The devil is in the details: Transposable element analysis of the Tasmanian devil genome

Nilsson, Maria A.

doi:10.1080/2159256x.2015.1119926

Cited by 5 publications

(7 citation statements)

References 39 publications

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“…Despite the limited number of retrocompetent elements, retrotransposition of LINEs and/or SINEs persists in mouse, human, and most other mammal genomes examined to date. TE quiescence of LINEs and/or SINES has only been observed in the ground squirrel (Platt II and Ray 2012 ), Tasmanian devil (Nilsson 2016 ), Ateles spider monkeys (Boissinot et al 2004 ), sigmodontine rodents (Grahn et al 2005 ; Rinehart et al 2005 ), and pteropodid bats (Cantrell et al 2008 ) but, given the timing and phylogenetic distribution of these silencing events, it is plausible that quiescence has impacted in as many as 15% of all mammal species (Platt II and Ray 2012 ). Understanding the genomic mechanisms, population genetic parameters, and random factors that reduce or eliminate TE activity is one of the major questions in vertebrate genome evolution (Goodier 2016 ).…”

Section: Mammalian Te Content and Evolutionmentioning

confidence: 99%

Mammalian transposable elements and their impacts on genome evolution

2018

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Transposable elements (TEs) are genetic elements with the ability to mobilize and replicate themselves in a genome. Mammalian genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. As a result, TEs have had significant impacts on mammalian evolution. Here we summarize the current understanding of TE content in mammal genomes and find that, with a few exceptions, most fall within a predictable range of observations. First, one third to one half of the genome is derived from TEs. Second, most mammalian genomes are dominated by LINE and SINE retrotransposons, more limited LTR retrotransposons, and minimal DNA transposon accumulation. Third, most mammal genome contains at least one family of actively accumulating retrotransposon. Finally, horizontal transfer of TEs among lineages is rare. TE exaptation events are being recognized with increasing frequency. Despite these beneficial aspects of TE content and activity, the majority of TE insertions are neutral or deleterious. To limit the deleterious effects of TE proliferation, the genome has evolved several defense mechanisms that act at the epigenetic, transcriptional, and post-transcriptional levels. The interaction between TEs and these defense mechanisms has led to an evolutionary arms race where TEs are suppressed, evolve to escape suppression, then are suppressed again as the defense mechanisms undergo compensatory change. The result is complex and constantly evolving interactions between TEs and host genomes.

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Section: Mammalian Te Content and Evolutionmentioning

confidence: 99%

Mammalian transposable elements and their impacts on genome evolution

2018

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“…2011; Nilsson et al. 2012; Nilsson 2016). As with other therians, large fractions of TEs correspond to non-LTR elements, such as LINEs and SINEs, including a high fraction of RTEs that are widely distributed across all marsupial orders (Gentles et al.…”

Section: Te Patterns In the Major Vertebrate Lineagesmentioning

confidence: 99%

“…2013). SINE activity is thought to have ceased before the radiation of the Dasyuridae (marsupial mice, quolls, and Tasmanian devils) ∼30 Mya, followed by L1 extinction in the lineage of the Tasmanian devil (but see Nilsson, 2016, for further comments). The opossum however, harbors transcriptionally active L1 and SINEs (Gu et al.…”

Section: Te Patterns In the Major Vertebrate Lineagesmentioning

confidence: 99%

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

Sotero-Caio

Platt

Suh

et al. 2017

Genome Biology and Evolution

247

227

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Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4–60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.

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“…2016). The repetitive nature of TE sequences, in combination with short-read sequencing technologies, exacerbates the correct assembly of TEs, especially for TE families exhibiting high sequence identity, high copy number or complex genomic arrangements (Nilsson 2016).…”

Section: Resultsmentioning

confidence: 99%

“…In fungi, 0-30% of the genome consists of transposable elements, with LTR (Long Terminal Repeats)-retrotransposons usually representing the largest fraction (Castanera et al 2016). The repetitive nature of TE sequences, in combination with short-read sequencing technologies, exacerbates the correct assembly of TEs, especially for TE families exhibiting high sequence identity, high copy number or complex genomic arrangements (Nilsson 2016).…”

Section: Transposable Elementsmentioning

confidence: 99%

The draft genome of the lichen-forming fungusLasallia hispanica(Frey) Sancho & A. Crespo

et al. 2018

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Lasallia hispanica (Frey) Sancho & A. Crespo is one of three Lasallia species occurring in central-western Europe. It is an orophytic, photophilous Mediterranean endemic which is sympatric with the closely related, widely distributed, highly clonal sister taxon L. pustulata in the supra- and oro-Mediterranean belts. We sequenced the genome of L. hispanica from a multispore isolate. The total genome length is 41·2 Mb, including 8488 gene models. We present the annotation of a variety of genes that are involved in protein secretion, mating processes and secondary metabolism, and we report transposable elements. Additionally, we compared the genome of L. hispanica to the closely related, yet ecologically distant, L. pustulata and found high synteny in gene content and order. The newly assembled and annotated L. hispanica genome represents a useful resource for future investigations into niche differentiation, speciation and microevolution in L. hispanica and other members of the genus.

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The devil is in the details: Transposable element analysis of the Tasmanian devil genome

Cited by 5 publications

References 39 publications

Mammalian transposable elements and their impacts on genome evolution

Mammalian transposable elements and their impacts on genome evolution

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

The draft genome of the lichen-forming fungusLasallia hispanica(Frey) Sancho & A. Crespo

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