Chloroplast genome organization of bromegrass,Bromus inermis Leyss

Summary A physical map of the Bromus inermis chloroplast genome was constructed using heterologous probes of barley and wheat chloroplast DNA (cpDNA) to locate restriction sites. The map was aligned from data obtained from filter hybridization experiments on single and double enzyme digests. Cleavage sites for the enzymes PstI, SalI, KpnI, XhoI and PvuII were mapped. The chloroplast genome of B. inermis is similar in physical organization to that of other grasses. The circular cpDNA molecule of B. inermis has the typical small (12.8 kbp) and large (81.3 kbp) single-copy regions separated by a pair of inverted repeat (21 kbp) regions. The cpDNA molecule of B. inermis is collinear in sequence to that of wheat, rye, barley and oats. No structural rearrangements or major deletions were observed, indicating that the cpDNA of Bromus is a useful tool in phylogenetic studies.     

Principles of prokaryotic genome organization]

The peculiarities of bacterial chromosome organization are discussed, based mainly on the data on Escherichia coli. Highly important for bacterial genome organization is its division into two approx. equal half-genomes undergoing periodically "exchanges" of some kind displayed as continuous inversions including the oriC region of replication initiation. It is believed that short oligonucleotides are comprised in either of half-genomes. The former are predominantly oriented as direct repeats, which ensures the possibility of formation of tandem duplications consisting of identical genes--under conditions when selection for enhancing functions of corresponding genes takes place. Multiple tandem duplications capable of excision of plasmatic gene copies seem to initiate horizontal gene transfer in bacteria. Tandem gene duplications are probably being formed in the process of bacterial genetic recombination as well, when, as a result of non-equal crossing over, gene alleles derived from different strains are united into a tandem.     

Ribosomal genes in the human genome: Identification of four fractions,their organization in the nucleolus and metaphase chromosomes

Completion of human genome reading stimulated intense studies in the field of functional genomics and characterization of individual genomes. Of considerable importance is the study of the complex of multicopy ribosomal genes (RGs), but its thorough analysis was not a task of the “Human Genome” program. In this short review we present our data on the copy number of rRNA genes in individual human genomes and on their heterogeneity in the functional respect. Fractions of active and potentially active RGs as well as fractions of inactive and silent RGs intensively methylated in the transcribed region are characterized. Their location in the nucleolus structures and in metaphase chromosomes is discussed.     

Rice genome organization: the centromere and genome interactions

Over the last decade, many varied resources have become available for genome studies in rice. These resources include over 4000 DNA markers, several bacterial artificial chromosome (BAC) libraries, P-1 derived artificial chromosome (PAC) libraries and yeast artificial chromosome (YAC) libraries (genomic DNA clones, filters and end-sequences), retrotransposon tagged lines, and many chemical and irradiated mutant lines. Based on these, high-density genetic maps, cereal comparative maps, YAC and BAC physical maps, and quantitative trait loci (QTL) maps have been constructed, and 93 % of the genome has also been sequenced. These data have revealed key features of the genetic and physical structure of the rice genome and of the evolution of cereal chromosomes. This Botanical Briefing examines aspects of how the rice genome is organized structurally, functionally and evolutionarily. Emphasis is placed on the rice centromere, which is composed of long arrays of centromere-specific repetitive sequences. Differences and similarities amongst various cereal centromeres are detailed. These indicate essential features of centromere function. Another view of various kinds of interactive relationships within and between genomes, which could play crucial roles in genome organization and evolution, is also introduced. Constructed genetic and physical maps indicate duplication of chromosomal segments and spatial association between specific chromosome regions. A genome-wide survey of interactive genetic loci has identified various reproductive barriers that may drive speciation of the rice genome. The significance of these findings in genome organization and evolution is discussed.     

Chloroplast genome of an extremely endangered conifer Thuja sutchuenensis Franch.: gene organization,comparative and phylogenetic analysis

Physiology and Molecular Biology of Plants - Thuja sutchuenensis is a critically endangered tertiary relict species of Cupressaceae from southwestern China. We sequenced the complete chloroplast...     

