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 Analysis of 19 Heliconiine Butterflies Shows Rapid TE-based Diversification and Multiple SINE Births and Deaths

2019 ◽  
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 ◽  
Phenotypic Diversification ◽  
And Function

AbstractTransposable 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. Finally, a burst of TE origination corresponds temporally to a burst of speciation in the clade, potentially providing support to hypotheses that TEs are drivers of genotypic and phenotypic diversification. This diversity in TE content and activity has the potential to impact how heliconiine butterflies continue to evolve and diverge.

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.

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 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

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 The Mobilome of Reptiles: Evolution, Structure, and Function

2019 ◽  
Vol 157 (1-2) ◽  
pp. 21-33 ◽  
Author(s):  
Stéphane Boissinot ◽  
Yann Bourgeois ◽  
Joseph D. Manthey ◽  
Robert P. Ruggiero
Keyword(s):  
Gene Flow ◽  
Transposable Elements ◽  
Genome Size ◽  
Local Adaptation ◽  
Size Structure ◽  
Structure And Function ◽  
Genomic Diversity ◽  
Genomic Features ◽  
And Function

Transposable elements (TE) constitute one of the most variable genomic features among vertebrates, impacting genome size, structure, and composition. Despite their important role in shaping genomic diversity, they have mostly been studied in mammals, which display one of the least diverse genomes in terms of TE diversity. Recent new resources in reptilian genomics have opened a broader perspective about TE evolution in amniotes. We discuss these recent results by showing that TE diversity is high in reptiles, particularly in squamates, with strong heterogeneity in the number of TE classes retained in each lineage, even at short evolutionary scales. More research is needed to uncover the exact mechanisms that regulate TE proliferation in reptiles and to what extent these selfish elements can play a role in local adaptation or in the emergence of barriers to gene flow.

Sign in / Sign up

Export Citation Format

Share Document