Reptiles: a group of transition in the evolution of genome size and of the nucleotypic effect

A comparison between genome size and some phenotypic parameters, such as developmental length and metabolic rate, showed in reptiles a nucleotypic correlation similar to the one observed in birds and mammals. Indeed, like homeotherms, reptiles exhibit a highly significant, inverse correlation of genome size with metabolic rate but unlike amphibians, no relationship with developmental length. Several lines of evidence suggest that these nucleotypic correlations are influenced by body temperature, which also affects the guanine + cytosine nuclear percentage, and that they play an important role in the adaptation of these amniotes. However, the reptilian suborders exhibit differences in the quantitative and compositional characters of the genome that do not completely correspond to differences in the phenotypic parameters commonly involved in the nucleotypic effect. Thus, additional factors could have influenced genome size in this class. These data could be explained with the model of Hartl and Petrov, who observed an inverse correlation between genome size, non-coding portion of the genome and rate of DNA loss and hypothesized a strong role for different spectra of spontaneous insertions and deletions (indels) in the variations of genome size. It is thus reasonable to surmise that variations in the reptilian genome were initially influenced by different indels spectra typical of the diverse lineages, possibly related to different chromosome compartmentalizations. The consequent size increases or decreases would have influenced various morphological and functional cell parameters, and through these some phenotypic characteristics of the whole organism, especially the metabolic rate, very important for environmental adaptation and thus subject to natural selection. Through this "nucleotypic" bond, natural selection would also have controlled genome size variations.     

Genome variations in the transition from amphibians to reptiles

Summary Many characters differentiate amphibian from reptilian genomes. The former have, on the average, larger and more variable genome sizes, a greater repetitive DNA percentage, and a higher interspersion level among DNAs with different degrees of repetitivity. Reptiles have more reduced and uniform genome sizes, a repetitive DNA percentage generally lower than 50%, and a lower interspersion level. Other differences can be observed in the chromosome banding and in the correlations between genome size and other morphometric and functional parameters of the cell.The differences found in amphibians and reptiles seem to indicate that in these two vertebrate classes there is a different tendency toward or tolerance of the accumulation and preservation of genetically dispensable DNA fractions. This might depend either on a different propensity toward genic amplification or on the appearance, in reptiles, of stricter and more efficient constraints regulating genome size.     

Characterization of nuclear DNA in 12 species of Chlorella (Chlorococcales, Chlorophyta) by DNA reassociation

Strains of 12 different species of the genus Chlorella were analyzed for amount, reiteration frequency and kinetic complexity of chromosomal DNA components by C0t analysis. The resulting C0t curves reveal at least two different DNA components consisting of single copy DNA (up to 95%) and of repetitive DNA with complexities of 4.1 x 10(3) base pairs (bp) to approximately 11.7 x 10(3) bp and a reiteration frequency of 100-760. The total amount of repetitive DNA is less than 9% of the nuclear genome and similar in all strains studied. In contrast, the total kinetic complexity varies in a wide range from 1.26 x 10(7) bp to 8.08 x 10(7) bp which is mainly due to differences in the size of single copy DNA. The genome sizes in Chlorella seem not to be correlated with biochemical and physiological characteristics and therefore are unlikely to be useful as a taxonomical marker. A comparison of thermal denaturation profiles showed that the melting points of repetitive and single copy DNA differ by approximately 7 degrees C which may result from base mismatch and/or from a distinct base composition of the repetitive DNA.     

