Molecular organisation of the plant genome: Its relation to structure,recombination and evolution of chromosomes

Large scale changes in nuclear DNA amount accompany the evolution of species of higher plants. Much of the nuclear DNA accrued during the evolution of species does not encode genetic information and is selectively neutral. Nonetheless, the pattern of distribution of the excess DNA within and between chromosome complements suggests that there are rigid constraints underlying evolutionary changes in genome organisation. A five-fold increase in the amount of nuclear DNA has occurred in the evolution ofLathyrus species. Not withstanding this massive DNA variation, species show consistently similar patterns in base sequence proliferation, divergence and DNA distribution within and between chromosome complements. Within chromosome complements, the excess DNA is distributed evenly in all chromosomes irrespective of the large differences in chromosome size and, between complements, DNA distribution is discontinuous; species cluster into DNA groups with remarkably regular intervals. Similar constraints govern the frequency and distribution of chiasmata in the chromosome complements. Between species chiasma frequency and nuclear DNA amounts are not correlated but within complements it is positively correlated with the amount of DNA contained in each chromosome.     

DNA amounts and chromatin compactness in Vicia

2C DNA amounts and areas of chromatin were determined with a M 86 Vickers microdensitometer in 56 species of Vicia (x=5, 6, 7), exhibiting large differences in chromosome size. There were significant differences between the species both in DNA content and chromatin area. The nuclear DNA amounts range from 3.85 to 27.07 pg. DNA distribution appears discontinuous; species cluster into distinct groups and the average nuclear DNA amount separating each successive pair is approximately the same (2.23 pg). The compaction of DNA in interphase nuclei increases with increasing DNA amount, which is, at least partly, due to a disproportionate increase in the heterochromatin relative to the euchromatin component of DNA. Comparisons of DNA readings at various stages of the cell cycle show that the DNA amounts are underestimated by microdensitometry in nuclei with high DNA density. Estimation of relative DNA content and area of individual chromosomes were made in twelve species. The results show that changes in DNA content within chromosomes affect the degree of metaphase coiling in an orderly fashion.     

Karyotype differences in the crenaticeps-group of Atractomorpha (orthoptera,acridoidea, pyrgomorphidae)

The four known species of the crenaticeps-group of the genus Atractomorpha have 2n ()=18+X0. All members of the complement are rod-chromosomes and the smallest autosome (no. 9) is megameric. The four species have similar amounts of euchromatin but differ markedly in the amount of heterochromatin present in their genomes. In A. similis, A. crenaticeps and the unnamed species, Species-1, there are distinct proximal segments of heterochromatin in the eight large autosomes. In A. similis these chromosomes also have prominent distal segments of heterochromatin. The fourth species, A. australis, has no visible heterochromatin in its eight large autosomes except for a small segment at the proximal end of autosome 4. In all four species, the heterochromatic segments influence chiasma frequency and chiasma position. Moreover the overall chiasma frequency is lowest in A. similis with most heterochromatin and highest in A. australis with least heterochromatin.     

Recombination and genome size

Summary Within complements the chiasma frequency per chromosome, which directly reflects the amount of recombination, is generally closely correlated with chromosome length, i.e. the chromosomal DNA content. The correlation does not apply when comparisons are made between the complements of different species. Analyses of results from three Angiosperm genera show a progressive decrease in the chiasma frequency per picogram of DNA with increase in nuclear DNA amount.     

