Asexual reproduction drives the reduction of transposable element load

Bast, Jens; Jaroň, Kamil S.; Schuseil, Donovan; Roze, Denis; Schwander, Tanja

doi:10.1101/501361

Cited by 4 publications

(3 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Although the major classes of TEs are found across taxa, their relative abundances differ [ 34 ] and there is no clear consensus as to the factors that explain the diversity of TEs within a genome [ 35 – 38 ]. One approach to understand the diversity of TEs is to consider the genome as a community and apply principles of community ecology to understand their distribution and abundance [ 39 ].…”

Section: Introductionmentioning

confidence: 99%

The genomic ecosystem of transposable elements in maize

et al. 2021

View full text Add to dashboard Cite

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. 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 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 attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. 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.

show abstract

Section: Introductionmentioning

confidence: 99%

The genomic ecosystem of transposable elements in maize

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Although the major classes of TEs are found across taxa, their relative abundances differ (Elliott and Gregory, 2015) and there is no clear consensus as to the factors that explain the diversity of TEs within a genome (Ågren and Wright, 2011;Ågren et al, 2015;Sotero-Caio et al, 2017;Bast et al, 2018). One approach to understand the diversity of TEs is to consider the genome as a community and apply principles of community ecology to understand their distribution and abundance (Brookfield, 2005).…”

Section: Introductionmentioning

confidence: 99%

The Genomic Ecosystem of Transposable Elements in Maize

Stitzer¹,

Anderson

Springer

et al. 2019

Preprint

View full text Add to dashboard Cite

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. transposable elements | ecology | maize Correspondence: mcstitzer@ucdavis.edu 'Lumping our beautiful collection of transposons into a single category is a crime' -Michael R. Freeling,

show abstract

“…Asexuality is potentially linked to lower repetitive element burden (45), but monogonont rotifers are cyclical parthenogens. Thus, one might argue that it is even more surprising that the genomes of our studied species contain such high proportions of repetitive DNA.…”

Section: Repetitive Element Expansion and Activitymentioning

confidence: 99%

Small, but surprisingly repetitive genomes: Transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

Blommaert

Riß

Hecox-Lea

et al. 2019

Preprint

View full text Add to dashboard Cite

Background: The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly examined variation among larger taxonomic units (e.g., orders, or genera), while comparisons among closely related species are rare. Rotifers of the Brachionus plicatilis species complex exhibit a seven-fold variation in genome size and thus represent a unique opportunity to study such changes on a relatively short evolutionary timescale. Here, we sequenced and analysed the genomes of four species of this complex with nuclear DNA contents spanning 110- 422 Mbp. To establish the likely mechanisms of genome size change, we analysed both sequencing read libraries and assemblies for signatures of polyploidy and repetitive element content. We also compared these genomes to that of B. calyciflorus, the closest relative with a sequenced genome (293 Mbp nuclear DNA content). Results summary: Despite the very large differences in genome size, we saw no evidence of ploidy level changes across the B. plicatilis complex. However, repetitive element content explained a large portion of genome size variation (at least 54%). The species with the largest genome, B. asplanchnoidis, has a strikingly high 44% repetitive element content, while the smaller B. plicatilis genomes contain between 14% and 25% repetitive elements. According to our analyses, the B. calyciflorus genome contains 39% repetitive elements, which is substantially higher than previously reported (21%), and suggests that high repetitive element load could be widespread in monogonont rotifers. Conclusions: Even though the genome sizes of these species are at the low end of the Metazoan spectrum, their genomes contain substantial amounts of repetitive elements. Polyploidy does not appear to play a role in genome size variations in these species, and these variations can be mostly explained by changes in repetitive element content. This contradicts the naïve expectation that small genomes are streamlined, or less complex, and that large variations in nuclear DNA content between closely related species are due to polyploidy.

show abstract

Asexual reproduction drives the reduction of transposable element load

Cited by 4 publications

References 31 publications

The genomic ecosystem of transposable elements in maize

The genomic ecosystem of transposable elements in maize

The Genomic Ecosystem of Transposable Elements in Maize

Small, but surprisingly repetitive genomes: Transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

Contact Info

Product

Resources

About