Structural characteristics of genome organization in amphibians: Differential staining of chromosomes and DNA structure

Summary Differential staining patterns on amphibian chromosomes are in some respects distinct from those on mammalian chromosomes; C-bands are best obtained, whereas G- and Q-bands are either unobtainable (on anuran chromosomes) or coincide with C-bands (chromosomes of urodeles). In amphibians, rRNA genes are located at secondary constrictions, but in urodeles they are also found at other chromosome sites, the positions of these sites being strictly heritable. DNA content in amphibian cells is tens and hundreds times higher than in mammals. DNA contents in anurans and urodeles differ within certain limits: from 2 to 25 pg/N and from 30 to over 160 pg/N respectively. Species characterized by slow morphogenesis have larger genomes. Genome growth is normally due to an increase in the amount of repetitive DNA (mostly intermediate repetitive sequences), the amount of unique sequences being almost constant (11 pg/genome in urodeles, and 1.5 pg/genome in anurans). In anurans in general no satellite DNA was found, whereas such fractions were found in manyUrodela species. Nucleosome chromatin structure in amphibians is identical to that of other eukariotes. It is postulated that differences in chromosome banding between amphibians and mammals are due to differences in chromatin packing which in turn is related to the distinct organization of DNA repetitive sequences. It is likely that fish chromosomes have a similiar structure. A comparison of such properties as the chromosome banding patterns, variations in nuclear DNA content and some genome characteristics enable us to group fishes and amphibians together as regards chromosome structure, as distinct from amniotes - reptiles, birds and mammals. It is probable that in the ancient amphibians - ancestors of reptiles - chromatin packing underwent a radical transformation, following changes in the organization of DNA repetitive sequences.     

Nuclear DNA changes within Helianthus annuus L.: cytophotometric,karyological and biochemical analyses

Summary Cytophotometric measurement of the root meristems of seedlings after Feulgen-staining reveals that large differences (up to 58.16%) in nuclear DNA content may occur in the thirty-one cultivated varieties or lines of Helianthus annuus tested. Significant variations (not exceeding 25%) in the amount of DNA, which does not differ between the root and the shoot meristems of a single seedling, are also found to exist within cultivars or lines; even seedlings obtained from seeds collected from different portions of single heads of plants belonging to a selfed line may vary one from the other in this respect. Variations in the number of chromosomes or alterations in the chromosome structure do not account for the differences observed in nuclear DNA content. Karyometric analyses demonstrate that the surface area of squashed interphase nuclei and metaphase chromosomes and the total length of the latter increase with the increase in Feulgen/DNA absorption. DNA thermal denaturation and reassociation kinetics indicate that a frequency variation in repeated DNA sequences goes hand in hand with changes in the size of the genome. These results, supporting the concept that a plant genome is highly flexible, are discussed in relation to other data to be found in the literature on the intraspecific variation in the nuclear DNA content and in relation to the way in which it is produced in H. annuus.     

Genome size and A-T rich DNA in selachians

The nuclear DNA content of 23 selachian species (10 Batoidea, 11 Galeomorphii, and 2 Squalomorphii) was histophotometrically studied. Their genome sizes range from 7.5 pg/N in Raja fillae (Batoidea) to 34.1 pg/N in Oxynotus centrina (Squalomorphii).Results show slight differences in the pattern of quantitative variations between the superorders Batoidea and Galeomorphii; Squalomorphii preserve their peculiar wide interspecific variability at the intrafamilial level, with values sited between 13.1 and 34.1 pg/N.In 21 species also the DNA base composition was determined by means of DAPI. The study shows that in the species examined the DAPI positive fraction varies from a minimum of 27.7% in Oxynotus centrina, which possesses the largest genome size among all the Selachians studied, to a maximum of 72.5% in Carcharhinus limbatus. As a whole the data show an inverse correlation between the DNA content and the DAPI positive fraction, a condition common to all cold-blooded vertebrates.The low percentage of DAPI positive DNA found in Oxynotus centrina could be attributable to a lower stainability by the fluorochrome caused by a higher chromatin condensation in the erythrocytes.The validity of the DAPI method was verified by comparison with the biochemical assay according to the thermal denaturation method in 6 selachian species.     

