scholarly journals Wheat Genomics: Present Status and Future Prospects

2008 ◽  
Vol 2008 ◽  
pp. 1-36 ◽  
Author(s):  
P. K. Gupta ◽  
R. R. Mir ◽  
A. Mohan ◽  
J. Kumar
Keyword(s):  
Repetitive Sequences ◽  
Genomic Research ◽  
Large Set ◽  
Economic Traits ◽  
Physical Maps ◽  
Gene Space ◽  
Genome Wide ◽  
Genomics Research ◽  
Number Of Genes ◽  
Molecular Maps

Wheat (Triticum aestivum L.), with a large genome (16000 Mb) and high proportion (∼80%) of repetitive sequences, has been a difficult crop for genomics research. However, the availability of extensive cytogenetics stocks has been an asset, which facilitated significant progress in wheat genomic research in recent years. For instance, fairly dense molecular maps (both genetic and physical maps) and a large set of ESTs allowed genome-wide identification of gene-rich and gene-poor regions as well as QTL including eQTL. The availability of markers associated with major economic traits also allowed development of major programs on marker-assisted selection (MAS) in some countries, and facilitated map-based cloning of a number of genes/QTL. Resources for functional genomics including TILLING and RNA interference (RNAi) along with some new approaches like epigenetics and association mapping are also being successfully used for wheat genomics research. BAC/BIBAC libraries for the subgenome D and some individual chromosomes have also been prepared to facilitate sequencing of gene space. In this brief review, we discuss all these advances in some detail, and also describe briefly the available resources, which can be used for future genomics research in this important crop.

Distinctive patterns of age-dependent hypomethylation in interspersed repetitive sequences

2010 ◽  
Vol 41 (2) ◽  
pp. 194-200 ◽  
Author(s):  
Pornrutsami Jintaridth ◽  
Apiwat Mutirangura
Keyword(s):  
Mononuclear Cells ◽  
Repetitive Sequences ◽  
Endogenous Retrovirus ◽  
Human Endogenous Retrovirus ◽  
Cellular Functions ◽  
Peripheral Blood Mononuclear ◽  
Global Methylation ◽  
Short Interspersed Elements ◽  
Genome Wide ◽  
Age Dependent

Interspersed repetitive sequences (IRSs) are a major contributor to genome size and may contribute to cellular functions. IRSs are subdivided according to size and functionally related structures into short interspersed elements, long interspersed elements (LINEs), DNA transposons, and LTR-retrotransposons. Many IRSs may produce RNA and regulate genes by a variety of mechanisms. The majority of DNA methylation occurs in IRSs and is believed to suppress IRS activities. Global hypomethylation, or the loss of genome-wide methylation, is a common epigenetic event not only in senescent cells but also in cancer cells. Loss of LINE-1 methylation has been characterized in many cancers. Here, we evaluated the methylation levels of peripheral blood mononuclear cells of LINE-1, Alu, and human endogenous retrovirus K (HERV-K) in 177 samples obtained from volunteers between 20 and 88 yr of age. Age was negatively associated with methylation levels of Alu (r = −0.452, P < 10−3) and HERV-K (r = −0.326, P < 10−3) but not LINE-1 (r = 0.145, P = 0.055). Loss of methylation of Alu occurred during ages 34–68 yr, and loss of methylation of HERV-K occurred during ages 40–63 yr and again during ages 64–83 yr. Interestingly, methylation of Alu and LINE-1 are directly associated, particularly at ages 49 yr and older (r = 0.49, P < 10−3). Therefore, only some types of IRSs lose methylation at certain ages. Moreover, Alu and HERV-K become hypomethylated differently. Finally, there may be several mechanisms of global methylation. However, not all of these mechanisms are age-dependent. This finding may lead to a better understanding of not only the biological causes and consequences of genome-wide hypomethylation but also the role of IRSs in the aging process.

scholarly journals The Report of Marine Life Genomic Research

2018 ◽  
Author(s):  
Guangyi Fan ◽  
Jianwei Chen ◽  
Tao Jin ◽  
Chengcheng Shi ◽  
Xiao Du ◽  
...  
Keyword(s):  
Recent Progress ◽  
Ethical Issues ◽  
Marine Invertebrates ◽  
Marine Species ◽  
White Paper ◽  
Genomic Research ◽  
Research Progress ◽  
Biological Research ◽  
Marine Microorganisms ◽  
Genomics Research

