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.     

Identification of two new repetitive elements and chromosomal mapping of repetitive DNA sequences in the fish Gymnothorax unicolor (Anguilliformes: Muraenidae)

Muraenidae is a species-rich family, with relationships among genera and species and taxonomy that have not been completely clarified. Few cytogenetic studies have been conducted on this family, and all of them showed the same diploid chromosome number (2n=42) but with conspicuous karyotypic variation among species. The Mediterranean moray eel Gymnothorax unicolor was previously cytogenetically studied using classical techniques that allowed the characterization of its karyotype structure and the constitutive heterochromatin and argyrophilic nucleolar organizer regions (Ag-NORs) distribution pattern. In the present study, we describe two new repetitive elements (called GuMboI and GuDdeI) obtained from restricted genomic DNA of G. unicolor that were characterized by Southern blot and physically localized by in situ hybridization on metaphase chromosomes. As they are highly repetitive DNA sequences, they map in heterochromatic regions. However, while GuDdeI was localized in the centromeric regions, the GuMboI fraction was distributed on some centromeres and was co-localized with the nucleolus organizer region (NOR). Comparative analysis with other Mediterranean species such as Muraena helena pointed out that these DNA fractions are species-specific and could potentially be used for species discrimination. As a new contribution to the karyotype of this species, we found that the major ribosomal genes are localized on acrocentric chromosome 9 and that the telomeres of each chromosome are composed of a tandem repeat derived from a poly-TTAGGG DNA sequence, as it occurs in most vertebrate species. The results obtained add new information useful in comparative genomics at the chromosomal level and contribute to the cytogenetic knowledge regarding this fish family, which has not been extensively studied.     

Dating primate divergences through an integrated analysis of palaeontological and molecular data

Estimation of divergence times is usually done using either the fossil record or sequence data from modern species. We provide an integrated analysis of palaeontological and molecular data to give estimates of primate divergence times that utilize both sources of information. The number of preserved primate species discovered in the fossil record, along with their geological age distribution, is combined with the number of extant primate species to provide initial estimates of the primate and anthropoid divergence times. This is done by using a stochastic forwards-modeling approach where speciation and fossil preservation and discovery are simulated forward in time. We use the posterior distribution from the fossil analysis as a prior distribution on node ages in a molecular analysis. Sequence data from two genomic regions (CFTR on human chromosome 7 and the CYP7A1 region on chromosome 8) from 15 primate species are used with the birth-death model implemented in mcmctree in PAML to infer the posterior distribution of the ages of 14 nodes in the primate tree. We find that these age estimates are older than previously reported dates for all but one of these nodes. To perform the inference, a new approximate Bayesian computation (ABC) algorithm is introduced, where the structure of the model can be exploited in an ABC-within-Gibbs algorithm to provide a more efficient analysis.     

小麦属核型分析和BG染色体组及4A染色体的起源

应用植物有丝分裂染色体标本制备新方法和N—带技术对小麦属(Triticum)9个六倍体种(AABBDD),8个四倍体种(AABB,AAGG),3个二倍体种(AA,A~uA~u)及B组的可能供体沙融山羊草(Ae. shronensis)体细胞核型和N—带进行了分析。结果表明,小麦属全部为具中部或次中部着丝点染色体,核型属于“2A”类型,不对称性随倍性提高而有所增加。种问核型有一定差异。所有小麦B染色体组、G染色体组和4A染色体均显N—带,其它染色体则不显带或只显很浅的着丝点带。六倍体种B染色体组带型基本相同,四倍体小麦B组N—带种间有一定差异。提莫菲维小麦(T.Timopheevi)G组带纹数目和分布与B梁色体组有显著差别,作者认为两者非同源。沙融山羊草核型和带型都与小麦B组相近,是B组的可能供体。一粒系小麦A染色体组基本不显N—带,其中无与4A带型相同的染色体,4A起源尚待研究。     

(dC-dA)n.(dG-dT)n sequences have evolutionarily conserved chromosomal locations in Drosophila with implications for roles in chromosome structure and function.

