共查询到20条相似文献,搜索用时 46 毫秒
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Background
Systematic genome comparisons are an important tool to reveal gene functions, pathogenic features, metabolic pathways and genome evolution in the era of post-genomics. Furthermore, such comparisons provide important clues for vaccines and drug development. Existing genome comparison software often lacks accurate information on orthologs, the function of similar genes identified and genome-wide reports and lists on specific functions. All these features and further analyses are provided here in the context of a modular software tool "inGeno" written in Java with Biojava subroutines. 相似文献2.
Apocalyptic views on the natural order, chimeras and genetic engineering should not detract from the fact that medical research, similar to the promotion of health, is a public good. Genomics crosses all species, thereby requiring a global approach that respects human rights and public health priorities. Public trust and public participation in research demand clear stewardship as well as transparent and accountable oversight. Characterizing fundamental genomic data as a public resource might counterbalance the current overemphasis on individual rights but this will not be simple. It is only through an attachment to justice and solidarity that the dignity and well-being of persons, both as humans and as citizens, can truly be fostered. 相似文献
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Ruth Müller Clare Hanson Mark Hanson Michael Penkler Georgia Samaras Luca Chiapperino John Dupré Martha Kenney Christopher Kuzawa Joanna Latimer Stephanie Lloyd Astrid Lunkes Molly Macdonald Maurizio Meloni Brigitte Nerlich Francesco Panese Martyn Pickersgill Sarah Richardson Joëlle Rüegg Sigrid Schmitz Aleksandra Stelmach Paula‐Irene Villa 《EMBO reports》2017,18(10):1677-1682
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Greely HT 《Nature reviews. Genetics》2001,2(3):222-227
Although the Human Genome Project has been successful, the Human Genome Diversity Project, proposed in 1991, has so far failed to thrive. One of the main values in studying the human genome, however, will come from examining its variations and their effects. To do that in a systematic way, an active Human Genome Diversity Project, or something very similar, will ultimately prove vital. Such an effort will confront difficult ethical and political issues; this article reviews those issues and tries to show how they might be overcome. 相似文献
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A report from the 14th Genome Sequencing and Analysis Conference, Boston, USA, 2-5 October 2002. 相似文献
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Nuclear–cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number
Matheus Fernandes Gyorfy Emma R. Miller Justin L. Conover Corrinne E. Grover Jonathan F. Wendel Daniel B. Sloan Joel Sharbrough 《The Plant journal : for cell and molecular biology》2021,108(1):219-230
The plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication (WGD) events in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follows WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat and Arabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated the organellar genome copy number in Arabidopsis synthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages. 相似文献
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Adam C English William J Salerno Oliver A Hampton Claudia Gonzaga-Jauregui Shruthi Ambreth Deborah I Ritter Christine R Beck Caleb F Davis Mahmoud Dahdouli Singer Ma Andrew Carroll Narayanan Veeraraghavan Jeremy Bruestle Becky Drees Alex Hastie Ernest T Lam Simon White Pamela Mishra Min Wang Yi Han Feng Zhang Pawel Stankiewicz David A Wheeler Jeffrey G Reid Donna M Muzny Jeffrey Rogers Aniko Sabo Kim C Worley James R Lupski Eric Boerwinkle Richard A Gibbs 《BMC genomics》2015,16(1)
Background
Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental and computational demands of SV analysis. Here, we characterize the SV content of a personal genome with Parliament, a publicly available consensus SV-calling infrastructure that merges multiple data types and SV detection methods.Results
We demonstrate Parliament’s efficacy via integrated analyses of data from whole-genome array comparative genomic hybridization, short-read next-generation sequencing, long-read (Pacific BioSciences RSII), long-insert (Illumina Nextera), and whole-genome architecture (BioNano Irys) data from the personal genome of a single subject (HS1011). From this genome, Parliament identified 31,007 genomic loci between 100 bp and 1 Mbp that are inconsistent with the hg19 reference assembly. Of these loci, 9,777 are supported as putative SVs by hybrid local assembly, long-read PacBio data, or multi-source heuristics. These SVs span 59 Mbp of the reference genome (1.8%) and include 3,801 events identified only with long-read data. The HS1011 data and complete Parliament infrastructure, including a BAM-to-SV workflow, are available on the cloud-based service DNAnexus.Conclusions
HS1011 SV analysis reveals the limits and advantages of multiple sequencing technologies, specifically the impact of long-read SV discovery. With the full Parliament infrastructure, the HS1011 data constitute a public resource for novel SV discovery, software calibration, and personal genome structural variation analysis.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1479-3) contains supplementary material, which is available to authorized users. 相似文献11.
《Current opinion in biotechnology》2013,24(1):39-47
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Weill JC Radman M 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》2004,359(1441):95-98
Our genome has evolved to perpetuate itself through the maintenance of the species via an uninterrupted chain of reproductive somas. Accordingly, evolution is not concerned with diseases occurring after the soma's reproductive stage. Following Richard Dawkins, we would like to reassert that we indeed live as disposable somas, slaves of our germline genome, but could soon start rebelling against such slavery. Cancer and its relation to the TP53 gene may offer a paradigmatic example. The observation that the latency period in cancer can be prolonged in mice by increasing the number of TP53 genes in their genome, suggests that sooner or later we will have to address the question of heritable disease avoidance via the manipulation of the human germline. 相似文献
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Tyler A. Elliott T. Ryan Gregory 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》2015,370(1678)
Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of ‘complete’ genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future. 相似文献
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Mannhaupt G Montrone C Haase D Mewes HW Aign V Hoheisel JD Fartmann B Nyakatura G Kempken F Maier J Schulte U 《Nucleic acids research》2003,31(7):1944-1954
The German Neurospora Genome Project has assembled sequences from ordered cosmid and BAC clones of linkage groups II and V of the genome of Neurospora crassa in 13 and 12 contigs, respectively. Including additional sequences located on other linkage groups a total of 12 Mb were subjected to a manual gene extraction and annotation process. The genome comprises a small number of repetitive elements, a low degree of segmental duplications and very few paralogous genes. The analysis of the 3218 identified open reading frames provides a first overview of the protein equipment of a filamentous fungus. Significantly, N.crassa possesses a large variety of metabolic enzymes including a substantial number of enzymes involved in the degradation of complex substrates as well as secondary metabolism. While several of these enzymes are specific for filamentous fungi many are shared exclusively with prokaryotes. 相似文献
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Alekshun MN 《Nature biotechnology》2001,19(12):1124-1125
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