A Unified Framework to Analyze Transposable Element Insertion Polymorphisms using Graph Genomes

Groza, Cristian; Chen, Xun; Wheeler, Travis J.; Bourque, Guillaume; Goubert, Clément

doi:10.1101/2023.09.11.557209

Cited by 5 publications

(2 citation statements)

References 104 publications

(168 reference statements)

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“…The pangenomic graph approach emerges as a computationally efficient method for comparing multiple whole genome assemblies when characterizing TE insertions at sites with complex variations (Ebler et al 2020;Groza et al 2023) . Notably, our findings reveal a striking 74.65% of structural variant regions attributable to TEs.…”

Section: Discussionmentioning

confidence: 99%

A pangenomic perspective of the Lake Malawi cichlid radiation reveals extensive structural variation driven by transposable elements

Quah,

Almeida,

Blumer

et al. 2024

Preprint

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The East African Rift Lakes, namely Lake Malawi, Victoria, and Tanganyika, host a remarkable diversity of cichlid fishes, representing one of nature's most striking vertebrate radiations. Despite rich phenotypic diversity, single nucleotide polymorphism (SNP)-based sequencing studies have revealed little sequence divergence between cichlids, with 0.1 to 0.25% pairwise divergence within Lake Malawi. These studies were based on aligning short reads to a single linear reference genome, which ignores the contribution of larger scale structural variants (SVs). To complement existing SNP-based studies, we adopted a pangenomic approach by constructing a multiassembly graph of haplochromine cichlids in Lake Malawi. We produced six new long read genome assemblies, alongside two publicly available ones, to span most of the major eco-morphological clades in the lake. This approach not only identifies longer SVs, but also visually represents complex and nested variation. Strikingly, the SV landscape is dominated by large insertions, many exclusive to individual assemblies. From a pangenomic perspective, we observed an exceptional amount of extra sequence, totaling up to 33.1% additional bases with respect to a single cichlid genome. Approximately 4.73 to 9.86% of the cichlid assemblies were estimated to be interspecies structural variation, suggesting substantial genomic diversity underappreciated in previous SNP-based studies. While coding regions remain highly conserved, our analysis uncovers a significant contribution of SVs from transposable element (TE) insertions, especially DNA, LINE, and LTR transposons. These findings underscore the intricate interplay of evolutionary forces shaping cichlid genome diversity, including both small nucleotide mutations and large TE-derived sequence alterations.

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Section: Discussionmentioning

confidence: 99%

A pangenomic perspective of the Lake Malawi cichlid radiation reveals extensive structural variation driven by transposable elements

Quah,

Almeida,

Blumer

et al. 2024

Preprint

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“…GraffiTE 61 uses several assembled genomes from the same species. It aligns each assembled genome against the reference but without aligning the others pairwise.…”

Section: Discussionmentioning

confidence: 99%

TheBrachypodium distachyonpangenome highlights Transposable Element dynamics in the species

Saidi,

Blaison,

del Pilar Rodríguez-Ordóñez

et al. 2024

Preprint

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The role of transposable elements (TEs) in host adaptation can be explored with a pangenomic approach. Individuals of the same species undergo independent TE insertions, causing genetic variability upon which natural selection acts. This can lead to improved adaptation of individuals to their environment. The advent of third-generation sequencing has enabled use of multiple whole-genomede novoassemblies for a given species, avoiding bias introduced by a single reference genome. We developed a new pipeline, panREPET, for such data. It compares TE copies between each pair of individuals then identifies copies shared by a group of individuals. This gives the exact sequence and genomic context of each TE copy. We describe here TE insertions shared among 54Brachypodium distachyon genomes. We were able to date two major TE bursts corresponding to major climate events: 22 kya during the Last Glacial Maximum and 10 kya during the Holocene.

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Regulation and function of transposable elements in cancer genomes

Lee,

Ahmad,

2024

Cell. Mol. Life Sci.

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Over half of human genomic DNA is composed of repetitive sequences generated throughout evolution by prolific mobile genetic parasites called transposable elements (TEs). Long disregarded as “junk” or “selfish” DNA, TEs are increasingly recognized as formative elements in genome evolution, wired intimately into the structure and function of the human genome. Advances in sequencing technologies and computational methods have ushered in an era of unprecedented insight into how TE activity impacts human biology in health and disease. Here we discuss the current views on how TEs have shaped the regulatory landscape of the human genome, how TE activity is implicated in human cancers, and how recent findings motivate novel strategies to leverage TE activity for improved cancer therapy. Given the crucial role of methodological advances in TE biology, we pair our conceptual discussions with an in-depth review of the inherent technical challenges in studying repeats, specifically related to structural variation, expression analyses, and chromatin regulation. Lastly, we provide a catalog of existing and emerging assays and bioinformatic software that altogether are enabling the most sophisticated and comprehensive investigations yet into the regulation and function of interspersed repeats in cancer genomes.

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A Unified Framework to Analyze Transposable Element Insertion Polymorphisms using Graph Genomes

Cited by 5 publications

References 104 publications

A pangenomic perspective of the Lake Malawi cichlid radiation reveals extensive structural variation driven by transposable elements

A pangenomic perspective of the Lake Malawi cichlid radiation reveals extensive structural variation driven by transposable elements

TheBrachypodium distachyonpangenome highlights Transposable Element dynamics in the species

Regulation and function of transposable elements in cancer genomes

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