Structure and DNA methylation pattern of partially heterochromatinised endosperm nuclei in Gagea lutea (Liliaceae)

Pentaploid endosperm nuclei in certain Gagea species exhibit large masses of sticky and dense chromatin, not observed in somatic nuclei. These heterochromatin masses most probably stem from the triploid chalasal polar nucleus of the embryo sac, thus representing an example of facultative heterochromatinisation in plants. In the present investigation, we studied the nuclei in Gagea lutea (L.) Ker-Gawl. endosperm tissue. The position of the heterochromatin in interphase nuclei was observed by confocal laser scanning microscopy (CLSM) and the DNA methylation status of the euchromatin and heterochromatin was analysed by immunolabelling with an antibody raised against 5-methylcytosine (anti-5-mC). In young endosperms, heterochromatin was relatively dispersed, occupying some peripheral and inner parts of the nuclei. In a later endosperm development, the nuclei became smaller and more pycnotic, and the heterochromatin masses were placed predominantly near the nuclear periphery. The distribution of anti-5-mC labelling on the heterochromatic regions was unequal: some parts appeared hypermethylated while other parts were, like the euchromatin, not labelled. During mitosis, the labelling intensity of all the chromosomes was approximately the same, thus indicating that there are no cytologically detectable methylation differences among the individual sets of chromosomes. However, differences in the anti-5-mC signal intensity along individual chromosomes were observed, resulting in banding patterns with highly positive bands apparently representing constitutive heterochromatic regions. From these results it is obvious that facultative heterochromatinisation, in contrast to constitutive heterochromatinisation, need not be strictly accompanied by a prominent DNA hypermethylation. Received: 24 April 1997 / Accepted: 28 July 1997     

Nuclear DNA variation in Lathyrus

In the genus Lathyrus the divergence and evolution of species was accompanied by large scale changes in nuclear DNA amount. All the species are diploids with 14 chromosomes so that the DNA changes were the result of amplification or deletion of segments within chromosomes. Our evidence indicates that the quantitative changes involve mainly the repetitive, as distinct from the non-repetitive fraction of the chromosomal DNA and, on a cytological basis, mainly heterochromatin in contrast to euchromatin. There is an element of discontinuity in the distribution of DNA amounts among species which suggests that the DNA variation results from a series of separate, spasmodic events. The discontinuities may be viewed, also, as steady states from the standpoint of genetic balance and biological fitness.     

Cytogenetic studies of the Australian rodent,Uromys caudimaculatus,a species showing extensive heterochromatin variation

The Australian rodent, Uromys caudimaculatus, consists of two chromosome races, a) The Southern Race is characterized by the possession of two to twelve B-chromosomes. These vary considerably in size, morphology, and C- and G-banding characteristics, they behave as univalent at meiosis and are inherited in a random manner, b) The Northern Race lacks Bchromosomes, but possesses large blocks of distal C-positive heterochromatin on between 18 and 28 of the 46 chromosomes. The C-blocks may be entirely G-positive, entirely G-negative, or G-banded, suggesting heterogeneity within the C-blocks. There is extensive variation both between and within populations of the northern race in the number and size of the distal heterochromatic blocks. There is no apparent difference between the races in chiasma frequency. The northern race does have a much higher proportion of interstitial versus distal chiasmata, although it is probable that this is merely a reflection of lack of crossing over in the heterochromatic blocks rather than an actual shift of chiasma localisation within the euchromatin. Despite the extensive differences between the races in the amount and organization of constitutive heterochromatin, hybrids show no abnormalities at meiosis and they are fully fertile.     

Pachytene pairing and metaphase I configurations in a tetraploid somatic Lycopersicon esculentum x L. peruvianum hybrid.

In the tetraploid somatic hybrid between the diploid Lycopersicon species L. esculentum (tomato) and L. peruvianum, synaptonemal complexes formed quadrivalents in 73 of the 120 sets of four chromosomes (60.8%) in 10 cells studied in detail at pachytene. Of these, 43 had one pairing partner exchange, 22 had two, and 8 had three, very close to a Poisson distribution. The points of pairing partner exchange were concentrated at the middle of the two arms. The frequency per arm corresponded with physical arm length. There was a sharp drop around the centromere, and pericentric heterochromatin had a slightly lower probability of being involved in pairing partner exchange than euchromatin. The chromosomes align before pairing and there are several points of pairing initiation, with concentrations at or near the ends and the centromere. From zygotene to late pachytene the quadrivalent frequency decreased considerably. At late pachytene it was lower than expected with the observed high frequency of pairing partner exchange. Pairing affinity between species was only slightly lower than affinity within species, in spite of considerable genetic differentiation. The frequency of recombination nodules increased from early to late zygotene and then decreased strongly to full pachytene. There is a highly significant negative correlation between percent pairing and SC length. At metaphase I the frequency of quadrivalents was 0.444, and branched quadrivalents were rare, probably caused by interference and restriction of chiasma formation to distal euchromatin. Metaphase I quadrivalent frequency is a relatively good indication of pairing affinity in this material.     

