e., broadly expressed) genes in the heart and liver of human and mouse (6585 homologous genes were analyzed). These species have inverse patterns of polyploidization in cardiomyocytes and hepatocytes. The between-species comparison of two pairs of homologous tissues with crisscross contrast in ploidy levels allows the removal of the effects of species and tissue specificity on the profile of gene activity. The different tests performed from the standpoint of modular biology revealed a consistent picture of ploidy-associated alteration in a wide range of functional gene groups. The major effects consisted of hypoxia-inducible factor-triggered changes in main cellular processes and signaling pathways, activation of defense against DNA lesions, acceleration of protein turnover and transcription, and the impairment of apoptosis, the immune response, and cytoskeleton maintenance. We also found a severe decline in aerobic respiration and stimulation of sugar and fatty acid metabolism. These metabolic rearrangements create a special type of metabolism that can be considered intermediate between aerobic and anaerobic. The metabolic and physiological changes revealed (reflected in the alteration of gene expression) help explain the unique ability of polyploid tissues to combine proliferation and differentiation, which are separated in diploid tissues. We argue that genome multiplication promotes cell survival and tissue regeneration under stressful conditions.