Clustered organization of reproductive genes in the C. elegans genome

Defining the forces that sculpt genome organization is fundamental for understanding the origin, persistence, and diversification of species. The genomic sequences of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae provide an excellent opportunity to explore the dynamics of chromosome evolution. Extensive chromosomal rearrangement has accompanied divergence from their common ancestor, an event occurring roughly 100 million years ago (Mya); yet, morphologically, these species are nearly indistinguishable and both reproduce primarily by self-fertilization. Here, we show that genes expressed during spermatogenesis (sperm genes) are nonrandomly distributed across the C. elegans genome into three large clusters located on two autosomes. In addition to sperm genes, these chromosomal regions are enriched for genes involved in the hermaphrodite sperm/oocyte switch and in the reception of sperm signals that control fertilization. Most loci are present in single copy, suggesting that cluster formation is largely due to gene aggregation and not to tandem duplication. Comparative mapping indicates that the C. briggsae genome differs dramatically from the C. elegans genome in clustering. Because clustered genes have a direct role in reproduction and thus fitness, their aggregated pattern might have been shaped by natural selection, perhaps as hermaphroditism evolved.     

The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome

Eukaryotic ribosomes are made of two components, four ribosomal RNAs, and approximately 80 ribosomal proteins (r-proteins). The exact number of r-proteins and r-protein genes in higher plants is not known. The strong conservation in eukaryotic r-protein primary sequence allowed us to use the well-characterized rat (Rattus norvegicus) r-protein set to identify orthologues on the five haploid chromosomes of Arabidopsis. By use of the numerous expressed sequence tag (EST) accessions and the complete genomic sequence of this species, we identified 249 genes (including some pseudogenes) corresponding to 80 (32 small subunit and 48 large subunit) cytoplasmic r-protein types. None of the r-protein genes are single copy and most are encoded by three or four expressed genes, indicative of the internal duplication of the Arabidopsis genome. The r-proteins are distributed throughout the genome. Inspection of genes in the vicinity of r-protein gene family members confirms extensive duplications of large chromosome fragments and sheds light on the evolutionary history of the Arabidopsis genome. Examination of large duplicated regions indicated that a significant fraction of the r-protein genes have been either lost from one of the duplicated fragments or inserted after the initial duplication event. Only 52 r-protein genes lack a matching EST accession, and 19 of these contain incomplete open reading frames, confirming that most genes are expressed. Assessment of cognate EST numbers suggests that r-protein gene family members are differentially expressed.     

Cerebellum and organization of behavior: A comparative-physiological aspect

The ontophylogenetic analysis of morphofunctional peculiarities of the cerebellum shows its extremely high adaptability to the requirements for the organization of the nervous activity of the organism corresponding to the level of its evolutionary development and ecological habitat conditions. The changes of the cerebellum in the course of its onto- and phylogenetic development appear to be more pronounced as compared with other cerebral regions. Depending on the level of the development, revealed are different aspects of the cerebellar integrative activity which contributed, if necessary, a quite new directions of the nervous activity, such as learning and cognition, which demonstrates astonishingly wide limits of the adaptability. This explains that the cerebellum in various vertebrates is considerably different by its shape, location of neurons in the cerebellar cortex, and the main peculiarities of afferent, internal, and efferent pathways. There is a reason to suggest that the future study of these aspects of the cerebellar activity will bring us to a clearer understanding of the cerebellar mechanisms of learning.     

Chloroplast DNA insertions into the nuclear genome of rice: the genes,sites and ages of insertion involved

Rice (Oryza sativa) is one of three predominant grain crops, and its nuclear and organelle genomes have been sequenced. Following genome analysis revealed many exchanges of DNA sequences between the nuclear and organelle genomes. In this study, a total of 45 chloroplast DNA insertions more than 2 kb in length were detected in rice nuclear genome. A homologous recombination mechanism is expected for those chloroplast insertions with high similarity between their flanking sequences. Only five chloroplast insertions with high sequence similarity between two flanking sequences from an insertion were found in the 45 insertions, suggesting that rice might follow the non-homologous end-joining (NHEJ) repair of double-stranded breaks mechanism, which is suggested to be common to all eukaryotes. Our studies indicate that the most chloroplast insertions occurred at a nuclear region characterized by a sharp change of repetitive sequence density. One potential explanation is that regions such as this might be susceptible target sites or “hotspots” of DNA damage. Our results also suggest that the insertion of retrotransposon elements or non-chloroplast DNA into chloroplast DNA insertions may contribute significantly to their fragmentation process. Moreover, based on chloroplast insertions in nuclear genomes of two subspecies (indica and japonica) of cultivated rice, our results strongly suggest that they diverged during 0.06–0.22 million years ago. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Co-evolution of base composition and codon usage in Xenopus laevis and human globin genes with long-range DNA organization of their genome

