scholarly journals Transposable elements contribute to dynamic genome content in maize

2019 ◽  
Author(s):  
Sarah N Anderson ◽  
Michelle C Stitzer ◽  
Alex B. Brohammer ◽  
Peng Zhou ◽  
Jaclyn M Noshay ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genomic Variation ◽  
Gene Content ◽  
Maize Genome ◽  
Large Scope ◽  
Shared Ancestry ◽  
Dynamic Genome ◽  
Genomic Studies ◽  
Genome Assemblies

AbstractTransposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genomic organization. The majority of maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17, and PH207). Among these genomes we identified 1.6 Gb of variable TE sequence representing a combination of recent TE movement and deletion of previously existing TEs. Although recent TE movement only accounted for a portion of the TE variability, we identified 4,737 TEs unique to one genome with defined insertion sites in all other genomes. Variable TEs are found for all superfamilies and are distributed across the genome, including in regions of recent shared ancestry among individuals. There are 2,380 genes annotated in the B73 genome located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in gene content among these genotypes. The large scope of TE variation present in this limited sample of temperate maize genomes highlights the major contribution of TEs in driving variation in genome organization and gene content.Significance StatementThe majority of the maize genome is comprised of transposable elements (TEs) that have the potential to create genomic variation within species. We developed a method to identify shared and non-shared TEs using whole genome assemblies of four maize inbred lines. Variable TEs are found throughout the maize genome and in comparisons of any two genomes we find ~20% of the genome is due to non-shared TEs. Several thousand maize genes are found within TEs that are variable across lines, highlighting the contribution of TEs to gene content variation. This study creates a comprehensive resource for genomic studies of TE variability among four maize genomes, which will enable studies on the consequences of variable TEs on genome function.

scholarly journals Dynamic patterns of transcript abundance of transposable element families in maize

2019 ◽  
Author(s):  
Sarah N Anderson ◽  
Michelle C Stitzer ◽  
Peng Zhou ◽  
Jeffrey Ross-Ibarra ◽  
Cory D Hirsch ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Dna Sequences ◽  
Germ Line ◽  
Transcript Abundance ◽  
Maize Genome ◽  
Rna Seq ◽  
Specific Expression ◽  
Poor Predictor ◽  
Repetitive Nature ◽  
Genomic Studies

AbstractTransposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in >800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes.

scholarly journals Eight soybean reference genome resources from varying latitudes and agronomic traits

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Jeffrey Shih-Chieh Chu ◽  
Bo Peng ◽  
Kuanqiang Tang ◽  
Xingxing Yi ◽  
Huangkai Zhou ◽  
...  
Keyword(s):  
De Novo ◽  
Agronomic Traits ◽  
Genomic Variation ◽  
Functional Studies ◽  
Technical Assessment ◽  
Genome Assemblies ◽  
Agronomical Traits ◽  
Multiple Reference ◽  
Reference Genomes

AbstractComparative analysis of multiple reference genomes representing diverse genetic backgrounds is critical for understanding the role of key alleles important in domestication and genetic breeding of important crops such as soybean. To enrich the genetic resources for soybean, we describe the generation, technical assessment, and preliminary genomic variation analysis of eight de novo reference-grade soybean genome assemblies from wild and cultivated accessions. These resources represent soybeans cultured at different latitudes and exhibiting different agronomical traits. Of these eight soybeans, five are from new accessions that have not been sequenced before. We demonstrate the usage of these genomes to identify small and large genomic variations affecting known genes as well as screening for genic PAV regions for identifying candidates for further functional studies.

A Problem Based Learning Exercise on Food Security: Understanding the Role of Genomic Variation and Plant Breeding

2018 ◽  
Author(s):  
Jolie WAX ◽  
Zhu Zhuo ◽  
Anna Bower ◽  
Jessica Cooper ◽  
Susan Gachara ◽  
...  
Keyword(s):  
Food Security ◽  
Plant Breeding ◽  
Problem Based Learning ◽  
Genomic Variation

scholarly journals Molecular Genetics in Epstein–Barr Virus-Associated Malignancies

Life ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 593
Author(s):  
Srikanth Umakanthan ◽  
Maryann M Bukelo
Keyword(s):  
Epstein Barr Virus ◽  
Diagnostic Tools ◽  
Main Role ◽  
Genetic Changes ◽  
Barr Virus ◽  
Cancer Pathogenesis ◽  
Genomic Studies ◽  
Epstein Barr ◽  
Oncogenic Form