In situ hybridization of (dC-dA)n.(dG-dT)n to the polytene chromosomes of Drosophila melanogaster reveals a clearly non-random distribution of chromosomal sites for this sequence. Sites are distributed over most euchromatic regions but the density of sites along the X chromosome is significantly higher than the density over the autosomes. All autosomes show approximately equal levels of hybridization except chromosome 4 which has no detectable stretches of (dC-dA)n.(dG-dT)n. Another striking feature is the lack of hybridization of the beta-heterochromatin of the chromocenter. The specific sites are conserved between different strains of D. melanogaster. The same overall chromosomal pattern of hybridization is seen for the other Drosophila species studied, including D. simulans, a sibling species with a much lower content of middle repetitive DNA, and D. virilis, a distantly related species. The evolutionary conservation of the distribution of (dC-dA)n.(dG-dT)n suggests that these sequences are of functional importance. The distribution patterns seen for D. pseudoobscura and D. miranda raise interesting speculations about function. In these species a chromosome equivalent to an autosomal arm of D. melanogaster has been translocated onto the X chromosome and acquired dosage compensation. In each species the new arm of the X also has a higher density of (dC-dA)n.(dG-dT)n similar to that seen on other X chromosomes. In addition to correlations with dosage compensation, the depletion of (dC-dA)n.(dG-dT)n in beta-heterochromatin and chromosome 4 may also be related to the fact that these regions do not normally undergo meiotic recombination.     

Life history, diversity and distribution: a study of Japanese pteridophytes

Many studies address the relationships between diversity or distribution and attributes of the physical environment. However, how these relationships are connected to variation in life history is poorly understood. This is particularly true in the case of pteridophytes. Japanese ferns and their allies comprise one of the best-known pteridophyte floras in the world. We analyzed ca 600 species of Japanese pteridophytes for which there is detailed information on distribution, reproduction, and chromosome number. Species richness was greatest in groups with a single reproductive mode (sexual, followed by apogamous), but distribution was greatest in species groups with multiple reproductive modes: sexual plus either sterile (irregular in meiosis) or apogamous. Geographical ranges varied greatly among species with small chromosome numbers but were uniformly small among species having high chromosome numbers. Seasonally green (mostly summer green) species had significantly larger distribution ranges than evergreen species. Endemic species had higher proportions of apogamy and sterility than non-endemic species. Seasonally green species had significantly larger distributional ranges, and a smaller proportion of species with apogamous reproduction, than evergreen species. There was no clear relationship between distribution and spore size, either among endemic species, non-endemic species, or all species combined. There was no relationship between spore size and chromosome number when all species were combined. However, positive relationships were detected within three of the nine largest genera, suggesting potential phylogenetic effects. We concluded that habitat availability, rather than dispersability, may be the limiting factor for the distribution of pteridophytes in Japan.     

Constraints upon the organisation and evolution of chromosomes in Allium

Summary In terms of chromosome morphology, karyotype organisation, taxonomy and genetic relationship as judged from chromosome pairing in the Fl hybrid, A. cepa and A.fistulosum are two closely related species. But large variation in nuclear DNA amounts has occurred during the evolution of the two species. A comparison of the molecular composition of DNA in the two species has confirmed that the excess DNA acquired during evolution was predominantly repetitive sequences (sequences which do not encode genetic information). However, its distribution within the chromosome complements was equal in all chromosomes irrespective of the differences in chromosome size. The even distribution of the excess DNA within complements suggests strong constraints underlying evolutionary changes in genome organisation. The nature of the constraints is discussed, and it is shown that such constraints can influence the direction of karyotype evolution during speciation.     

Evidence for chromosome number reduction and chromosomal homosequentiality in the 24-chromosome Korean frog Rana dybowskii and related species

The karyotype of the Korean frog Rana dybowskii with its pattern of C-band heterochromatin distribution was numerically analyzed. There are 2n = 24 chromosomes in the karyotype representing a reduction in number from the typical 2n = 26 chromosome karyotype of Rana. The karyotype shows other evidence of reorganization relative to 26-chromosome species. The chromosomes grade smoothly in size from largest to smallest without the two size classes that are characteristic for 26-chromosome species. In contrast to many 26-chromosome species, there are few centromeric C-bands but many interstitial ones. C-bands for each homologous chromosome pair are distinctive. A prominent secondary constriction is located on one of the smallest chromosomes, chromosome 11, in a position similar to that seen in most 26-chromosome species. The karyotype of R. dybowskii is compared to those of other species of Rana known to have 2n = 24 chromosomes; it is most similar to that of R. chensinensis, less so that of R. ornativentris and less still to that of R. arvalis in terms of the positions of centromeres and secondary constrictions. C-bands as well as secondary constrictions in the karyotypes of these frogs show evidence of chromosomal homosequentiality. The process and possible consequences of chromosome number reduction from an ancestral 26-chromosome karyotype is also evident in the karyotypes of these closely allied palearctic frogs. Pericentric inversions followed by fusion of two small elements apparently produced a new chromosome, chromosome 6, occurring originally among northeast Asian populations.     