With the continuing development of sequencing technology, genomics has been applied in a variety of biological research areas. In particular, the application of genomics to marine species, which boast a high diversity, promises great scientific and industrial potential. Significant progress has been made in marine genomics especially over the past few years. Consequently, BGI, leveraging its prominent contributions in genomics research, established BGI-Qingdao, an institute specifically aimed at exploring marine genomics. In order to accelerate marine genomics research and related applications, BGI-Qingdao initiated the International Conference on Genomics of the Ocean (ICG-Ocean) to develop international collaborations and establish a focused and coherent global research plan. Last year, the first ICG-Ocean conference was held in Qingdao, China, during which 47 scientists in marine genomics from all over the world reported on their research progress to an audience of about 300 attendees. This year, we would like to build on that success, drafting a report on marine genomics to draw global attention to marine genomics. We summarized the recent progress, proposed future directions, and we would like to enable additional profound insights on marine genomics. Similar to the annual report on plant and fungal research by Kew Gardens, and the White Paper of ethical issues on experimental animals, we hope our first report on marine genomics can provide some useful insights for researchers, funding agencies as well as industry, and that future versions will expand upon the foundation established here in both breadth and depth of knowledge.This report summarizes the recent progress in marine genomics in six parts including: marine microorganisms, marine fungi, marine algae and plants, marine invertebrates, marine vertebrates and genomics-based applications.

scholarly journals Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases

2020 ◽  
Author(s):  
Elle M Weeks ◽  
Jacob C Ulirsch ◽  
Nathan Y Cheng ◽  
Brian L Trippe ◽  
Rebecca S Fine ◽  
...  
Keyword(s):  
Complex Traits ◽  
Association Studies ◽  
Gene Prioritization ◽  
Protein Interaction Data ◽  
Large Set ◽  
Genome Wide Association Studies ◽  
Protein Protein Interaction ◽  
Genome Wide ◽  
Causal Genes ◽  
Red Blood Cell Count

Genome-wide association studies (GWAS) are a valuable tool for understanding the biology of complex traits, but the associations found rarely point directly to causal genes. Here, we introduce a new method to identify the causal genes by integrating GWAS summary statistics with gene expression, biological pathway, and predicted protein-protein interaction data. We further propose an approach that effectively leverages both polygenic and locus-specific genetic signals by combining results across multiple gene prioritization methods, increasing confidence in prioritized genes. Using a large set of gold standard genes to evaluate our approach, we prioritize 8,402 unique gene-trait pairs with greater than 75% estimated precision across 113 complex traits and diseases, including known genes such as SORT1 for LDL cholesterol, SMIM1 for red blood cell count, and DRD2 for schizophrenia, as well as novel genes such as TTC39B for cholelithiasis. Our results demonstrate that a polygenic approach is a powerful tool for gene prioritization and, in combination with locus-specific signal, improves upon existing methods.

scholarly journals Restricted nucleation and piRNA-mediated establishment of heterochromatin during embryogenesis in Drosophila miranda

2021 ◽  
Author(s):  
Kevin H.-C. Wei ◽  
Carolus Chan ◽  
Doris Bachtrog
Keyword(s):  
Genome Stability ◽  
Repetitive Sequences ◽  
Developmental Time ◽  
Wide Distribution ◽  
Promoter Regions ◽  
Architectural Feature ◽  
Genome Wide ◽  
Nucleation Sites ◽  
Zygotic Transcription ◽  
Initial Nucleation

