Transposons, Genome Size, and Evolutionary Insights in Animals

Canapa, Adriana; Barucca, Marco; Biscotti, Maria Assunta; Forconi, Marikò; Olmo, Ettore

doi:10.1159/000444429

Cited by 127 publications

(113 citation statements)

References 263 publications

Supporting

Mentioning

104

Contrasting

Order By: Relevance

“…When many TEs of similar sequence identity are spread throughout the genome, they may induce ectopic recombination resulting in insertions, deletions, and chromosomal rearrangements such as inversions [Canapa et al, 2015]. Thus, not only does transposition provide a source of structural diversity via TE insertions, but the TE insertions themselves may help create additional heritable structural variation affecting evolutionary processes across populations [Piacentini et al, 2014].…”

Section: The Impact Of Transposable Elements On the Genome Of Their Hostmentioning

confidence: 99%

“…TEs can increase genome size through copy number increase via transposition, TE-induced ectopic recombination resulting in changes in genome size, and by TE-mediated satellite expansions [Canapa et al, 2015;Klein and O'Neill, 2018]. While genomes may increase in size with TE activity, recombination-driven deletions counteract this effect, in some cases maintaining genome size even in the face of TE activity .…”

Section: The Impact Of Transposable Elements On the Genome Of Their Hostmentioning

confidence: 99%

“…TE content varies across the genomic landscape, especially in cases where species have microchromosomes such as in squamates and birds; microchromosomes are typically enriched in gene content and contain relatively fewer TEs [Ellegren, 2010]. Similarly, across the tree of life, cladespecific factors lead to the lack of a clear association between genome size and genomic TE content, while a strong association can be found within individual clades [Pagel and Johnstone, 1992;Canapa et al, 2015]. Based on published genomes, the reptile clade has a positive relationship between genome size and overall genomic TE content, including additional clade-specific patterns ( Fig.…”

Section: The Impact Of Transposable Elements On the Genome Of Their Hostmentioning

confidence: 99%

See 2 more Smart Citations

The Mobilome of Reptiles: Evolution, Structure, and Function

Boissinot¹,

Bourgeois²,

Manthey

et al. 2019

Cytogenet Genome Res

View full text Add to dashboard Cite

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.

show abstract

Section: The Impact Of Transposable Elements On the Genome Of Their Hostmentioning

confidence: 99%

Section: The Impact Of Transposable Elements On the Genome Of Their Hostmentioning

confidence: 99%

Section: The Impact Of Transposable Elements On the Genome Of Their Hostmentioning

confidence: 99%

See 1 more Smart Citation

The Mobilome of Reptiles: Evolution, Structure, and Function

Boissinot¹,

Bourgeois²,

Manthey

et al. 2019

Cytogenet Genome Res

View full text Add to dashboard Cite

show abstract

“…genome size evolution | DNA loss | transposable elements | amniotes | flight T he nature and relative importance of the molecular mechanisms and evolutionary forces underlying genome size variation has been the subject of intense research and debate (1)(2)(3)(4)(5)(6)(7). Variation in genome sizes may not always occur at a level where natural selection is strong enough to prevent genetic drift to determine their fate (neutral or effectively neutral variation) (3).…”

mentioning

confidence: 99%

Dynamics of genome size evolution in birds and mammals

Kapusta

Suh

Feschotte

2017

Proc. Natl. Acad. Sci. U.S.A.

337

306

View full text Add to dashboard Cite

Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified "accordion" model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.genome size evolution | DNA loss | transposable elements | amniotes | flight T he nature and relative importance of the molecular mechanisms and evolutionary forces underlying genome size variation has been the subject of intense research and debate (1-7). Variation in genome sizes may not always occur at a level where natural selection is strong enough to prevent genetic drift to determine their fate (neutral or effectively neutral variation) (3). Additionally, the fixation probability of slightly deleterious deletions or insertions would be higher in species with smaller effective population sizes, where natural selection acts less efficiently (3,8). On the other hand, a number of correlative associations between genome size and phenotypic traits, such as cell size (9, 10) and metabolic rate associated with powered flight (11, 12), suggest that natural selection and adaptive processes also shape genome size evolution. Teasing apart the relative importance of these two forces (drift and selection) requires a better understanding of the mode and processes by which DNA is gained and lost over long evolutionary periods in different taxa. Thus, establishing an integrated view of the contribution of gain and loss of DNA to genome size variation (or lack thereof) remains an important goal in genome biology (e.g., refs. 1, 2, 13, and 14).Most studies of genome size evolution have focused on taxa with extensive variation in genome sizes, such as flowering plants (15)(16)(17)(18)(19)(20), conifers (21), insects (22-...

show abstract

“…In regards to eukaroytes, some patterns in genome size have been discussed (Lynch and Conery 2003;Daubin and Moran 2004;Lynch 2004). Additionally, a handful of studies have analyzed genome size in connection to other parameters such as indels (Pettersson et al 2009), transposon content (Kidwell 2002;Elliott and Gregory 2015a;Canapa et al 2016), average intron length (Deutsch and Long 1999;Zhu et al 2009) or total intron length (Elliott and Gregory 2015b). Despite these advances, none of these studies have estimated the amount of the genome that is genic (exonic plus intronic, including noncoding) based on independent examination of single genomes and without averaging over a whole kingdom.…”

Section: Introductionmentioning

confidence: 99%

Similar ratios of introns to intergenic sequence across animal genomes

Francis

Wörheide

2016

Preprint

View full text Add to dashboard Cite

One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here, we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of nonmodel organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought.

show abstract

Transposons, Genome Size, and Evolutionary Insights in Animals

Cited by 127 publications

References 263 publications

The Mobilome of Reptiles: Evolution, Structure, and Function

The Mobilome of Reptiles: Evolution, Structure, and Function

Dynamics of genome size evolution in birds and mammals

Similar ratios of introns to intergenic sequence across animal genomes

Contact Info

Product

Resources

About