Chromosome-specific desynapsis in the n = 2 race of Haplopappus gracilis (Compositae)

During cytological screening for pollen sterility in a wild population of Haplopappus gracilis (n = 2), several partially sterile plants were found that had good pachytene pairing but varying numbers of univalents. Some plants had chromosome A bivalents or A univalents, while in the same cells chromosome B had only bivalents. In other plants the reverse condition occurred; the B chromosome had B bivalents or B univalents and only A bivalents. This demonstrates a chromosome-specific effect for the desynapsis genes. Hybridization between the two homozygous mutant genotypes produced only normal bivalents; this indicates the two mutants are not alleles and each is recessive. An F2 generation showed independent assortment of the desynaptic mutations. The chromosome A bivalent is the larger of the two and normally has one or two chiasmata; the B bivalent normally has a single chiasma. Chiasmata distribution was tested in the desynaptic mutant A bivalents and showed an acceptable fit to a binomial distribution. This occurs also in heterozygous, asynaptic pairing control gene mutations. Analysis of the NOR bivalent in two hologenomic desynaptic mutations in tomato also showed a good fit to a binomial distribution of chiasmata. This indicates the same methods are applicable to diverse species.     

Additional chromosome numbers inPelargonium (Geraniaceae)

Mitotic chromosome counts were made from field collected and subsequently cultivated plants of 61Pelargonium species from 14 sections. The 33 new results are presented. 47 of the species have a basic number of x = 11, nine spp. of x = 9 and five spp. of x = 8. 17 spp. are polyploid. In two sections species with different basic numbers occur, which is of interest for the subgeneric classification. The size of the chromosomes varies between the investigated species. Most but not all species with x = 11 have short, those with x = 8, 9 large, and only exceptionally short chromosomes. Within sections chromosome size is not always uniform. The relationship between the different basic chromosome numbers is discussed.     

Unlocking Holocentric Chromosomes: New Perspectives from Comparative and Functional Genomics?

The presence of chromosomes with diffuse centromeres (holocentric chromosomes) has been reported in several taxa since more than fifty years, but a full understanding of their origin is still lacking. Comparative and functional genomics are nowadays furnishing new data to better understand holocentric chromosome evolution thus opening new perspectives to analyse karyotype rearrangements in species with holocentric chromosomes in particular evidencing unusual common features, such as the uniform GC content and gene distribution along chromosomes.     

Extraordinary conservation of entire chromosomes in insects over long evolutionary periods

Comparison of the genomes of different Drosophila species has shown that six different chromosomes, the so‐called ‘‘Muller elements,” constitute the building blocks for all Drosophila species. Here, we confirm previous results suggesting that this conservation of the Muller elements extends far beyond Drosophila, to at least tephritid fruit flies, thought to have diverged from drosophilids 60–70 mYr ago. Less than 10 percent of genes differ in chromosome location between the two insect groups. Within chromosomes, however, the order is highly scrambled, as expected from the comparison between Drosophila species. The data also support the notion that the sex chromosomes of tephritid flies originated from an ancestor of the dot chromosome 4 of Drosophila. Overall, therefore, no new chromosome has been created for perhaps a billion generations over the two evolutionary lines. This stability at the chromosome level, which appears to extend to all Diptera including mosquitoes, is in stark contrast to other groups such as mammals, birds, fish and plants, in which chromosome numbers and organization vary enormously among species that have diverged over much fewer generations.     

Multigenic and morphometric differentiation of ground squirrels (Spermophilus, Scuiridae, Rodentia) in Turkey, with a description of a new species

This study reports on the molecular phylogenetics of ground squirrels, genus Spermophilus, in Turkey using cytochrome b (1140bp), part of the D-loop and flanking tRNAs (572bp), X chromosome (867-1051bp) and Y chromosome (983-989bp) DNA sequences. Individuals also were characterized by karyotype and with geometric morphometric analyses of mandibles and skulls. Two hundred fourteen individuals from 91 localities were studied. All the data support the recognition of a new species in SW Anatolia: the Taurus ground squirrel Spermophilus taurensis sp. nov. The new species has a small distribution in the Taurus Mountains in an area that is a hotspot for biodiversity. Molecular clock analysis suggests that the new species diverged from the European ground squirrel, Spermophilus citellus, about 2.5 million years ago and that the ancestor of these two species diverged from the widespread Anatolian ground squirrel, Spermophilus xanthoprymnus, about 5 million years ago. Morphometric differentiation in skull and mandible shape among the three species is incomplete, but statistically significant. S. xanthoprymnus is subdivided into five cytochrome b phylogroups and we use these data to infer the location of glacial refugia where the species lived during the last glacial maximum. This study illustrates the potential of combined molecular and morphometric studies to uncover new Anatolian species and to reconstruct their phylogeographic history. The new species is important for squirrel taxonomy and for understanding Eurasian mammal evolution.     

