Genome Size and the Role of Transposable Elements

2015 ◽  
pp. 81-106 ◽  
Author(s):  
Alan H. Schulman
Keyword(s):  
Transposable Elements ◽  
Genome Size

scholarly journals Recombination involving transposable elements: role of target molecule replication in Tn1 delta Ap-mediated replicon fusion.

1983 ◽  
Vol 80 (8) ◽  
pp. 2314-2317 ◽  
Author(s):  
C. J. Muster ◽  
J. A. Shapiro ◽  
L. A. MacHattie
Keyword(s):  
Transposable Elements ◽  
Target Molecule

Role of transposable elements in the propagation of minisatellites in the rice genome

2004 ◽  
Vol 271 (2) ◽  
pp. 220-227 ◽  
Author(s):  
T. Inukai
Keyword(s):  
Transposable Elements ◽  
Rice Genome

scholarly journals Variation and Evolution of Genome Size in Gymnosperms

2021 ◽  
Vol 70 (1) ◽  
pp. 156-169
Author(s):  
Deepak Ohri
Keyword(s):  
Transposable Elements ◽  
Genome Size ◽  
Narrow Range ◽  
Ltr Retrotransposons ◽  
General Survey ◽  
Efficient Mechanism ◽  
Repeat Sequences ◽  
Adaptive Value ◽  
Epigenetic Machinery ◽  
Large Genomes

Abstract Gymnosperms show a significantly higher mean (1C=18.16, 1Cx=16.80) and a narrow range (16.89-fold) of genome sizes as compared with angiosperms. Among the 12 families the largest ranges of 1C values is shown by Ephedraceae (4.73-fold) and Cupressaceae (4.45-fold) which are partly due to polyploidy as 1Cx values vary 2.41 and 1.37-fold respectively. In rest of the families which have only diploid taxa the range of 1C values is from 1.18-fold (Cycadaeae) to 4.36-fold (Podocarpaceae). The question is how gymnosperms acquired such big genome sizes despite the rarity of recent instances of polyploidy. A general survey of different families and genera shows that gymnosperms have experienced both increase and decrease in their genome size during evolution. Various genomic components which have accounted for these large genomes have been discussed. The major contributors are the transposable elements particularly LTR-retrotransposons comprising of Ty3gypsy, Ty1copia and gymny superfamilies which are most widespread. The genomes of gymnosperms have been acquiring diverse LTR-RTs in their long evolution in the absence of any efficient mechanism of their elimination. The epigenetic machinery which silences these large tracts of repeat sequences into the stretches of heterochromatin and the adaptive value of these silenced repeat sequences need further investigation.

scholarly journals The Genomic Ecosystem of Transposable Elements in Maize

2019 ◽  
Author(s):  
Michelle C. Stitzer ◽  
Sarah N. Anderson ◽  
Nathan M. Springer ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Flowering Plant ◽  
Genome Wide ◽  
Family Level ◽  
Genomic Environment ◽  
Single Category ◽  
The Impact

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.‘Lumping our beautiful collection of transposons into a single category is a crime’-Michael R. Freeling, Mar. 10, 2017

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 The role of transposable elements in functional evolution of amphioxus genome: the case of opsin gene family

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Chrysoula N. Pantzartzi ◽  
Jiri Pergner ◽  
Zbynek Kozmik
Keyword(s):  
Transposable Elements ◽  
Gene Family ◽  
Opsin Gene ◽  
Functional Evolution ◽  
Amphioxus Genome

scholarly journals The role of transposable elements activity in aging and their possible involvement in laminopathic diseases

2020 ◽  
Vol 57 ◽  
pp. 100995 ◽  
Author(s):  
Davide Andrenacci ◽  
Valeria Cavaliere ◽  
Giovanna Lattanzi
Keyword(s):  
Transposable Elements

scholarly journals “What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

Biology ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 25 ◽  
Author(s):  
Roberta Moschetti ◽  
Antonio Palazzo ◽  
Patrizio Lorusso ◽  
Luigi Viggiano ◽  
René Massimiliano Marsano
Keyword(s):  
Transposable Elements ◽  
Transcriptional Control ◽  
Environmental Changes ◽  
Model Organism ◽  
Model Organisms ◽  
Regulatory Sequences ◽  
Transcriptional Pattern ◽  
Constitutive Components ◽  
Host Genes

Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. Drosophila is undoubtedly among the most powerful model organisms used for the purpose of studying the role of transposons and their effects on the stability and evolution of genes and genomes. Besides their most intuitive role as insertional mutagens, TEs can modify the transcriptional pattern of host genes by juxtaposing new cis-regulatory sequences. A key element of TE biology is that they carry transcriptional control elements that fine-tune the transcription of their own genes, but that can also perturb the transcriptional activity of neighboring host genes. From this perspective, the transposition-mediated modulation of gene expression is an important issue for the short-term adaptation of physiological functions to the environmental changes, and for long-term evolutionary changes. Here, we review the current literature concerning the regulatory and structural elements operating in cis provided by TEs in Drosophila. Furthermore, we highlight that, besides their influence on both TEs and host genes expression, they can affect the chromatin structure and epigenetic status as well as both the chromosome’s structure and stability. It emerges that Drosophila is a good model organism to study the effect of TE-linked regulatory sequences, and it could help future studies on TE–host interactions in any complex eukaryotic genome.

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