Genome size, GC percentage and 5mC level in the Indonesian coelacanth Latimeria menadoensis

The living fossil Latimeria menadoensis is important to understand sarcopterygian evolution. To gain further insights into this fish species we studied its genome size, GC% and 5mC level. The genome size and the GC% of the Indonesian coelacanth seem to be very similar to those of the African coelacanth. Moreover the GC%, the CpG frequency and the 5mC level of L. menadoensis are more similar to those of fish and amphibians than to those of mammals, birds and reptiles and this is in line with the hypothesis that two different DNA methylation and CpG shortage equilibria arose during vertebrate evolution. Our results suggest that the genome of L. menadoensis has remained unchanged for several million years, maybe since the origin of the lineage which from lobe-finned fish led to tetrapods. These data fit a conservative evolutionary landscape and suggest that the genome of the extant crossopterygians may be a sort of evolutionarily frozen genome.     

Nuclear DNA changes within Helianthus annum L.: changes within single progenies and their relationships with plant development

Summary The variations in the basic nuclear DNA content, which previous results indicated to occur within one and the same progeny of Helianthus annuus, were studied in detail and correlated with certain developmental features of the plants. The size and organization of the genome of seedlings obtained from seeds (achenes) collected at the periphery (P-seedlings) or in the middle (M-seedlings) of the flowering heads of plants belonging to a line selfed for 10 years were compared. Cytophotometric determinations indicated that the nuclear DNA content of P-seedlings is 14.7% higher than that of M-seedlings. Thermal denaturation and reassociation kinetics of extracted DNAs showed that variations in the redundancy of repetitive DNA, in particular of a family of medium repeated sequences with a Cot range of 2–100, account for the differences in genome size. These findings were confirmed by the results of molecular hybridizations (slot blots), which also indicated a higher amount of ribosomal DNA in the P-seedlings than in the M-seedlings. Cell proliferation is affected by DNA content, and mitotic cycle time is 1h30 longer in the P-seedlings. By studying mature plants, positive correlations were also found between genome size and both the surface area of leaf epidermal cells (P0.01) and flowering time (P0.001). It is suggested that the variations of nuclear DNA content and organization observed play a role in determining developmental variability in plant populations, which may be of importance in buffering the effects of changing environmental conditions.     

Genome size and «C-heterochromatic-DNA» in man and the african apes

The genome sizes and the amounts of DNA after C-banding pretreatments (C-heterochromatic DNA) were measured by quantitative cytochemical methods in man and the African apes,Gorilla gorilla andPan troglodytes. As evaluated by flow cytometry on propidium-iodide-stained lymphocytes, gorilla and chimpanzee have genome sizes larger than man. On the basis of the different resistance of metaphase chromosome DNA to the C-banding procedure, two genome compartments were defined, i.e.,C-heterochromatic-DNA andeuchromatic-DNA. The latter proved to be fairly constant in man and the African apes (as well as in two hylobatid species), whereas the variable amounts ofC-heterochromatic-DNA account well for the interspecific differences of genome size among the hominoid species studied so far. During karyotype diversification, quantitative changes (with either gains or losses) ofC-heterochromatic-DNA seem to have taken place independently in the hylobatid and the man/African ape lineages.     

Packaging of transducing DNA by bacteriophage P1

Summary P1 transduces bacterial chromosomal markers with widely differing frequencies. We use quantitative Southern hybridisations here to show that, despite this, most markers are packaged at similar levels. Exceptions are a group of markers near 2 min and another at 90 min which seem to be packaged at levels two-to threefold higher. We thus conclude that certain marker frequency variations in transduction can be explained by differences in packaging level, but that most cannot. The limited range in packaging levels suggests that P1 can initiate the packaging of chromosomal DNA from many sites. This idea is supported by our failure to find any chromosomal sequences with homology to the phage pac site and by the occurrence of hybridising bands which seem to suggest sequential packaging from a large number of specific sites. We eliminate the possibility that chromosomal DNA packaging is the result of endonucleolytic cutting by the P1 res enzyme.     