Global genomic studies have detected the role of genomic alterations in the pathogenesis of Epstein–Barr virus (EBV)-associated tumors. EBV oncoproteins cause a vital shift of EBV from an infectious virus to an oncogenic form during the latent and lytic phase within the lymphoid B cells and epithelial cells. This epigenetic alteration modulates the virus and host genomes and inactivates and disrupts numerous tumor suppressors and signaling pathways. Genomic profiling has played the main role in identifying EBV cancer pathogenesis and its related targeted therapies. This article reviews the role of genetic changes in EBV-associated lymphomas and carcinomas. This includes the prolific molecular genesis, key diagnostic tools, and target-specific drugs that have been in recent clinical use.

scholarly journals Regression Modeling and Meta-Analysis of Diagnostic Accuracy of SNP-Based Pathogenicity Detection Tools for UGT1A1 Gene Mutation

2013 ◽  
Vol 2013 ◽  
pp. 1-7
Author(s):  
Fakher Rahim ◽  
Hamid Galehdari ◽  
Javad Mohammadi-asl ◽  
Najmaldin Saki
Keyword(s):  
Meta Analysis ◽  
Genomic Variation ◽  
Missense Mutations ◽  
Suggested Model ◽  
Pathogenicity Prediction ◽  
Mutation Score ◽  
Functional Scores ◽  
Comprehensive Search ◽  
Overall Performance

Aims. This review summarized all available evidence on the accuracy of SNP-based pathogenicity detection tools and introduced regression model based on functional scores, mutation score, and genomic variation degree. Materials and Methods. A comprehensive search was performed to find all mutations related to Crigler-Najjar syndrome. The pathogenicity prediction was done using SNP-based pathogenicity detection tools including SIFT, PHD-SNP, PolyPhen2, fathmm, Provean, and Mutpred. Overall, 59 different SNPs related to missense mutations in the UGT1A1 gene, were reviewed. Results. Comparing the diagnostic OR, our model showed high detection potential (diagnostic OR: 16.71, 95% CI: 3.38–82.69). The highest MCC and ACC belonged to our suggested model (46.8% and 73.3%), followed by SIFT (34.19% and 62.71%). The AUC analysis showed a significance overall performance of our suggested model compared to the selected SNP-based pathogenicity detection tool (P=0.046). Conclusion. Our suggested model is comparable to the well-established SNP-based pathogenicity detection tools that can appropriately reflect the role of a disease-associated SNP in both local and global structures. Although the accuracy of our suggested model is not relatively high, the functional impact of the pathogenic mutations is highlighted at the protein level, which improves the understanding of the molecular basis of mutation pathogenesis.

scholarly journals Self-Regulation of Genomic Studies and Prospects of Personified Medicine

Lex Russica ◽  
2020 ◽  
pp. 54-61
Author(s):  
K. V. Mashkova ◽  
M. V. Varlen ◽  
A. Yu. Shirokov
Keyword(s):  
Self Regulation ◽  
Genetic Research ◽  
Personal Data ◽  
Professional Associations ◽  
Legal Framework ◽  
State Regulation ◽  
Personal Genomic ◽  
Demographic Situation ◽  
Genomic Studies

A secular trend of the development of medicine in the 20th century was on the ways of strengthening the foundations of public health, formation of systems of affordable medical care. Human genome deciphering opens wide prospects for using the obtained data in medicine. In recent years commercial medical organizations have been developing genetic research and personal genomic testing services. The paper is devoted to the analysis of the importance of legal self-regulation in the field of genomic counseling in the Russian Federation. The authors investigate the prospects of the introduction of personalized medicine and limitations that arise today in one of the areas of the approach under consideration, namely: forecasting predisposition to diseases of mixed nature, which is related to the peculiarities of development of medical and demographic situation in the world. The question is raised about the need for broad population studies to verify the risk values for diseases with low genetic determinacy. The authors conclude that it is impossible to predict what medicine of the future will be, but the results of genome decryption and increasing availability of personal data represent a unique social phenomenon that should be developed within the legal framework. In the coming years, the debate on the role of legal mechanisms in the self-regulation of genetic research and genetic services will become increasingly important. At the international level, this discussion will be focused on the fundamental issue of respect for individual rights in the interpretation of the data received. As genetic advice evolves, the issue of responsibility for the information provided and the availability of national regulatory mechanisms within the framework of state regulation or self-regulated professional associations will become a key concern.

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