Organization and Evolution of Subtelomeric Satellite Repeats in the Potato Genome

Subtelomeric domains immediately adjacent to telomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes. A common feature associated with subtelomeric regions in different eukaryotes is the presence of long arrays of tandemly repeated satellite sequences. However, studies on molecular organization and evolution of subtelomeric repeats are rare. We isolated two subtelomeric repeats, CL14 and CL34, from potato (Solanum tuberosum). The CL14 and CL34 repeats are organized as independent long arrays, up to 1-3 Mb, of 182 bp and 339 bp monomers, respectively. The CL14 and CL34 repeat arrays are directly connected with the telomeric repeats at some chromosomal ends. The CL14 repeat was detected at the subtelomeric regions among highly diverged Solanum species, including tomato (Solanum lycopersicum). In contrast, CL34 was only found in potato and its closely related species. Interestingly, the CL34 repeat array was always proximal to the telomeres when both CL14 and CL34 were found at the same chromosomal end. In addition, the CL34 repeat family showed more sequence variability among monomers compared with the CL14 repeat family. We conclude that the CL34 repeat family emerged recently from the subtelomeric regions of potato chromosomes and is rapidly evolving. These results provide further evidence that subtelomeric domains are among the most dynamic regions in eukaryotic genomes

Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

BACKGROUND: Silene latifolia is a dioecious [corrected] plant with well distinguished X and Y chromosomes that is used as a model to study sex determination and sex chromosome evolution in plants. However, efficient utilization of this species has been hampered by the lack of large-scale sequencing resources and detailed analysis of its genome composition, especially with respect to repetitive DNA, which makes up the majority of the genome. METHODOLOGY/PRINCIPAL FINDINGS: We performed low-pass 454 sequencing followed by similarity-based clustering of 454 reads in order to identify and characterize sequences of all major groups of S. latifolia repeats. Illumina sequencing data from male and female genomes were also generated and employed to quantify the genomic proportions of individual repeat families. The majority of identified repeats belonged to LTR-retrotransposons, constituting about 50% of genomic DNA, with Ty3/gypsy elements being more frequent than Ty1/copia. While there were differences between the male and female genome in the abundance of several repeat families, their overall repeat composition was highly similar. Specific localization patterns on sex chromosomes were found for several satellite repeats using in situ hybridization with probes based on k-mer frequency analysis of Illumina sequencing data. CONCLUSIONS/SIGNIFICANCE: This study provides comprehensive information about the sequence composition and abundance of repeats representing over 60% of the S. latifolia genome. The results revealed generally low divergence in repeat composition between the sex chromosomes, which is consistent with their relatively recent origin. In addition, the study generated various data resources that are available for future exploration of the S. latifolia genome

Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula

<p>Abstract</p> <p>Background</p> <p>Extraordinary size variation of higher plant nuclear genomes is in large part caused by differences in accumulation of repetitive DNA. This makes repetitive DNA of great interest for studying the molecular mechanisms shaping architecture and function of complex plant genomes. However, due to methodological constraints of conventional cloning and sequencing, a global description of repeat composition is available for only a very limited number of higher plants. In order to provide further data required for investigating evolutionary patterns of repeated DNA within and between species, we used a novel approach based on massive parallel sequencing which allowed a comprehensive repeat characterization in our model species, garden pea (<it>Pisum sativum</it>).</p> <p>Results</p> <p>Analysis of 33.3 Mb sequence data resulted in quantification and partial sequence reconstruction of major repeat families occurring in the pea genome with at least thousands of copies. Our results showed that the pea genome is dominated by LTR-retrotransposons, estimated at 140,000 copies/1C. Ty3/gypsy elements are less diverse and accumulated to higher copy numbers than Ty1/copia. This is in part due to a large population of Ogre-like retrotransposons which alone make up over 20% of the genome. In addition to numerous types of mobile elements, we have discovered a set of novel satellite repeats and two additional variants of telomeric sequences. Comparative genome analysis revealed that there are only a few repeat sequences conserved between pea and soybean genomes. On the other hand, all major families of pea mobile elements are well represented in <it>M. truncatula</it>.</p> <p>Conclusion</p> <p>We have demonstrated that even in a species with a relatively large genome like pea, where a single 454-sequencing run provided only 0.77% coverage, the generated sequences were sufficient to reconstruct and analyze major repeat families corresponding to a total of 35–48% of the genome. These data provide a starting point for further investigations of legume plant genomes based on their global comparative analysis and for the development of more sophisticated approaches for data mining.</p