Genetic diversity patterns in Curcuma reflect differences in genome size

The relationships between genome size and the systematic and evolutionary patterns in vascular plants are equivocal, although a close relationship between genome size and evolutionary patterns has been previously reported. However, several studies have also revealed the dynamic nature of genome size evolution and its considerable ‘ups’ and ‘downs’. Thus, in this study, the phylogenetic relationships among three previously revealed genome size groups and among species of the highly polyploid genus Curcuma were evaluated using AFLP. Our results suggest two main lineages within Indian Curcuma reflecting evolution of genome size. The first one includes hexaploids and higher polyploids of the previously recognized genome size group I, and the second one includes mainly hexaploids of genome size groups II and III. Within genome size group I, relationships among species seem to be influenced by reticulate evolution and higher polyploids are likely to be of allopolyploid origin. Reproductive systems in Indian Curcuma vary considerably among ploidy levels and these differences considerably affect morphological and genetic variation. In general, clonally reproducing species are expected to exhibit low genotypic diversity, but, at the same time, species of allopolyploid origin are expected to maintain higher levels of heterozygosity compared with their progenitors. We investigated intra‐populational genetic variability in Curcuma spp. to evaluate whether mode of reproduction or ploidy represent the main factor influencing the degree of genetic diversity. We found that hexaploid species exhibited significantly higher genetic diversity than higher polyploids (9x, 15x). Our results suggest that this genetic diversity pattern is largely influenced by the mode of reproduction, as higher polyploids reproduce exclusively vegetatively, whereas hexaploids reproduce mainly sexually. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 388–401.     

Genome complexity of the maize rust fungus,Puccinia sorghi

The base composition and complexity of genomic DNA fromPuccinia sorghi have been estimated by thermal denaturation, analytical ultracentrifugation, and reassociation kinetics. The buoyant density of genomic DNA in CsCl was found to be 1.7021 g/ml, which corresponds to a GC content of 43%. From thermal denaturation curves the GC content was estimated to be 41%. The haploid genome size ofP. sorghi was estimated to be 4.7 × 10⁷ bp, half of which represented a moderately repetitive fraction. The size of theP. sorghi genome is similar to that of other basidiomycete fungi; however, the amount of repetitive DNA is greater than that reported for most other fungi.     

Genome size of two cebus species (primates: platyrrhini) with a fertile hybrid and their quantitative genomic differences

Genome size or C-value is defined as the total amount of DNA contained within a haploid chromosome set and is regarded as a species-specific constant. Speciation among neotropical primates seems to be accompanied by marked quantitative changes in DNA content. A direct correlation between genome size and the presence of heterochromatin has also been proposed. In this work, we analyzed the genome of a female fertile hybrid between Cebus libidinosus and C. nigritus using interspecies comparative genomic hybridization (iCGH), in order to detect quantitative differences between the hybrid and the parental genomes. We also estimated the genome sizes of C. libidinosus and C. nigritus. Both species, considered subspecies of C. apella until 2001, have a highly homologous karyotype but are easily distinguishable at the chromosomal level due to the noncentromeric heterochromatin block on C. libidinosus chromosome 11. Our findings on C-value quantification support the species status for C. libidinosus and C. nigritus, each having a different genome size. The iCGH analysis of the hybrid revealed quantitative differences in comparison to both parental species. The hybrid genome contains a greater amount of DNA in the heterochromatic blocks related to those in the genomes of both parental species. In view of observations in previous and the present work, some hypotheses about genome dynamics of neotropical primates are proposed and discussed.     

