Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium

2007 ◽  
Vol 58 (6) ◽  
pp. 470 ◽  
Author(s):  
P. Moolhuijzen ◽  
D. S. Dunn ◽  
M. Bellgard ◽  
M. Carter ◽  
J. Jia ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Physical Map ◽  
Genome Structure ◽  
Genetic Research ◽  
Structure And Function ◽  
Wheat Genome ◽  
D Genome ◽  
Genome Sequencing Consortium ◽  
And Function ◽  
Bac Contigs

Genome sequencing and the associated bioinformatics is now a widely accepted research tool for accelerating genetic research and the analysis of genome structure and function of wheat because it leverages similar work from other crops and plants. The International Wheat Genome Sequencing Consortium addresses the challenge of wheat genome structure and function and builds on the research efforts of Professor Bob McIntosh in the genetics of wheat. Currently, expressed sequence tags (ESTs; ~500 000 to date) are the largest sequence resource for wheat genome analyses. It is estimated that the gene coverage of the wheat EST collection is ~60%, close to that of Arabidopsis, indicating that ~40% of wheat genes are not represented in EST collections. The physical map of the D-genome donor species Aegilops tauschii is under construction (http://wheat.pw.usda.gov/PhysicalMapping). The technologies developed in this analysis of the D genome provide a good model for the approach to the entire wheat genome, namely compiling BAC contigs, assigning these BAC contigs to addresses in a high resolution genetic map, filling in gaps to obtain the entire physical length of a chromosome, and then large-scale sequencing.

scholarly journals Impact of DNA methylation on 3D genome structure

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Diana Buitrago ◽  
Mireia Labrador ◽  
Juan Pablo Arcon ◽  
Rafael Lema ◽  
Oscar Flores ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Chromatin Structure ◽  
Chromatin Condensation ◽  
Genome Structure ◽  
Dna Methyltransferases ◽  
Model System ◽  
Structure And Function ◽  
3D Genome ◽  
Cellular Machinery ◽  
And Function

AbstractDetermining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, budding yeast, that lacks DNA methylation machinery making it a perfect model system to study the intrinsic role of DNA methylation in chromatin structure and function. We expressed the murine DNA methyltransferases in Saccharomyces cerevisiae and analyzed the correlation between DNA methylation, nucleosome positioning, gene expression and 3D genome organization. Despite lacking the machinery for positioning and reading methylation marks, induced DNA methylation follows a conserved pattern with low methylation levels at the 5’ end of the gene increasing gradually toward the 3’ end, with concentration of methylated DNA in linkers and nucleosome free regions, and with actively expressed genes showing low and high levels of methylation at transcription start and terminating sites respectively, mimicking the patterns seen in mammals. We also see that DNA methylation increases chromatin condensation in peri-centromeric regions, decreases overall DNA flexibility, and favors the heterochromatin state. Taken together, these results demonstrate that methylation intrinsically modulates chromatin structure and function even in the absence of cellular machinery evolved to recognize and process the methylation signal.

scholarly journals Histone chaperone FACT and curaxins: effects on genome structure and function

2019 ◽  
Vol 2019 ◽  
Author(s):  
Han-Wen Chang ◽  
Ekaterina V. Nizovtseva ◽  
Sergey V. Razin ◽  
Tim Formosa ◽  
Katerina V. Gurova ◽  
...  
Keyword(s):  
Genome Structure ◽  
Histone Chaperone ◽  
Structure And Function ◽  
And Function

Microsporidian Genome Structure and Function

Microsporidia ◽  
2014 ◽  
pp. 221-229 ◽  
Author(s):  
Patrick J. Keeling ◽  
Naomi M. Fast ◽  
Nicolas Corradi
Keyword(s):  
Genome Structure ◽  
Structure And Function ◽  
And Function

Basic mechanisms and treatment planning/targets for attention-deficit/hyperactivity disorder

2020 ◽  
pp. 309-317
Author(s):  
Barbara Franke ◽  
Jan K. Buitelaar
Keyword(s):  
Treatment Options ◽  
Disease Onset ◽  
Genetic Research ◽  
Structure And Function ◽  
Reward Processing ◽  
Hyperactivity Disorder ◽  
Brain Structure And Function ◽  
Genetic Level ◽  
And Function ◽  
Different Levels