Grand Celebration: 10th Anniversary of the Human Genome Project

In 1990, scientists began working together on one of the largest biological research projects ever proposed. The project proposed to sequence the three billion nucleotides in the human genome. The Human Genome Project took 13 years and was completed in April 2003, at a cost of approximately three billion dollars. It was a major scientific achievement that forever changed the understanding of our own nature. The sequencing of the human genome was in many ways a triumph for technology as much as it was for science. From the Human Genome Project, powerful technologies have been developed (e.g., microarrays and next generation sequencing) and new branches of science have emerged (e.g., functional genomics and pharmacogenomics), paving new ways for advancing genomic research and medical applications of genomics in the 21st century. The investigations have provided new tests and drug targets, as well as insights into the basis of human development and diagnosis/treatment of cancer and several mysterious humans diseases. This genomic revolution is prompting a new era in medicine, which brings both challenges and opportunities. Parallel to the promising advances over the last decade, the study of the human genome has also revealed how complicated human biology is, and how much remains to be understood. The legacy of the understanding of our genome has just begun. To celebrate the 10th anniversary of the essential completion of the Human Genome Project, in April 2013 Genes launched this Special Issue, which highlights the recent scientific breakthroughs in human genomics, with a collection of papers written by authors who are leading experts in the field

A genome-wide transcriptional activity survey of rice transposable element-related genes

BACKGROUND: Transposable element (TE)-related genes comprise a significant portion of the gene catalog of grasses, although their functions are insufficiently characterized. The recent availability of TE-related gene annotation from the complete genome sequence of rice (Oryza sativa) has created an opportunity to conduct a comprehensive evaluation of the transcriptional activities of these potentially mobile elements and their related genes. RESULTS: We conducted a genome-wide survey of the transcriptional activity of TE-related genes associated with 15 developmental stages and stress conditions. This dataset was obtained using a microarray encompassing 2,191 unique TE-related rice genes, which were represented by oligonucleotide probes that were free from cross-hybridization. We found that TE-related genes exhibit much lower transcriptional activities than do non-TE-related genes, although representative transcripts were detected from all superfamilies of both type I and II TE-related genes. The strongest transcriptional activities were detected in TE-related genes from among the MULE and CACTA superfamilies. Phylogenetic analyses suggest that domesticated TE-related genes tend to form clades with active transcription. In addition, chromatin-level regulations through histone and DNA modifications, as well as enrichment of certain cis elements in the promoters, appear to contribute to the transcriptional activation of representative TE-related genes. CONCLUSION: Our findings reveal clear, albeit low, general transcription of TE-related genes. In combination with phylogenetic analysis, transcriptional analysis has the potential to lead to the identification of domesticated TEs with adapted host functions