Genome size evolution in Sapindaceae at subfamily level: a case study of independence in relation to karyological and palynological traits

Sapindaceae s.l. is a moderately large family of trees, shrubs and lianas. Current knowledge on genome size and how it varies in this family is scarce. This research aims to characterize the DNA content in 39 species of Sapindaceae, mainly in tribe Paullinieae s.s., by the analysis of the variation in genome size relative to karyotypic and palynological features. Nuclear DNA amount was measured by flow cytometry, and linear regression analyses were conducted to analyse the relationship between genome size variation and various karyotypic and palynological features. Genome size varied nine‐fold among species, ranging from 1C = 0.305 pg (Lophostigma plumosum) to 2.710 pg (Cardiospermum heringeri). The low regression coefficients obtained suggest that genome size mainly varies independently of karyotypic and palynological features. With regard to karyotype evolution, the constant chromosome number but variable genome size in Houssayanthus, Paullinia and Serjania suggest that structural changes mainly caused by changes in the amounts of repetitive DNA are more important than numerical change. In contrast, in Cardiospermum and Urvillea, variation in chromosome number and genome size supports the suggestion that numerical and structural changes are important in the karyotype evolution of these genera. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 589–600.     

DNA reassociation kinetics in relation to genome size in four amphibian species

DNA reassociation kinetics were studied, by means of the hydroxyapatite chromatography method, for four species of Amphibians with different nuclear DNA content: Xenopus laevis (3 pg DNA per haploid genome) and Bufo bufo (7 pg) of the Anura subclass and Trituras cristatus (23 pg) and Necturus maculosus (52 pg) of the Urodela subclass.Within each subclass the two species studied were found to have about the same absolute amount of unique DNA. The differences of total nuclear DNA can be accounted for by quantitative variations of the repetitive sequence classes, at least in part due to changes in the number of copies of the various sequences. On the contrary the great difference in nuclear DNA between the two subclasses, Anura and Urodela, involves all sequence classes in parallel; the slowly reassociating fraction appears to be unique in spite of a tenfold difference in absolute amount.The dependence of reassociation kinetics on DNA fragment length for the four species indicates for all of them an interspersed organization of the various sequence classes.     

Evolution of genome size in Drosophila. is the invader's genome being invaded by transposable elements?

Genome size varies considerably between species, and transposable elements (TEs) are known to play an important role in this variability. However, it is far from clear whether TEs are involved in genome size differences between populations within a given species. We show here that in Drosophila melanogaster and Drosophila simulans the size of the genome varies among populations and is correlated with the TE copy number on the chromosome arms. The TEs embedded within the heterochromatin do not seem to be involved directly in this phenomenon, although they may contribute to differences in genome size. Furthermore, genome size and TE content variations parallel the worldwide colonization of D. melanogaster species. No such relationship exists for the more recently dispersed D. simulans species, which indicates that a quantitative increase in the TEs in local populations and fly migration are sufficient to account for the increase in genome size, with no need for an adaptation hypothesis.     

Climate and growth form: the consequences for genome size in plants

The adaptive significance of nuclear DNA variation in angiosperms is still widely debated. The discussion mainly revolves round the causative factors influencing genome size and the adaptive consequences to an organism according to its growth form and environmental conditions. Nuclear DNA values are now known for 3874 angiosperm species (including 773 woody species) from over 219 families (out of a total of 500) and 181 species of woody gymnosperms, representing all the families. Therefore, comparisons have been made on not only angiosperms, taken as a whole, but also on the subsets of data based on taxonomic groups, growth forms, and environment. Nuclear DNA amounts in woody angiosperms are restricted to less than 23.54 % of the total range of herbaceous angiosperms; this range is further reduced to 6.8 % when woody and herbaceous species of temperate angiosperms are compared. Similarly, the tropical woody dicots are restricted to less than 50.5 % of the total range of tropical herbaceous dicots, while temperate woody dicots are restricted to less than 10.96 % of the total range of temperate herbaceous dicots. In the family Fabaceae woody species account for less than 14.1 % of herbaceous species. Therefore, in the total angiosperm sample and in subsets of data, woody growth form is characterized by a smaller genome size compared with the herbaceous growth form. Comparisons between angiosperm species growing in tropical and temperate regions show highly significant differences in DNA amount and genome size in the total angiosperm sample. However, when only herbaceous angiosperms were considered, significant differences were obtained in DNA amount, while genome size showed a non-significant difference. An atypical result was obtained in the case of woody angiosperms where mean DNA amount of tropical species was almost 25.04 % higher than that of temperate species, which is because of the inclusion of 85 species of woody monocots in the tropical sample. The difference becomes insignificant when genome size is compared. Comparison of tropical and temperate species among dicots and monocots and herbaceous monocots taken separately showed significant differences both in DNA amount and genome size. In herbaceous dicots, while DNA amount showed significant differences the genome size varies insignificantly. There was a non-significant difference among tropical and temperate woody dicots. In three families, i.e., Poaceae, Asteraceae, and Fabaceae the temperate species have significantly higher DNA amount and genome size than the tropical ones. Woody gymnosperms had significantly more DNA amount and genome size than woody angiosperms, woody eudicots, and woody monocots. Woody monocots also had significantly more DNA amount and genome size than woody eudicots. Lastly, there was no significant difference between deciduous and evergreen hardwoods. The significance of these results in relation to present knowledge on the evolution of genome size is discussed.     