The distribution of SCEs within and between the genomes of an interspecific hybrid

The distribution of sister chromatid exchanges has been examined in the chromosomes of a hybrid male wallaby (Macropus rufogriseus x Wallabia bicolor ), and in the X chromosomes of M. parryi and M. rufus. Comparisons were made of SCE frequency between the two genomes of the hybrid, only one of which has an appreciable amount of constitutive heterochromatin, and between the euchromatic and heterochromatic regions of the M. rufogriseus genome. The frequency of SCEs is closely correlated with the DNA content of the individual chromosomes. The distribution of the SCEs between the euchromatin and heterochromatin in the M. rufogriseus genome showed a deficiency of SCEs observed in the heterochromatin compared with the euchromatin. —A substantial excess of SCEs occurred at the nucleolar organiser region of the M. rufogriseus X chromosome. This excess was absent from the nucleolar organiser region of the X chromosome of the two other macropodine species studied and is accounted for by the presence of an adjacent euchromatin-heterochromatin junction.     

Cytogenetics of pearl millet

Summary The somatic karyotype of pearl millet Pennisetum americanum (L.) Leeke. (2n = 14) has been studied in several cultivars, but few cytological markers have been discovered which could help in the easy identification of the chromosomes. Analysis of pachytene bivalents permits such identification but is feasible only in a few cultivars. Recently, several lines having telocentric chromosomes have been produced and classified but their potentialities as cytogenetic tools have yet to be explored. Some African populations of pearl millet carry B-chromosomes in their karyotype. Cytogenetics of B-chromosomes has been reported in great detail. Bs undergo spontaneous changes to produce deficient- and iso-chromosomes. The main effect of B-chromosomes is on chiasma frequency which is exerted by the relative amounts of chiasma promoting euchromatin and the chiasma depressing heterochromatin in the Bs. Haploid plants occur occasionally and sometimes show a low degree of seed set, offering a possibility of establishing homozygous inbred lines. Cytogenetics of several spontaneous and induced autotetraploids have been reported. In general quadrivalent formation between the seven sets of four homologues was random. Seed set of the autotetraploids could be improved by selection; improved seed fertility was found to be associated with increased chiasma frequency, increased quadrivalent frequency and regular distribution of chromosomes at anaphase I. Genes controlling morphological characters of plant phenotype segregate independent of those controlling fertility and in pearl millet polyploidy per se is not limiting to plant vigour. Primary trisomics represent the best studied among the aneuploids of pearl millet. All the seven primary trisomics have been identified and described. Some were used in assigning genes to specific chromosomes but in general trisomies have poor vigour and fertility, and show low frequency of transmission. Apart from B-chromosomes, cytogenetics of interchanges has been the best studied aspect of pearl millet. The frequency of co-orientation of an interchange complex at metaphase I, which determines the fertility or sterility of the interchange heterozygote, is influenced by the genetic background and thus is theoretically amenable for selection leading to improved fertility of the heterozygote. Interchange tester-stocks have been assembled which can be used to identify the chromosomes involved in any newly obtained interchange. A complex interchange line involving all the chromosomes of the complement has also been produced, but the ring-of-fourteen produces total male and female sterility.Genotypic control of mitosis and meiosis has been reported, with reference to chromosome numerical mosaicism, multiploid sporocytes, desynapsis and chromosome fragmentation, and male sterility. Pearl millet being a largely outbreeding species, forced inbreeding was mainly found to result in loss of morphological vigour and reduction in mean chiasma frequency per PMC. Interspecific hybrids between pearl millet and several related species have been cytologically investigated and homology of the seven chromosomes of pearl millet with seven of the fourteen chromosomes of P. purpureum has been demonstrated. Cytogenetic evidence from haploids, autopolyploids and interspecific hybrids has indications to suggest that the haploid number of x = 7 is derived from x = 5, but the evidence is inconclusive and needs critical evaluation.     

