TEPEAK : A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations

Burke, Devin; Chuong, Edward; Taylor, William; Layer, Ryan

doi:10.1101/2023.10.13.562297

Cited by 2 publications

(2 citation statements)

References 72 publications

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“…In our work we follow the opposite direction to show how a pangenome can be used to obtain a new TE library whose elements will be close in most cases to the complete sequence of the TE, even before any manual curation. Recently a related method has been made available, which starts from short read whole genome shotgun data to identify polymorphic structural variants as candidates for TEs (Burke et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Identification of transposable element families from pangenome polymorphisms

Sierra,

Durbin

2024

Preprint

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Background: Transposable Elements (TEs) are fragments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have the ability to generate new copies of themselves in the genome. Most existing methods used to identify TEs in a newly sequenced genome are based on their repetitive character, together with detection based on homology and structural features. As new high quality assemblies become more common, including the availability of multiple independent assemblies from the same species, an alternative strategy for identification of TE families becomes possible in which we focus on the polymorphism at insertion sites caused by TE mobility. Results: We develop the idea of using the structural polymorphisms found in pangenomes to create a library of the TE families recently active in a species, or in a closely related group of species. We present a tool, pantera, that achieves this task, and illustrate its use both on species with well-curated libraries, and on new assemblies. Conclusions: Our results show that pantera is sensitive and accurate, tending to correctly identify complete elements with precise boundaries, and is particularly well suited to detect larger, low copy number TEs that are often undetected with existing de novo methods.

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Section: Introductionmentioning

confidence: 99%

Identification of transposable element families from pangenome polymorphisms

Sierra,

Durbin

2024

Preprint

View full text Add to dashboard Cite

show abstract

Section: Introductionmentioning

confidence: 99%

Identification of transposable element families from pangenome polymorphisms

Sierra,

Durbin

2024

Mobile DNA

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Background Transposable Elements (TEs) are segments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have the ability to generate new copies of themselves in the genome. Most existing methods used to identify TEs in a newly sequenced genome are based on their repetitive character, together with detection based on homology and structural features. As new high quality assemblies become more common, including the availability of multiple independent assemblies from the same species, an alternative strategy for identification of TE families becomes possible in which we focus on the polymorphism at insertion sites caused by TE mobility. Results We develop the idea of using the structural polymorphisms found in pangenomes to create a library of the TE families recently active in a species, or in a closely related group of species. We present a tool, pantera, that achieves this task, and illustrate its use both on species with well-curated libraries, and on new assemblies. Conclusions Our results show that pantera is sensitive and accurate, tending to correctly identify complete elements with precise boundaries, and is particularly well suited to detect larger, low copy number TEs that are often undetected with existing de novo methods.

show abstract

TEPEAK : A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations

Cited by 2 publications

References 72 publications

Identification of transposable element families from pangenome polymorphisms

Identification of transposable element families from pangenome polymorphisms

Identification of transposable element families from pangenome polymorphisms

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