Chromosome numbers in three species groups of freshwater flatworms increase with increasing latitude

Polyploidy in combination with parthenogenesis offers advantages for plasticity and the evolution of a broad ecological tolerance of species. Therefore, a positive correlation between the level of ploidy and increasing latitude as a surrogate for environmental harshness has been suggested. Such a positive correlation is well documented for plants, but examples for animals are still rare. Species of flatworms (Platyhelminthes) are widely distributed, show a remarkably wide range of chromosome numbers, and offer therefore good model systems to study the geographical distribution of chromosome numbers. We analyzed published data on counts of chromosome numbers and geographical information of three flatworm “species” (Phagocata vitta, Polycelis felina and Crenobia alpina) sampled across Europe (220 populations). We used the mean chromosome number across individuals of a population as a proxy for the level of ploidy within populations, and we tested for relationships of this variable with latitude, mode of reproduction (sexual, asexual or both) and environmental variables (annual mean temperature, mean diurnal temperature range, mean precipitation and net primary production). The mean chromosome numbers of all three species increased with latitude and decreased with mean annual temperature. For two species, chromosome number also decreased with mean precipitation and net primary production. Furthermore, high chromosome numbers within species were accompanied with a loss of sexual reproduction. The variation of chromosome numbers within individuals of two of the three species increased with latitude. Our results support the hypothesis that polyploid lineages are able to cope with harsh climatic conditions at high latitudes. Furthermore, we propose that asexual reproduction in populations with high levels of polyploidization stabilizes hybridization events. Chromosomal irregularities within individuals tend to become more frequent at the extreme environments of high latitudes, presumably because of mitotic errors and downsizing of the genome.     

Predicting the distribution of cryptic species: the case of the spur-thighed tortoise in Andalusia (southern Iberian Peninsula)

Some species are very difficult to observe in the wild, and some of these present an apparently incongruent distribution, as is the case of the spur-thighed tortoise Testudo graeca in the southern Iberian Peninsula. This species has a discontinuous distribution with two main reproductive areas: one in the contiguous provinces of Almeria and Murcia, and the other in Huelva province. Both populations are thought to maintain reproductive isolation. However, we present new records obtained from two areas (the provinces of Malaga and Cadiz) which are outside their previously known range. Malaga province and Cadiz province are located between the two traditional reproductive areas. The new records were based on 16 interviews with shepherds as well as information provided by three naturalists. The aim of this work was to analyze the spatial distribution of areas favourable to the spur-thighed tortoise in the southern Iberian Peninsula, using different models with the same group of variables but with a different number of records: known records, new records and a combination of them. We obtained a distribution model for the species in Andalusia consistent with all observations, which was related to climatic stability, climatic disturbances, and spatial situation. This model presented three main favourable areas: two are coincident with the two known nuclei, and the other is situated in the southern part of the region, in the contiguous provinces of Cadiz and Malaga. We conclude that it is important to consider all the observations in the distribution models because records outside the traditional reproductive areas can include other environmental characteristics appropriate for the species.     

Human chromosome 11 carries at least four genes controlling expression of cell-surface antigens

We have mapped two new genes to chromosome 11 which control the cell-surface expression of two distinct antigens defined by monoclonal antibodies. One of the antigens has a general tissue distribution and is associated with a molecular complex of two polypeptides of 80,000 dalton and 40,000 dalton molecular weight. The second antigen has a restricted tissue distribution and is carried on a polypeptide of 100,000 daltons. We have used a combination of genetic and biochemical techniques to demonstrate that these new markers are distinct from the antigens defined by the monoclonal antibodies F10.44.2 and W6/34 which are also encoded by genes on chromosome 11. It is concluded that human chromosome 11 carries at least four distinct genes controlling cell-surface antigen expression.     