Contrasting DNA sequence organisation patterns in sauropsidian genomes

The genomic DNA organisation patterns of four sauropsidian species, namely Python reticularis, Caiman crocodilus, Terrapene carolina triungius and Columba livia domestica were investigated by reassociation of short and long DNA fragments, by hyperchromicity measurements of reannealed fragments and by length estimations of S₁-nuclease resistant repetitive duplexes. While the genomic DNA of the three reptilian species shows a short period interspersion pattern, the genome of the avian species is organised in a long period interspersion pattern apparently typical for birds. These findings are discussed in view of the close phylogenetic relationships of birds and reptiles, and also with regard to a possible relationship between the extent of sequence interspersion and genome size.     

Chondrichthyan cytogenetics: A comparison with teleosteans

Summary Cytogenetic studies on cartilaginous fish conducted in recent years have shown that these vertebrates have peculiarities associated both with the karyotypes and the size and composition of their DNAs. Although the data for this group, which includes about 1000 extant species, are still fragmentary, there appear to be more differences than similarities with teleosts; e.g., chromosome sets are characterized by a high diploid number (2n=up to 106) and are often rich in acrocentric elements and in microchromosomes. From the quantitative standpoint, chondrichthyan genomes are relatively large (2C=up to 34 pg DNA/n), exhibiting sometimes wide interspecific variability (Squalidae).The few studies on genome composition for these species have revealed marked difference between chondrichthyans and teleosteans in the ratio of the amount of GC-rich DNA to the total increase in genome. Moreover, thermal denaturation of the genomes of six selachians revealed derived curves that are characteristic of heterogeneity in nucleotide distribution, which has not been evidenced in most of the teleosteans investigated thus far.Finally, for the first time in selachians, an investigation was conducted using restriction enzymes, the results of which showed a pattern of chromosome labeling that was in some cases (Alu I) similar to and in others (Hae III, Hind III) different from that of teleosteans.     

Is genome size influenced by colonization of new environments in dipteran species?

Genome size differences are usually attributed to the amplification and deletion of various repeated DNA sequences, including transposable elements (TEs). Because environmental changes may promote modifications in the amount of these repeated sequences, it has been postulated that when a species colonizes new environments this could be followed by an increase in its genome size. We tested this hypothesis by estimating the genome size of geographically distinct populations of Drosophila ananassae, Drosophila malerkotliana, Drosophila melanogaster, Drosophila simulans, Drosophila subobscura, and Zaprionus indianus, all of which have known colonization capacities. There was no strong statistical differences between continents for most species. However, we found that populations of D. melanogaster from east Africa have smaller genomes than more recent populations. For species in which colonization is a recent event, the differences between genome sizes do not thus seem to be related to colonization history. These findings suggest either that genome size is seldom modified in a significant way during colonization or that it takes time for genome size of invading species to change significantly.