Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila

Regulation of DNA replication and copy number is necessary to promote genome stability and maintain cell and tissue function. DNA replication is regulated temporally in a process known as replication timing (RT). Rap1-interacting factor 1 (Rif1) is a key regulator of RT and has a critical function in copy number control in polyploid cells. Previously, we demonstrated that Rif1 functions with SUUR to inhibit replication fork progression and promote underreplication (UR) of specific genomic regions. How Rif1-dependent control of RT factors into its ability to promote UR is unknown. By applying a computational approach to measure RT in Drosophila polyploid cells, we show that SUUR and Rif1 have differential roles in controlling UR and RT. Our findings reveal that Rif1 acts to promote late replication, which is necessary for SUUR-dependent underreplication. Our work provides new insight into the process of UR and its links to RT.     

The Drosophila melanogaster genome sequencing and annotation projects: a status report.

The sequence and genome annotations of Drosophila melanogaster were initially published in late 1999 and early 2000. Since then, the Berkeley Drosophila Genome Project (BDGP) and FlyBase have improved the quality of the sequence and reviewed the annotations by hand, respectively, to produce an account of the fruit fly genome that is of the highest quality. This review discusses the main features of this process, both from the point of view of the biology revealed in the end result and in the development of software that has been central to this genome sequencing and annotation project.     

Chromosome topology and genome size of selected actinomycetes species

Information about the genome organization of actinomycetes species is restricted to a few genera: Corynebacterium, Mycobacterium, Rhodococcus, Saccharopolyspora and Streptomyces. Streptomyces species and Saccharopolyspora erythraea were shown to contain a single linear 8 Mb chromosome. In contrast, the Corynebacterium, Mycobacterium and Rhodococcus species studied were demonstrated to possess a smaller (3 Mb–6.5 Mb) single circular chromosome. To investigate whether linear chromosome topology and genome sizes above 7 Mb are unique features of Streptomyces and S. erythraea we have started to investigate the chromosome topology, the genome size and the status of accessory elements of additional actinomycetes species: Actinoplanes philippinensis, Amycolatopsis orientalis, Micromonospora chalcea, Nocardia asteroides, Rhodococcus opacus and Streptoverticillium abikoense. Our data which are based on PFGE experiments clearly suggest that large genome sizes and chromosome linearity are seen in mycelium forming actinomycetes genera. In addition we have identified large linear plasmids in Nocardia asteroides, Streptoverticillium abikoense and Rhodococcus opacus.     

Egg size,embryonic development time and ovoviviparity in Drosophila species

Lengths, widths and volumes of eggs from 11 species of Drosophila whose genomes have been fully sequenced exhibit significant variation that is not explained by their phylogenetic relationships. Furthermore, egg size differences are unrelated to embryonic development time in these species. In addition, two of the species, Drosophila sechellia and, to a lesser degree, D. yakuba, both ecological specialists, exhibit ovoviviparity, suggesting that female control over oviposition in these species differs from what is observed in D. melanogaster. The interspecific differences in these reproductive characters, coupled with the availability of whole genome sequences for each, provide an unprecedented opportunity to examine their evolution.     

The dynamic ups and downs of genome size evolution in Brassicaceae

Crucifers (Brassicaceae, Cruciferae) are a large family comprisingsome 338 genera and c. 3,700 species. The family includes importantcrops as well as several model species in various fields ofplant research. This paper reports new genome size (GS) datafor more than 100 cruciferous species in addition to previouslypublished C-values (the DNA amount in the unreplicated gameticnuclei) to give a data set comprising 185 Brassicaceae taxa,including all but 1 of the 25 tribes currently recognized. Evolutionof GS was analyzed within a phylogenetic framework based ongene trees built from five data sets (matK, chs, adh, trnLF,and ITS). Despite the 16.2-fold variation across the family,most Brassicaceae species are characterized by very small genomeswith a mean 1C-value of 0.63 pg. The ancestral genome size (ancGS)for Brassicaceae was reconstructed as ^anc1C = 0.50 pg. Approximately50% of crucifer taxa analyzed showed a decrease in GS comparedwith the ancGS. The remaining species showed an increase inGS although this was generally moderate, with significant increasesin C-value found only in the tribes Anchonieae and Physarieae.Using statistical approaches to analyze GS, evolutionary gainsor losses in GS were seen to have accumulated disproportionatelyfaster within longer branches. However, we also found that GShas not changed substantially through time and most likely evolvespassively (i.e., a tempo that cannot be distinguished betweenneutral evolution and weak forms of selection). The data revealan apparent paradox between the narrow range of small GSs overlong evolutionary time periods despite evidence of dynamic genomicprocesses that have the potential to lead to genome obesity(e.g., transposable element amplification and polyploidy). Toresolve this, it is suggested that mechanisms to suppress amplificationand to eliminate amplified DNA must be active in Brassicaceaealthough their control and mode of operation are still poorlyunderstood.     