Heterochromatin is a key architectural feature of eukaryotic genomes, crucial for silencing of repetitive elements and maintaining genome stability. Heterochromatin shows stereotypical enrichment patterns around centromeres and repetitive sequences, but the molecular details of how heterochromatin is established during embryogenesis are poorly understood. Here, we map the genome-wide distribution of H3K9me3-dependent heterochromatin in individual embryos of D. miranda at precisely staged developmental time points. We find that canonical H3K9me3 enrichment patterns are established early on before cellularization, and mature into stable and broad heterochromatin domains through development. Intriguingly, initial nucleation sites of H3K9me3 enrichment appear as early as embryonic stage3 (nuclear cycle 9) over transposable elements (TE) and progressively broaden, consistent with spreading to neighboring nucleosomes. The earliest nucleation sites are limited to specific regions of a small number of TE families and often appear over promoter regions, while late nucleation develops broadly across most TEs. Early nucleating TEs are highly targeted by maternal piRNAs and show early zygotic transcription, consistent with a model of co-transcriptional silencing of TEs by small RNAs. Interestingly, truncated TE insertions lacking nucleation sites show significantly reduced enrichment across development, suggesting that the underlying sequences play an important role in recruiting histone methyltransferases for heterochromatin establishment.

scholarly journals Functional Comparison of the Tup11 and Tup12 Transcriptional Corepressors in Fission Yeast

2005 ◽  
Vol 25 (2) ◽  
pp. 716-727 ◽  
Author(s):  
Fredrik Fagerström-Billai ◽  
Anthony P. H. Wright
Keyword(s):  
Gene Expression ◽  
Gene Duplication ◽  
Fission Yeast ◽  
Budding Yeast ◽  
Functional Difference ◽  
Evolutionary Mechanism ◽  
Genome Wide ◽  
Number Of Genes ◽  
Transcriptional Corepressors ◽  
Genome Wide Gene Expression

ABSTRACT Gene duplication is considered an important evolutionary mechanism. Unlike many characterized species, the fission yeast Schizosaccharomyces pombe contains two paralogous genes, tup11 + and tup12 + , that encode transcriptional corepressors similar to the well-characterized budding yeast Tup1 protein. Previous reports have suggested that Tup11 and Tup12 proteins play redundant roles. Consistently, we show that the two Tup proteins can interact together when expressed at normal levels and that each can independently interact with the Ssn6 protein, as seen for Tup1 in budding yeast. However, tup11 − and tup12 − mutants have different phenotypes on media containing KCl and CaCl2. Consistent with the functional difference between tup11 − and tup12 − mutants, we identified a number of genes in genome-wide gene expression experiments that are differentially affected by mutations in the tup11 + and tup12 + genes. Many of these genes are differentially derepressed in tup11 − mutants and are over-represented in genes that have previously been shown to respond to a range of different stress conditions. Genes specifically derepressed in tup12 − mutants require the Ssn6 protein for their repression. As for Tup12, Ssn6 is also required for efficient adaptation to KCl- and CaCl2-mediated stress. We conclude that Tup11 and Tup12 are at least partly functionally diverged and suggest that the Tup12 and Ssn6 proteins have adopted a specific role in regulation of the stress response.

Emergence and populations genomics of the highly invasive chestnut blight pathogen

2020 ◽  
Author(s):  
◽  
Lea Stauber
Keyword(s):  
Mating Type ◽  
Fungal Genome ◽  
Chestnut Blight ◽  
Mixed Mating ◽  
Large Set ◽  
Pathogen Evolution ◽  
Invasive Pathogens ◽  
Invasive Pathogen ◽  
Genome Wide

Invasive pathogens are a threat to forest and agroecosystems, as well as animal and human health. Identifying genomic determinants of pathogen evolution, as well as investigations into the genetic structure of invasive pathogen populations provide fundamental insights to why species can emerge as invasive pathogens. In this PhD project I investigated the emergence and population genomics of the invasive chestnut blight fungus Cryphonectria parasitica, using comparative and population genomic approaches. C. parasitica recently emerged as an invasive bark pathogen on non-Asian Castanea species in North America and Europe. In the first chapter, I investigated genomic determinants of lifestyle transitions in the genus Cryphonectria, by genome comparisons of C. parasitica and its sister species. The study uncovered a striking loss of genes associated with carbohydrate metabolism in the invasive pathogen C. parasitica, which may have promoted its pathogenicity on Castanea species. The second chapter explores the emergence and diversification of a highly invasive chestnut blight lineage across south-eastern Europe. By analyzing the genome-wide diversity of a large set of C. parasitica isolates of predominantly European origin, the study showed that a highly successful clonal pathogen lineage can emerge from a recombinant bridgehead population within Europe. Interestingly, the emergence of this clonal lineage was accompanied by an evolutionary transition from mixed mating type populations to single mating type outbreak populations. Lastly, in the third chapter I investigated temporal changes in genetic diversity of established C. parasitica populations in southern Switzerland, as well as potential links between the presence of the deleterious hyperparasitic mycovirus Cryphonectria hypovirus 1 (CHV1) and fungal genome-wide diversity. The results indicate increased mating among related fungal individuals, resulting in high genetic similarity of genotypes and facilitated CHV1 transmission. There were no substantial changes in fungal population structure and after ˜30 years and no detectable impact of CHV1 presence on fungal genome-wide diversity. Although our results show stable CHV1 incidence in fungal populations over three decades, the short-term interaction dynamics are likely highly volatile. The overall findings of this PhD thesis highlight the relevance of genomic determinants facilitating pathogen emergence and invasions. C. parasitica is a useful model to study fundamental questions of pathogen evolution and invasive processes, as well as antagonistic pathogen-hyperparasite interactions.