Assembly and repeat annotation of the nothobranchius furzeri genome

In der Alternsforschung an Vertebraten sind die relativ langen Lebensspannen der derzeitigen Modellorganismen ein Hindernis bei der Durchführung von Experimenten. Der Türkise Prachtgrundkärpfling Nothobranchius furzeri weist eine für Wirbeltiere sehr kurze Lebensspanne (4-12 Monate) auf, was ihn zu einem geeigneten Modellorganismus für die Alternsforschung macht. In der vorliegenden Arbeit wird der mehrstufige Prozess zur Erzeugung der Genomsequenz von N.furzeri beschrieben. Basierend auf umfangreichen Sequenzierungsadaten und zusätzlichen Kartenressourcen wurde eine qualitativ hochwertige Genomassemblierung mit einer Größe von 1,24 Gb (N50 57,4 Mb; 19 Chromosomen) erstellt. Weiterhin wurde die Zusammensetzung repetitiver Sequenzen im N. furzeri Genom untersucht. Neben etablierten Methoden zur Repeatanalyse wurde zudem eine neue Softwarelösung (RepARK) entwickelt und angewendet. Es wurden 35,5% der Genomassemblierung als Repeats eingestuft. Basierend auf dieser Repeatannotation zeigte sich, dass die Genomassemblierung zwar circa 90% der unikalen Sequenzen enthält aber rund 60% der Repeats fehlen. Eine Analyse von unassemblierten Sequenzen zeigt zudem einen genomischen Repeatanteil von 56-70%. Diesen fehlenden Sequenzanteil gilt es in Zukunft insbesondere mit Sequenziertechnologien der dritten Generation möglichst vollständig zu erfassen, um auf dieser Basis die Rolle von repetitiven Elementen in biologischen Prozessen wie dem Altern erforschen zu können.In aging research, the long lifespan of the current vertebrate model organisms challenges the feasibility of research efforts. The turquoise killifish Nothobranchius furzeri has the shortest lifespan for vertebrates known so far (4-12 months) making it to a valuable new model in aging research. In this thesis, the multi-step process of building genome reference sequence of N. furzeri is described. Based on a broad range of sequencing data and additional map resources, a high-quality genome assembly with a size of 1.24 Gb (N50 57.4 Mb, 19 chromosomes) was achieved. Furthermore, the composition of repetitive sequences in the N. furzeri genome was analyzed. In addition to established repeat detection methods a new software solution (RepARK) was developed and applied. In this analysis, 35.5% of the genome assembly was annotated as repetitive. Using this repeat annotation, it was estimated that the genome assembly contains 90% of the unique sequence while about 60% of the repeats are absent. An analysis in not-assembled data suggests a repeat content in the N. furzeri genome ranging from 56% to 70%. This missing fraction needs to be resolved by further third generation sequencing efforts to study the role of repeats in biological processes such as aging

Determining individual chromosome missegregation rates and the responses to aneuploidy in human cells

PhDGenomic instability and aneuploidy, which are ubiquitous hallmarks of cancer cells, encompass both structural and numerical chromosome aberrations. Strikingly, cancer cells often display recurrent patterns of aneuploidy which are thought to be contingent on selection pressures within the tumour microenvironment maintaining advantageous karyotypes. However, it is currently unknown if individual chromosomes are intrinsically vulnerable to missegregation, and therefore whether chromosome bias may also contribute to pathological aneuploidy patterns. Moreover, the earliest responses to chromosome missegregation in non-transformed cells, and how these are overcome in cancer, has remained elusive due to the difficult nature of isolating nascent aneuploid cells. Results. Individual chromosomes displayed recurrent patterns of biased missegregation in response to a variety of cellular stresses across cell lines. Likewise, a small subset of chromosomes accounted for a large fraction of segregation errors following one specific mechanism driving aneuploidy. This was supported by the discovery that chromosomes 1 and 2 are strikingly susceptible to the premature loss of sister chromatid cohesion during prolonged prometaphase arrest. Additionally, I have elucidated the arrangement of individual metaphase human chromosomes, highlighting missegregation vulnerabilities occurring at the metaphase plate periphery following nocodazole wash-out. Finally, I have developed a novel system for isolating nascent aneuploid cells, suggesting the earliest transcriptome responses to chromosome missegregation in non-transformed human cells involve ATM and BCL2-mediated apoptosis.Medical Research Counci

A study of the mechanisms of meiosis in wheat

Breeding programs have the objectives to develop more productive and more stable varieties. Hybridization and selection are frequently employed in plant breeding and the success of introgression of special traits such as disease resistance relies on genetic recombination between the host and alien chromosomes. During meiosis, homologous chromosomes recognized each other, align and pair which ensure their recombination and correct segregation at metaphase. This process controls aberrant chromosome number within the gametes, and ensures that genes are shuffled by recombination. 70% of flowering plants are polyploids including bread (hexaploid) and pasta wheat (tetraploid), and strict homologous pairing in species containing more than one genome is even more important. Wheat homologous chromosomes and their relative homoeologues are genetically close enough to pair during meiosis, however, the Ph1 locus ensures that only true homologues pair and recombine, stabilizing the wheat genome. Because the pairing is exclusive to homologues, alien chromosomes cannot recombine with wheat chromosome and are eliminated. Deletion lines for the Ph1 locus, allowing recombination of wheat and its relatives, are used for new wheat variety production.EThOS - Electronic Theses Online ServiceGBUnited Kingdo