Sympatric genome size variation and hybridization of four oak species as determined by flow cytometry genome size variation and hybridization

The Quercus species serve as a powerful model for studying introgression in relation to species boundaries and adaptive processes. Coexistence of distant relatives, or lack of coexistence of closely relative oak species, introgression may play a role. In the current study, four closely related oak species were found in Zijinshan, China. We generated a comprehensive genome size (GS) database for 120 individuals of four species using flow cytometry‐based approaches. We examined GS variability within and among the species and hybridization events among the four species. The mean GSs of Q. acutissima, Q. variabilis, Q. fabri, and Q. serrata var. brevipetiolata were estimated to be 1.87, 1.92, 1.97, and 1.97 pg, respectively. The intraspecific and interspecific variations of GS observed among the four oak species indicated adaptation to the environment. Hybridization occurred both within and between the sections. A hybrid offspring was produced from Q. fabri and Q. variabilis, which belonged to different sections. The GS evolutionary pattern for hybrid species was expansion. Hybridization between the sections may be affected by habitat disturbance. This study increases our understanding of the evolution of GS in Quercus and will help establish guidelines for the ecological protection of oak trees.     

Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms

MethodsNuclear genome sizes were measured from cultivated plant material for a comprehensive sampling of taxa, including nearly half of all species of Genlisea and representing all major lineages. Flow cytometric measurements were conducted in parallel in two laboratories in order to compare the consistency of different methods and controls. Chromosome counts were performed for the majority of taxa, comparing different staining techniques for the ultrasmall chromosomes.ConclusionsGenlisea is an ideal candidate model organism for the understanding of genome reduction as the genus includes species with both relatively large (∼1700 Mbp) and ultrasmall (∼61 Mbp) genomes. This comparative, phylogeny-based analysis of genome sizes and karyotypes in Genlisea provides essential data for selection of suitable species for comparative whole-genome analyses, as well as for further studies on both the molecular and cytogenetic basis of genome reduction in plants.     

The relationship between gene dosage,gene expression,and sex in Drosophila

In Drosophila, the ratio of the number of X chromosomes to sets of other chromosomes initiates a series of events which result in sexual differentiation. In addition, this ratio establishes dosage compensation, a mechanism which equalizes the products of X-linked genes in males and females. The present review discusses possible genetic entities responsible for the interpretation of chromosomal sex and subsequent sex-mediated regulation during development.     

Variation across amphibian species in the size of the nuclear genome supports a pluralistic, hierarchical approach to the C-value enigma

Amphibians have featured prominently in discussions of the C-value enigma, the still-unresolved puzzle regarding the evolution of genome size. Their wide range in nuclear DNA contents and diverse ecological and developmental lifestyles make them excellent subjects for addressing the key elements of the C-value enigma. However, in some cases the importance of work on amphibians appears to be overstated. This is especially true of claims that patterns of variation in salamanders support a particular theory of genome size evolution to the exclusion of others. This study provides a critical re-examination of some of these claims, as well as an investigation of the relationships between genome size, cell and nuclear size, and metabolism in amphibians. The results of these analyses, combined with an overview of previous amphibian genome size literature, strongly indicate the need for a pluralistic approach to the C-value enigma. In particular, it must be recognized that evolutionary forces operating and interacting at several levels of biological organization (of which the genome itself is one) are responsible for the observed patterns in amphibian genome size distributions.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 329–339.     

Nuclear DNA amounts in 112 species of tropical hardwoods -- new estimates

The 4C DNA values of 112 species, belonging to 37 families have a range from 0.83 pg (Bixa orellana) to 15.54 pg (Thryallis angustifolia), showing a 18.72-fold variation. The genome size varies from 0.21 pg (Bixa orellana) to 3.32 (Thespesia populnea), with a 15.8-fold difference. The Bombacaceae has the minimum range (1.08-fold) of variation, while the maximum (5.0-fold) is shown by the Fabaceae. The Boraginaceae, Lauraceae, Malpighiaceae, and Malvaceae generally have higher 4C DNA values of > 10 pg, while the Bixaceae, Caricaceae, Oxalidaceae, and Santalaceae have lower values of < 2.0 pg. These data add further to our knowledge on variation in DNA amount in tropical hardwoods.     