Phenotypic Screen and Transcriptomics Approach Complement Each Other in Functional Genomics of Defensive Stink Gland Physiology

2021 ◽  
Author(s):  
Sabrina Lehmann ◽  
Bibi Atika ◽  
Daniela Grossmann ◽  
Christian Schmitt-Engel ◽  
Nadi Strohlein ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Large Scale ◽  
Reverse Genetics ◽  
Expression Profiles ◽  
Forward Genetics ◽  
Large Set ◽  
Knock Down ◽  
Genome Wide ◽  
Phenotypic Screen ◽  
A Genome

Abstract Background Functional genomics uses unbiased systematic genome-wide gene disruption or analyzes natural variations such as gene expression profiles of different tissues from multicellular organisms to link gene functions to particular phenotypes. Functional genomics approaches are of particular importance to identify large sets of genes that are specifically important for a particular biological process beyond known candidate genes, or when the process has not been studied with genetic methods before. Results Here, we present a large set of genes whose disruption interferes with the function of the odoriferous defensive stink glands of the red flour beetle Tribolium castaneum. This gene set is the result of a large-scale systematic phenotypic screen using a reverse genetics strategy based on RNA interference applied in a genome-wide forward genetics manner. In this first-pass screen, 130 genes were identified, of which 69 genes could be confirmed to cause knock-down gland phenotypes, which vary from necrotic tissue and irregular reservoir size to irregular color or separation of the secreted gland compounds. The knock-down of 13 genes caused specifically a strong reduction of para-benzoquinones, suggesting a specific function in the synthesis of these toxic compounds. Only 14 of the 69 confirmed gland genes are differentially overexpressed in stink gland tissue and thus could have been detected in a transcriptome-based analysis. Moreover, of the 29 previously transcriptomics-identified genes causing a gland phenotype, only one gene was recognized by this phenotypic screen despite the fact that 13 of them were covered by the screen. Conclusion Our results indicate the importance of combining diverse and independent methodologies to identify genes necessary for the function of a certain biological tissue, as the different approaches do not deliver redundant results but rather complement each other. The presented phenotypic screen together with a transcriptomics approach are now providing a set of close to hundred genes important for odoriferous defensive stink gland physiology in beetles.

What genomic research has told us about the obesity and its possible gene therapy targets.

2021 ◽  
Author(s):  
Moataz Dowaidar
Keyword(s):  
Genetic Risk ◽  
Genomic Research ◽  
Activity Measurement ◽  
Unhealthy Lifestyle ◽  
Sweetened Beverages ◽  
Therapy Targets ◽  
New Information ◽  
Genome Wide ◽  
A Genome ◽  
Primary Advantage