The mechanisms underlying ADHD are complex and can be defined at different levels. Cognitive deficits are often part of the disorder, including problems in executive functioning, reward processing, and timing deficits. Alterations have also been reported in brain structure and function in people with the disorder. ADHD is known to be a highly heritable, multifactorial disorder, in which genetic factors—often in combination with environmental factors—are risk factors for disease onset. Early research at the genetic level has implicated monoaminergic neurotransmission, following the serendipitous finding that methylphenidate, a dopamine and noradrenaline transport inhibitor, treats ADHD symptoms. The current models to explain brain malfunctioning in ADHD indeed centre around these monoamine systems. In addition to dopamine, noradrenaline, and (to a lesser extent) serotonin, also glutamate, histamine, and the nicotinic acetylcholinergic system seem to be involved in ADHD aetiology. In the coming years, genetic research is expected to uncover more of the mechanisms underlying ADHD, hopefully resulting in improved treatment options.

scholarly journals Simultaneous TE Analysis of 19 Heliconiine Butterflies Yields Novel Insights into Rapid TE-Based Genome Diversification and Multiple SINE Births and Deaths

2019 ◽  
Vol 11 (8) ◽  
pp. 2162-2177 ◽  
Author(s):  
David A Ray ◽  
Jenna R Grimshaw ◽  
Michaela K Halsey ◽  
Jennifer M Korstian ◽  
Austin B Osmanski ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Common Ancestor ◽  
Genome Structure ◽  
Detailed Examination ◽  
Structure And Function ◽  
Evolutionary Processes ◽  
Repetitive Nature ◽  
Daunting Task ◽  
And Function

Abstract Transposable elements (TEs) play major roles in the evolution of genome structure and function. However, because of their repetitive nature, they are difficult to annotate and discovering the specific roles they may play in a lineage can be a daunting task. Heliconiine butterflies are models for the study of multiple evolutionary processes including phenotype evolution and hybridization. We attempted to determine how TEs may play a role in the diversification of genomes within this clade by performing a detailed examination of TE content and accumulation in 19 species whose genomes were recently sequenced. We found that TE content has diverged substantially and rapidly in the time since several subclades shared a common ancestor with each lineage harboring a unique TE repertoire. Several novel SINE lineages have been established that are restricted to a subset of species. Furthermore, the previously described SINE, Metulj, appears to have gone extinct in two subclades while expanding to significant numbers in others. This diversity in TE content and activity has the potential to impact how heliconiine butterflies continue to evolve and diverge.

scholarly journals A sampling of methods to study chromosome and genome structure and function

2020 ◽  
Vol 28 (1) ◽  
pp. 1-5
Author(s):  
Beth A. Sullivan
Keyword(s):  
Genome Structure ◽  
Structure And Function ◽  
And Function

scholarly journals Chromosome organization in bacteria: mechanistic insights into genome structure and function

2019 ◽  
Vol 21 (4) ◽  
pp. 227-242 ◽  
Author(s):  
Remus T. Dame ◽  
Fatema-Zahra M. Rashid ◽  
David C. Grainger
Keyword(s):  
Genome Structure ◽  
Structure And Function ◽  
Chromosome Organization ◽  
And Function

scholarly journals De NovoSequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicumL.)

2016 ◽  
Vol 2016 ◽  
pp. 1-6 ◽  
Author(s):  
Yi Wang ◽  
Chao Wang ◽  
Xiaolu Wang ◽  
Fan Peng ◽  
Ruijiao Wang ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Wheat Genome ◽  
The Other ◽  
Crucial Step ◽  
Functional Types ◽  
Other Hand ◽  
Genome Sequencing Consortium ◽  
Stems And Leaves ◽  
Wheat Transcriptome

Construction as well as characterization of a polish wheat transcriptome is a crucial step to study useful traits of polish wheat. In this study, a transcriptome, including 76,014 unigenes, was assembled from dwarf polish wheat (DPW) roots, stems, and leaves using the software of Trinity. Among these unigenes, 61,748 (81.23%) unigenes were functionally annotated in public databases and classified into differentially functional types. Aligning this transcriptome against draft wheat genome released by the International Wheat Genome Sequencing Consortium (IWGSC), 57,331 (75.42%) unigenes, including 26,122 AB-specific and 2,622 D-specific unigenes, were mapped on A, B, and/or D genomes. Compared with the transcriptome ofT. turgidum, 56,343 unigenes were matched with 103,327 unigenes ofT. turgidum. Compared with the genomes of rice and barley, 14,404 and 7,007 unigenes were matched with 14,608 genes of barley and 7,708 genes of rice, respectively. On the other hand, 2,148, 1,611, and 2,707 unigenes were expressed specifically in roots, stems, and leaves, respectively. Finally, 5,531 SSR sequences were observed from 4,531 unigenes, and 518 primer pairs were designed.

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