Eucaryotic DNA is punctuated by many A+T-rich segments that we named A+T-rich linkers. Two types of these A+T-rich linkers can be distinguished: (i) isolated A+T-rich linkers, and (ii) A+T-rich linkers crowded in clusters. We have analysed the distribution of A+T-rich linker across the alpha- and beta-globin gene domain in Xenopus laevis and human genomes using isodenaturation and electron microscopy. Comparison of our data with those previously obtained for the avian globin genes leads us to conclude that genes can be harboured indifferently in either domain. A correlation is established between the presence of A+T-rich linker inside introns and flanking regions and the A+T content of the coding sequence. For the coding sequence, a high A+T content is strongly correlated with high A+T content in the codon's third position and weakly in the first position.     

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes

Background

The polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, we report the first draft genome of Ch. tentans and characterize its gene expression machineries and genomic architecture of the BR genes.

Results

The genome of Ch. tentans is approximately 200 Mb in size, and has a low GC content (31%) and a low repeat fraction (15%) compared to other Dipteran species. Phylogenetic inference revealed that Ch. tentans is a sister clade to mosquitoes, with a split 150–250 million years ago. To characterize the Ch. tentans gene expression machineries, we identified potential orthologus sequences to more than 600 Drosophila melanogaster (D. melanogaster) proteins involved in the expression of protein-coding genes. We report novel data on the organization of the BR gene loci, including a novel putative BR gene, and we present a model for the organization of chromatin bundles in the BR2 puff based on genic and intergenic in situ hybridizations.

Conclusions

We show that the molecular machineries operating in gene expression are largely conserved between Ch. tentans and D. melanogaster, and we provide enhanced insight into the organization and expression of the BR genes. Our data strengthen the generality of the BR genes as a unique model system and provide essential background for in-depth studies of the biogenesis of messenger ribonucleoprotein complexes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-819) contains supplementary material, which is available to authorized users.     

Tri-nucleotide repeats and their association with genes in rice genome

Tri-nucleotide repeats (TNRs) are extremely abundant in rice genome, of which CCG/CGG repeats have an advantage over other repeats, with approximate half of all the TNRs in the genome. Our results show that rice genome has relatively abundant TNRs with high GC content, and containing only purines or pyrimidines under the same GC content. The AAT/ATT repeats that occur predominantly in intergenic and intronic regions have a considerably higher average length than that of other repeats. The highest frequency of TNRs occurs in 5'-UTR regions, followed by in coding and 5'-flanking regions. Purines-rich TNRs prefer to the coding regions, but pyrimidines-rich TNRs exhibit a stronger bias to upstream regions, suggesting that they might be considered as the regulatory elements in gene expression. As if TNRs located predominantly near the start of coding regions do not significantly influence on the protein function.     

Tri-nucleotide repeats and their association with genes in rice genome

Tri-nucleotide repeats (TNRs) are extremely abundant in rice genome, of which CCG/CGG repeats have an advantage over other repeats, with approximate half of all the TNRs in the genome. Our results show that rice genome has relatively abundant TNRs with high GC content, and containing only purines or pyrimidines under the same GC content. The AAT/ATT repeats that occur predominantly in intergenic and intronic regions have a considerably higher average length than that of other repeats. The highest frequency of TNRs occurs in 5′-UTR regions, followed by in coding and 5′-flanking regions. Purines-rich TNRs prefer to the coding regions, but pyrimidines-rich TNRs exhibit a stronger bias to upstream regions, suggesting that they might be considered as the regulatory elements in gene expression. As if TNRs located predominantly near the start of coding regions do not significantly influence on the protein function.