The discovery of a genome-wide correlation with obesity-related genes hasrevealed new information about the genetics of obesity. Given the lowproportion of obesity heritability explained by available SNPs, it's not shockingthat these SNPs aren't scientifically effective as methods for assessing whowould acquire obesity. The roles of the majority of loci, the majority of whichmap to non-coding sequences, will take thorough analysis to determine theresponsible gene at each locus, which may not be the closest gene. Thismechanistic information, as well as the resulting elucidation of thepathophysiology of obesity, will allow the creation of new therapies, whichcould be the primary advantage of these genetic discoveries.Fortunately, a lack of mechanistic information hasn't stopped researchers fromusing SNPs and genetic risk ratings to shed light on how obesity biologyinteracts with environmental and lifestyle influences. These findings suggestthat an unhealthy lifestyle may amplify the genetic risk of obesity, despite thefact that environmental studies of obesity genes may be distorted byinaccuracies in diet and physical activity measurement. More research isrequired to confirm this theory and to identify the specific dietary components(such as sugar-sweetened beverages) that interfere with genetic variants. Thisstudy could contribute to personalized obesity prevention and care measures inthe future (pending confirmation in clinical trials of genetic-risk-guidedinterventions). Obesity genetics has offered researchers the opportunity toexamine causal interactions between obesity and its various possiblecomplications. However, since the majority of the studies discussed above wereconducted on people of European ethnicity, more research is required inminority ethnic groups with a high risk of obesity to understand the role ofbiology, climate, and relationships among these factors in explaining theirincreased risk.

A porcine brain-wide RNA editing landscape

2020 ◽  
Author(s):  
Jinrong Huang ◽  
Lin Lin ◽  
Zhanying Dong ◽  
Ling Yang ◽  
Tianyu Zheng ◽  
...  
Keyword(s):  
Rna Editing ◽  
Repetitive Sequences ◽  
Brain Regions ◽  
Mammalian Brain ◽  
Protein Coding ◽  
Porcine Brain ◽  
Coding Regions ◽  
Pig Brain ◽  
Genome Wide ◽  
A Genome

Abstract Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is an essential post-transcriptional modification. Although hundreds of thousands of RNA editing sites have been reported in mammals, brain-wide analysis of the RNA editing in the mammalian brain remains rare. Here, a genome-wide RNA editing investigation is performed in 119 samples, representing 30 anatomically defined subregions in the pig brain. We identify a total of 682,037 A-to-I RNA editing sites of which 97% are not identified before. Within the pig brain, cerebellum and olfactory bulb are regions with most edited transcripts. The editing level of sites residing in protein-coding regions are similar across brain regions, whereas region-distinct editing is observed in repetitive sequences. Highly edited conserved recoding events in pig and human brain are found in neurotransmitter receptors, demonstrating the evolutionary importance of RNA editing in neurotransmission functions. The porcine brain-wide RNA landscape provides a rich resource to better understand the evolutionally importance of post-transcriptional RNA editing.

scholarly journals Alaska Native genomic research: perspectives from Alaska Native leaders, federal staff, and biomedical researchers

2020 ◽  
Vol 22 (12) ◽  
pp. 1935-1943
Author(s):  
Vanessa Y. Hiratsuka ◽  
◽  
Michael J. Hahn ◽  
R. Brian Woodbury ◽  
Sara Chandros Hull ◽  
...  
Keyword(s):  
Alaska Native ◽  
Genomic Research ◽  
Health Board ◽  
Socially Responsible ◽  
Health Organizations ◽  
Research Partnerships ◽  
Cultural Considerations ◽  
Research Perspectives ◽  
National Human ◽  
Genomics Research

AbstractMeaningful engagement of Alaska Native (AN) tribes and tribal health organizations is essential in the conduct of socially responsible and ethical research. As genomics becomes increasingly important to advancements in medicine, there is a risk that populations not meaningfully included in genomic research will not benefit from the outcomes of that research. AN people have historically been underrepresented in biomedical research; AN underrepresentation in genomics research is compounded by mistrust based on past abuses, concerns about privacy and data ownership, and cultural considerations specific to this type of research. Working together, the National Human Genome Research Institute and two Alaska Native health organizations, Southcentral Foundation and the Alaska Native Health Board, cosponsored a workshop in July 2018 to engage key stakeholders in discussion, strengthen relationships, and facilitate partnership and consideration of participation of AN people in community-driven biomedical and genomic research. AN priorities related to translation of genomics research to health and health care, return of genomic results, design of research studies, and data sharing were discussed. This report summarizes the perspectives that emerged from the dialogue and offers considerations for effective and socially responsible genomic research partnerships with AN communities.

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