The distribution of B chromosomes across species

In this review we look at the broad picture of how B chromosomes are distributed across a wide range of species. We review recent studies of the factors associated with the presence of Bs across species, and provide new analyses with updated data and additional variables. The major obstacle facing comparative studies of B chromosome distribution is variation among species in the intensity of cytogenetic study. Because Bs are, by definition, not present in all individuals of a species, they may often be overlooked in species that are rarely studied. We give examples of corrections for differences in study effort, and show that after a variety of such corrections, strong correlations remain. Several major biological factors are associated with the presence of B chromosomes. Among flowering plants, Bs are more likely to occur in outcrossing than in inbred species, and their presence is also positively correlated with genome size and negatively with chromosome number. They are no more frequent in polyploids than in diploids, nor in species with multiple ploidies. Among mammals, Bs are more likely to occur in species with karyotypes consisting of mostly acrocentric chromosomes. We find no evidence for an association with chromosome number or genome size in mammals, although the sample for genome size is small. The associations with breeding system and acrocentric chromosomes were both predicted in advance, but those with genome size and chromosome number were discovered empirically and we can offer only tentative explanations for the very strong associations we have uncovered. Our understanding of why B chromosomes are present in some species and absent in others is still in its infancy, and we suggest several potential avenues for future research.     

广义报春苣苔属 (苦苣苔科) 的染色体新计数及其分类学意义

报道了广义报春苣苔属14种3变种和7个未定名种的染色体数目,并对其近缘属——广义石山苣苔属的3个种也进行了细胞学研究。结合最近的分类处理和系统发育假设,对所得结果和以前发表的染色体数据进行了综合分析, 结果表明：广义报春苣苔属的染色体数目为2n=36,基数为x=18,表现出高度稳定性。染色体相对较小,以中间着丝粒和亚中间着丝粒染色体为主。尽管一些类群的染色体大小之间存在微小差异,但是染色体形态的均一性和染色体数目的一致性有力地支持分子系统学的研究结果。另外,相同的染色体数目及相似的染色体形态也表明广义报春苣苔属和广义石山苣苔属的亲缘关系较近,与分子系统学的结果一致。     

Comparative cytogenetic analysis of hexaploid Avena L. species

Using C-banding method and in situ hybridization with the 45S and 5S rRNA gene probes, six hexaploid species of the genus Avena L. with the ACD genome constitution were studied to reveal evolutionary karyotypic changes. Similarity in the C-banding patterns of chromosomal and in the patterns of distribution of the rRNA gene families suggests a common origin of all hexaploid species. Avena fatua is characterized by the broadest intraspecific variation of the karyotype; this species displays chromosomal variants typical of other hexaploid species of Avena. For instance, a translocation with the involvement of chromosome 5C marking A. occidentalis was discovered in many A. fatua accessions, whereas in other representatives of this species this chromosome is highly similar to the chromosome of A. sterilis. Only A. fatua and A. sativa show slight changes in the morphology and in the C-banding pattern of chromosome 2C. These results can be explained either by a hybrid origin of A. fatua or by the fact that this species is an intermediate evolutionary form of hexaploid oats. The 7C-17 translocation was identified in all studied accessions of wild and weedy species (A. sterilis, A. fatua, A. ludoviciana, and A. occidentalis) and in most A. sativa cultivars, but it was absent in A. byzantina and in two accessions of A. sativa. The origin and evolution of the Avena hexaploid species are discussed in context of the results.     

Divergent location of ribosomal genes in chromosomes of fish thorny-headed worms, <Emphasis Type="Italic">Pomphorhynchus laevis</Emphasis> and <Emphasis Type="Italic">Pomphorhynchus tereticollis</Emphasis> (Acanthocephala)

We studied distribution of ribosomal DNA (rDNA) sequences along with chromosomal location of the nucleolar organizer regions (NORs) in males of two fish parasites, Pomphorhynchus laevis and Pomphorhynchus tereticollis (Acanthocephala). Fluorescence in situ hybridization with 18S rDNA probe identified two clusters of rDNA in each species, but revealed a remarkable difference in their location on chromosomes. In P. laevis, the rDNA-FISH signals were found in long arms of the first chromosome pair and in short arms of the second pair. Whereas in P. tereticollis, rDNA clusters were located in long arms of both the first and second chromosome pairs. The divergent location of rDNA clusters in the chromosome No. 2 supports current classification of P. tereticollis, previously considered a synonym of P. laevis, as a separate species. A possible scenario of the second chromosome rearrangement during karyotype evolution of the two species involves two successive pericentric inversions. In both species, one or two prominent nucleoli were apparent within interphase nuclei stained with either silver nitrate or a fluorescent dye YOYO-1. However, a single large nucleolus was observed in early stages of mitosis and meiosis I regardless the number of rDNA clusters. Nevertheless, two bivalents with silver-stained NORs in diakinesis and two silver-stained sites in early prophase II nuclei indicated that all NORs are active. This means that each Pomphorhynchus NOR generates a nucleolus, but the resulting nucleoli have a strong tendency to associate in a large body.