Chromosome evolution in the genus Poecilimon (Orthoptera, Tettigonioidea, Phaneropteridae)

Cytotaxonomic analysis of 20 species and subspecies of the genus Poecilimon using C-banding pattern, chiasma frequency, and morphometric characteristics of the chromosomes were described. Using a cladistic analysis the chromosome data provided a basis to produce a phylogenetic tree which was compared with a tree based on morphological characters and DNA sequence data. There are important differences in the grouping of data sets to species obtained on the basis of morphology/DNA analyses and that based on chromosomes. The explanation of the differences between C-banding patterns and taxonomic proximity is probably that the C-banding pattern changes quickly as the result of the high degree of variation of constitutive heterochromatin.     

The supernumerary segment system of Stethophyma

Three species of the genus Stethophyma have been cytologically examined and all three show variation both for supernumerary heterochromatic segments and for the distribution of standard heterochromatin among the autosomes. The European species, S. grossum, for example, shows considerable interpopulation variation for standard heterochromatin while two of the populations, from Spain and Austria, show supernumerary segment polymorphism. The segments are located interstitially on the S₁₁ chromosome but occupy different positions in the different populations. — In all species, the presence of the extra heterochromatic segments increases the mean chiasma frequency. Moreover, the influence of the segments upon mean chiasma frequency is different in different populations and in different species. In the Spanish population, the increase is both intra- and interchromosomal whereas in Austria the influence of the segment is completely interchromosomal. — In the American species, S. gracile and S. lineatum, where supernumerary heterochromatic segments are carried on both S₁₀ and S₁₁ chromosomes, the effect on chiasma frequency shows a dosage relationship, an increase in the number of segments per individual being correlated with an increase in mean chiasma frequency. It is suggested that the interstitial segments found in all species have originated by direct duplication of chromosome material. By contrast the terminal segments in S. lineatum and S. gracile may be derived by translocation from a B-chromosome since such a chromosome has been found in one individual of the former species. — The variation in segment structure and the distribution of standard heterochromatin, among the European species of S. grossum suggests that these systems have evolved independently in different populations.On educational leave from the Forest Research Laboratory, Fredericton, N. B. Canada.     

Different types of plant chromatin associated with modified histones H3 and H4 and methylated DNA

Eukaryotic chromosomes are organized into two large and distinct domains, euchromatin and heterochromatin, which are cytologically characterized by different degrees of chromatin compaction during interphase/prophase and by post-synthesis modifications of histones and DNA methylation. Typically, heterochromatin remains condensed during the entire cell cycle whereas euchromatin is decondensed at interphase. However, a fraction of the euchromatin can also remain condensed during interphase and appears as early condensing prophase chromatin. 5S and 45S rDNA sites and telomere DNA were used to characterize these regions in metaphase and interphase nuclei. We investigated the chromosomal distribution of modified histones and methylated DNA in the early and late condensing prophase chromatin of two species with clear differentiation between these domains. Both species, Costus spiralis and Eleutherine bulbosa, additionally have a small amount of classical heterochromatin detected by CMA/DAPI staining. The distribution of H4 acetylated at lysine 5 (H4K5ac), H3 phosphorylated at serine 10 (H3S10ph), H3 dimethylated at lysine 4 or 9 (H3K4me2, H3K9me2), and 5-methylcytosine was compared in metaphase, prophase, and interphase cells by immunostaining with specific antibodies. In both species, the late condensing prophase chromatin was highly enriched in H4K5ac and H3K4me2 whereas the early condensing chromatin was very poor in these marks. H3K9me2 was apparently uniformly distributed along the chromosomes whereas the early condensing chromatin was slightly enriched in 5-methylcytosine. Signals of H3S10ph were restricted to the pericentromeric region of all chromosomes. Notably, none of these marks distinguished classical heterochromatin from the early condensing euchromatin. It is suggested that the early condensing chromatin is an intermediate type between classical heterochromatin and euchromatin.     

