Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data

Chu, Chong; Zhao, Boxun; Park, Peter J.; Lee, Eunjung Alice

doi:10.1002/cphg.102

Cited by 11 publications

(7 citation statements)

References 73 publications

(86 reference statements)

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“…The analysis of segmental duplications, which has seen considerable progress in recent years [38][39][40] also falls outside the scope of this review, though one should be aware of their existence as they can interfere with the discovery and analysis of TE families. We also do not address the genotyping of TE insertions compared to a reference genome (see reviews [41,42]) and more recently published tools [43][44][45].…”

Section: Introductionmentioning

confidence: 99%

Methodologies for the De novo Discovery of Transposable Element Families

Storer

Hubley

Rosen

et al. 2022

Genes

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The discovery and characterization of transposable element (TE) families are crucial tasks in the process of genome annotation. Careful curation of TE libraries for each organism is necessary as each has been exposed to a unique and often complex set of TE families. De Novo methods have been developed; however, a fully automated and accurate approach to the development of complete libraries remains elusive. In this review, we cover established methods and recent developments in De Novo TE analysis. We also present various methodologies used to assess these tools and discuss opportunities for further advancement of the field.

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Section: Introductionmentioning

confidence: 99%

Methodologies for the De novo Discovery of Transposable Element Families

Storer

Hubley

Rosen

et al. 2022

Genes

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“…With the recent advancement of genome sequencing technology, both shortreads and long-reads can be used to detect TE insertions (Zhou et al, 2020;Zook et al, 2020). Computer programs specialized for the detection of mobile element insertions (MEIs) from whole-genome sequences have been developed (Chu et al, 2020), and were used to detect MEIs in many species such as human (Sudmant et al, 2015), grape (Zhou et al, 2019), rice (Kou et al, 2020), and tomato (Alonge et al, 2020;Dominguez et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing

et al. 2021

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Genomic structural variants (SVs) are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout (Oncorhynchus mykiss), an important aquaculture species of cold freshwater. The objectives of this study were 1) to identify and validate high-confidence SVs in rainbow trout using whole-genome re-sequencing; and 2) to examine the contribution of transposable elements (TEs) to SVs in rainbow trout. A total of 96 rainbow trout, including 11 homozygous lines and 85 outbred fish from three breeding populations, were whole-genome sequenced with an average genome coverage of 17.2×. Putative SVs were identified using the program Smoove which integrates LUMPY and other associated tools into one package. After rigorous filtering, 13,863 high-confidence SVs were identified. Pacific Biosciences long-reads of Arlee, one of the homozygous lines used for SV detection, validated 98% (3,948 of 4,030) of the high-confidence SVs identified in the Arlee homozygous line. Based on principal component analysis, the 85 outbred fish clustered into three groups consistent with their populations of origin, further indicating that the high-confidence SVs identified in this study are robust. The repetitive DNA content of the high-confidence SV sequences was 86.5%, which is much higher than the 57.1% repetitive DNA content of the reference genome, and is also higher than the repetitive DNA content of Atlantic salmon SVs reported previously. TEs thus contribute substantially to SVs in rainbow trout as TEs make up the majority of repetitive sequences. Hundreds of the high-confidence SVs were annotated as exon-loss or gene-fusion variants, and may have phenotypic effects. The high-confidence SVs reported in this study provide a foundation for further rainbow trout SV studies.

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“…We have recently applied these technologies to demonstrate that there are at least 2-fold more polymorphic L1Hs sequences in human populations than previously thought 29 . Several existing tools and pipelines have the ability to resolve reference and non-reference MEIs in the human genomes; however, most require a whole-genome pipeline for haplotype assembly, local assembly, or cross-platform support [40][41][42][43] . This often necessitates whole genome long-read sequencing, which is currently cost-prohibitive at scale and precludes an in-depth exploration into the impact of MEIs on human biology and disease.…”

mentioning

confidence: 99%

Cas9 targeted enrichment of mobile elements using nanopore sequencing

McDonald

Zhou

Castro

et al. 2021

Preprint

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Mobile element insertions (MEIs) are highly repetitive genomic sequences that contribute to inter- and intra-individual genetic variation and can lead to genetic disorders. Targeted and whole-genome approaches using short-read sequencing have been developed to identify reference and non-reference MEIs; however, the read length hampers detection of these elements in complex genomic regions. Here, we pair Cas9 targeted nanopore sequencing with computational methodologies to capture active MEIs in human genomes. We demonstrate parallel enrichment for distinct classes of MEIs, averaging 44% of reads on targeted signals. We show an individual flow cell can recover a remarkable fraction of MEIs (97% L1Hs, 93% AluYb, 51% AluYa, 99% SVA_F, and 65% SVA_E). We identify twenty-one non-reference MEIs in GM12878 overlooked by modern, long-read analysis pipelines, primarily in repetitive genomic regions. This work introduces the utility of nanopore sequencing for MEI enrichment and lays the foundation for rapid discovery of elusive, repetitive genetic elements.

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Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data

Cited by 11 publications

References 73 publications

Methodologies for the De novo Discovery of Transposable Element Families

Methodologies for the De novo Discovery of Transposable Element Families

Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing

Cas9 targeted enrichment of mobile elements using nanopore sequencing

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