果蝇基因组与功能基因研究进展

黑腹果蝇Drosophila melanogaster是生物科学研究中重要的模式动物之一。2000年,黑腹果蝇全基因组测序完成,随后基因组序列质量不断完善,对其功能基因进行深入研究,为其他高等动物基因组和功能基因的研究提供了巨大帮助。本文综述了近年来基因组功能元件、比较基因组学等方面的最新研究成果,着重介绍了功能基因在Hh信号通路、细胞凋亡方面的研究进展,并对最新的功能基因研究技术进行了简要概述。     

The effect of genome size on detailed species traits within closely related species of the same habitat

In spite of the large number of studies on genome size, studies comparing genome size and growth‐related traits across a wider range of species from the same habitat, taking into account species phylogeny, are largely missing. I estimated the relationship between genome size and different seed and seedling traits in perennial herbs occurring in dry calcareous grasslands in northern Bohemia, Czech Republic. There was no relationship between genome size and plant traits in simple regression analyses, but several strong relationships emerged in analyses based on pairwise phylogenetically independent contrasts. There was a significant relationship between monoploid genome size and production of above‐ground biomass, seedling establishment success and seed weight and between holoploid genome size and seed dormancy. Because the results are based on phylogenetically independent contrasts over a range of species from the same type of habitat, they allow me to conclude that these patterns were not because of species group or habitat type, but really show a correlation with genome size. In contrast to previous studies, I found a higher number of relationships with monoploid than with holoploid genome size. This may be because the traits observed in this study are directly related to plant growth and thus to life‐cycle time, which is determined by monoploid genome size. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160 , 290–298.     

Transposable elements and the evolution of genome size in eukaryotes

It is generally accepted that the wide variation in genome size observed among eukaryotic species is more closely correlated with the amount of repetitive DNA than with the number of coding genes. Major types of repetitive DNA include transposable elements, satellite DNAs, simple sequences and tandem repeats, but reliable estimates of the relative contributions of these various types to total genome size have been hard to obtain. With the advent of genome sequencing, such information is starting to become available, but no firm conclusions can yet be made from the limited data currently available. Here, the ways in which transposable elements contribute both directly and indirectly to genome size variation are explored. Limited evidence is provided to support the existence of an approximately linear relationship between total transposable element DNA and genome size. Copy numbers per family are low and globally constrained in small genomes, but vary widely in large genomes. Thus, the partial release of transposable element copy number constraints appears to be a major characteristic of large genomes.     

Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies

While the evolutionary mechanisms driving eukaryote genome size evolution are still debated, repeated element content appears to be crucial. Here, we reconstructed the phylogeny and identified repeats in the genome of 26 Drosophila exhibiting a twofold variation in genome size. The content in transposable elements (TEs) is highly correlated to genome size evolution among these closely related species. We detected a strong phylogenetic signal on the evolution of both genome size and TE content, and a genome contraction in the Drosophila melanogaster subgroup.     

Satellite DNA and chromosomes in Neotropical fishes: methods,applications and perspectives

Constitutive heterochromatin represents a substantial portion of the eukaryote genome, and it is mainly composed of tandemly repeated DNA sequences, such as satellite DNAs, which are also enriched by other dispersed repeated elements, including transposons. Studies on the organization, structure, composition and in situ localization of satellite DNAs have led to consistent advances in the understanding of the genome evolution of species, with a particular focus on heterochromatic domains, the diversification of heteromorphic sex chromosomes and the origin and maintenance of B chromosomes. Satellite DNAs can be chromosome specific or species specific, or they can characterize different species from a genus, family or even representatives of a given order. In some cases, the presence of these repeated elements in members of a single clade has enabled inferences of a phylogenetic nature. Genomic DNA restriction, using specific enzymes, is the most frequently used method for isolating satellite DNAs. Recent methods such as C₀t–1 DNA and chromosome microdissection, however, have proven to be efficient alternatives for the study of this class of DNA. Neotropical ichthyofauna is extremely rich and diverse enabling multiple approaches with regard to the differentiation and evolution of the genome. Genome components of some species and genera have been isolated, mapped and correlated with possible functions and structures of the chromosomes. The 5SHindIII‐DNA satellite DNA, which is specific to Hoplias malabaricus of the Erythrinidae family, has an exclusively centromeric location. The As51 satellite DNA, which is closely correlated with the genome diversification of some species from the genus Astyanax, has also been used to infer relationships between species. In the Prochilodontidae family, two repetitive DNA sequences were mapped on the chromosomes, and the SATH 1 satellite DNA is associated with the origin of heterochromatic B chromosomes in Prochilodus lineatus. Among species of the genus Characidium and the Parodontidae family, amplifications of satellite DNAs have demonstrated that these sequences are related to the differentiation of heteromorphic sex chromosomes. The possible elimination of satellite DNA units could explain the genome compaction that occurs among some species of Neotropical Tetraodontiformes. These topics are discussed in the present review, showing the importance of satellite DNA analysis in the differentiation and karyotype evolution of Actinopterygii.