The constitutive heterochromatin in chromosomes of Fritillaria Sp., as revealed by Giemsa banding.

The incidence of C-bands (constitutive heterochromatin), as determined by differential Giemsa staining, was studied in the chromosomes of 56 species, varietal forms and subgenera of Fritillaria and 30 of them are illustrated. With the exception of the subgenera Korolkowi, a supposed link between lilies and fritillaries, and chromsome complements of all plants contained bands. There were wide differences in the size and number of these bands among species both within and between groups. In those with the largest and most abundant bands, there was a pronounced tendency for centromeric localization, both in Old and New World species. The Giemsa positive centromeres were masked when this occurred. Heteromorphy in respect of banding occurred in most species. The relation of repetitive DNA sequences with heterochromatin is discussed, as is also the problem of evolution in Fritillaria.     

Variation of genome size and organization within hexaploid Festuca arundinacea

Summary Cytophotometric, karyological, and biochemical analyses were carried out in the meristems of seedlings obtained from seeds collected from 35 natural populations of hexaploid Festuca amndinacea in Italy. Highly significant differences between populations were observed in the amount of nuclear DNA (up to 32.3%). These changes are linked to variations in the amount of heterochromatin and in the frequency of repeated DNA sequences, and particularly of a fraction of them. Differences between populations in the arm ratios and total length of the chromosomes were also observed. The genome sizes of the populations are correlated positively with the mean temperature during the year and with that of the coldest month at the stations, and correlate negatively with their latitudes. The intraspecific genome changes observed are discussed in relation to other pertinent data to be found in the literature and in relation to their possible role in environmental adaptation.     

Chromosomal DNA variation in Cucumis

Summary Variation in nuclear DNA amounts found in different species of Cucumis was surveyed. The DNA amounts varied from 1.373 to 2.483 pg in diploids and from 2.846 to 3.886 pg in tetraploids. DNA amount was not correlated with chromosome number and periodicity. Tetraploids were found to have double the quantity of nuclear DNA of diploids. A positive linear relationship was established between the nuclear DNA amounts and volume of chromosomes. The botanical varieties within a particular species do not differ significantly for 2C DNA amounts. A comparison of the distribution of DNA amounts among different chromosomes of haploid complement in different species revealed that the quantitative DNA changes associated with speciation affected all chromosomes. DNA changes were not however, of the same magnitude in all chromosomes of the complement. Speciation in Cucumis thus seems to have occurred through amplification or diminution of DNA proportionate to the size of chromosomes. The relationship between the basic numbers, x=7 and x=12, will have to be considered relative to the high DNA amount noticed in some species with x=12.     

Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome

Eleven sequenced BACs were annotated and localized via FISH to tomato pachytene chromosomes providing the first global insights into the compositional differences of euchromatin and pericentromeric heterochromatin in this model dicot species. The results indicate that tomato euchromatin has a gene density (6.7 kb/gene) similar to that of Arabidopsis and rice. Thus, while the euchromatin comprises only 25% of the tomato nuclear DNA, it is sufficient to account for approximately 90% of the estimated 38,000 nontransposon genes that compose the tomato genome. Moreover, euchromatic BACs were largely devoid of transposons or other repetitive elements. In contrast, BACs assigned to the pericentromeric heterochromatin had a gene density 10-100 times lower than that of the euchromatin and are heavily populated by retrotransposons preferential to the heterochromatin-the most abundant transposons belonging to the Jinling Ty3/gypsy-like retrotransposon family. Jinling elements are highly methylated and rarely transcribed. Nonetheless, they have spread throughout the pericentromeric heterochromatin in tomato and wild tomato species fairly recently-well after tomato diverged from potato and other related solanaceous species. The implications of these findings on evolution and on sequencing the genomes of tomato and other solanaceous species are discussed.     

Preferential occurrence of sister chromatid exchanges at heterochromatin-euchromatin junctions in the wallaby and hamster chromosomes

Chromosomes of two mammalian species, the white-throated wallaby and the rat-like hamster, possessed large amounts of constitutive heterochromatin which is detectable as C bands. By making use of this character, the frequency of sister chromatid exchanges (SCEs) was determined for the C band and the euchromatic regions of the chromosome. In both species, the distribution of SCEs in the euchromatin of chromosomes was found to be proportional to its metaphase length, while the number of SCEs localized in the C band regions was clearly fewer than expected on the basis of the relative length of those regions at metaphase. Many SCEs were, however, detected at the junctions between the euchromatin and the C band heterochromatin. All of these findings were consistent with previous observations on the Indian muntjac and the kangaroo rat chromosomes.     

Detection and location of three simple sequence DNAs in polytene chromosomes from virilis group species of Drosophila

In vitro synthesized RNAs complementary to the three satellite DNAs of Drosophila virilis have been used in a series of in situ hybridization experiments with polytene chromosomes from virilis group species. Gall and Atherton (1974) demonstrated that each of the satellites of D. virilis is comprised of many repeats of a distinct, seven base pair long, simple sequence. With few exceptions, copies of each of these simple sequences are detected in the chromocenters of all virilis group species. This is true even in species which do not possess satellite DNAs at buoyant densities corresponding to those of the satellite DNAs of D. virilis. Small quantities of the three simple sequences are also detected in euchromatic arms of several different species. The same euchromatic location may contain detectable copies of one, two, or all three simple sequence DNAs. The amounts of simple sequences at each location in the euchromatin may vary between species, between different stocks of the same species, and even between individuals of the same stock. The simple sequences located in the euchromatin appear to undergo DNA replication during formation of polytene chromosomes unlike those in heterochromatin. The locations of the euchromatic sequences are not the results of single chromosomal inversion events involving heterochromatic and euchromatic breakpoints.     

Alpha and beta heterochromatin in polytene chromosome 2 ofDrosophila melanogaster

The formation of alpha and beta heterochromatin in chromosomes of Drosophila melanogaster was studied in salivary glands (SGs) and pseudonurse cells (PNCs). In SGs of X0, XY, XYY, XX and XXY individuals the amounts of alpha heterochromatin were similar, suggesting that the Y chromosome does not substantially contribute to alpha heterochromatin formation. Pericentric heterochromatin developed a linear sequence of blocks in PNCs, showing morphology of both alpha and beta heterochromatin. In situ hybridization with Rsp sequences (H _o clone) revealed that the most proximal heterochromatic segment of the mitotic map (region h39) formed a polytenized block in PNCs. Dot analysis showed that the clone had a hybridization rate with PNC-DNA very close to that with DNA from mainly diploid head cells, whereas the homologous SG-DNA was dramatically underrepresented. A similar increase of DNA representation in PNC was found for AAGAC satellite DNA. The mitotic region h44 was found not to polytenize in the SG chromosome, whereas in PNC chromosome 2 this region was partly polytenized and presented as an array of several blocks of alpha and beta heterochromatin. The mapping of deficiencies with proximal breakpoints in the most distal heterochromatin segments h35 in arm 2L and h46 in 2R showed that the mitotic eu-heterochromatin transitions were located in SG chromosomes distally to the polytene 40E and 41C regions, respectively. Thus, the transition zones between mitotic hetero- and euchromatin are located in banded polytene euchromatin. A scheme for dynamic organization of pericentric heterochromatin in nuclei with polytene chromosomes is proposed. Received: 17 November 1995; in revised form: 10 April 1996 / Accepted: 18 September 1996