sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data

Kuzniar, Arnold; Maassen, Jason; Verhoeven, Stefan; Santuari, Luca; Shneider, Carl; Kloosterman, Wigard P.; Ridder, Jeroen de

doi:10.7717/peerj.8214

“…To predict SVs, we used the “sv-callers” workflow with few modifications that enabled parallel execution of multiple SV callers ( Kuzniar et al 2020 ), an approach that is considered optimal as it exploits often complementary information to predict SVs ( Goerner-Potvin and Bourque 2018 ; Cameron et al 2019 ). Briefly, the workflow takes every strain and maps the genomic reads to the reference genome V. dahliae JR2 using BWA-MEM v.0.7 with default options ( Li and Durbin 2010 ).…”

Section: Methodsmentioning

confidence: 99%

Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant PathogenVerticillium dahliae

Torres

¹

,

Thomma

²

,

Seidl

³

2021

Genome Biology and Evolution

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Transposable elements (TEs) are a major source of genetic and regulatory variation in their host genome and are consequently thought to play important roles in evolution. Many fungal and oomycete plant pathogens have evolved dynamic and TE-rich genomic regions containing genes that are implicated in host colonization and adaptation. TEs embedded in these regions have typically been thought to accelerate the evolution of these genomic compartments, but little is known about their dynamics in strains that harbor them. Here, we used whole-genome sequencing data of 42 strains of the fungal plant pathogen Verticillium dahliae to systematically identify polymorphic TEs that may be implicated in genomic as well as in gene expression variation. We identified 2,523 TE polymorphisms and characterize a subset of 8% of the TEs as polymorphic elements that are evolutionary younger, less methylated, and more highly expressed when compared with the remaining 92% of the total TE complement. As expected, the polyrmorphic TEs are enriched in the adaptive genomic regions. Besides, we observed an association of polymorphic TEs with pathogenicity-related genes that localize nearby and that display high expression levels. Collectively, our analyses demonstrate that TE dynamics in V. dahliae contributes to genomic variation, correlates with expression of pathogenicity-related genes, and potentially impacts the evolution of adaptive genomic regions.

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“…To predict structural variants, we used the 'sv-callers' workflow with few modifications that enabled parallel execution of multiple SV callers (Kuzniar, et al 2020). We used four different callers: DELLY v.0.8.1 (Rausch, et al 2012), LUMPY v.2.13 (Layer, et al 2014, Manta v.1.6.0 (Chen, et al 2016), and Wham v.1.0 (Kronenberg, et al 2015) in single-sample mode, using each 42 previously sequenced V. dahliae strains independently ( Supplementary Table 1).…”

Section: Structural Variant Calling and Analysismentioning

confidence: 99%

Transposable elements contribute to genome dynamics and gene expression variation in the fungal plant pathogenVerticillium dahliae

Torres

¹

,

Thomma

²

,

Seidl

³

2021

Preprint

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Transposable elements (TEs) are a major source of genetic and regulatory variation in their host genome and are consequently thought to play important roles in evolution. Many fungal and oomycete plant pathogens have evolved dynamic and TE-rich genomic regions containing genes that are implicated in host colonization. TEs embedded in these regions have typically been thought to accelerate the evolution of these genomic compartments, but little is known about their dynamics in strains that harbor them. Here, we used whole-genome sequencing data of 42 strains of the fungal plant pathogen Verticillium dahliae to systematically identify polymorphic TEs that may be implicated in genomic as well as in gene expression variation. We identified 2,523 TE polymorphisms and characterize a subset of 8% of the TEs as dynamic elements that are evolutionary younger, less methylated, and more highly expressed when compared with the remaining 92% of the TE complement. As expected, the dynamic TEs are enriched in the dynamic genomic regions. Besides, we observed an association of dynamic TEs with pathogenicity-related genes that localize nearby and that display high expression levels. Collectively, our analyses demonstrate that TE dynamics in V. dahliae contributes to genomic variation, correlates with expression of pathogenicity-related genes, and potentially impacts the evolution of dynamic genomic regions.Significance statementTransposable elements (TEs) are ubiquitous components of genomes and are major sources of genetic and regulatory variation. Many plant pathogens have evolved TE-rich genomic regions containing genes with roles in host colonization, and TEs are thought to contribute to accelerated evolution of these dynamic regions. We analyzed the fungal plant pathogen Verticillium dahliae to identify TE variation between strains and to demonstrate that polymorphic TEs have specific characteristic that separates them from the majority of TEs. Polymorphic TEs are enriched in dynamic genomic regions and are associated with structural variants and highly expressed pathogenicity-related genes. Collectively, our results provide evidence for the hypothesis that dynamic TEs contribute to increased genomic diversity, functional variation, and the evolution of dynamic genomic regions.

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“…Advises to improve the detection using short read technology have already been described such as the careful combination of complementary SV callers [ 7 ]. Meta SV callers such as Meta-sv, Parliament2 or sv-callers reconcile SV calls produced by different SV callers [ 25 – 27 ]. However, only the calls that are discovered concordantly between different tools are returned.…”

Section: Discussionmentioning

confidence: 99%

Towards a better understanding of the low recall of insertion variants with short-read based variant callers

Delage

¹

,

Thévenon

²

,

Lemaitre

³

2020

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Background Since 2009, numerous tools have been developed to detect structural variants using short read technologies. Insertions >50 bp are one of the hardest type to discover and are drastically underrepresented in gold standard variant callsets. The advent of long read technologies has completely changed the situation. In 2019, two independent cross technologies studies have published the most complete variant callsets with sequence resolved insertions in human individuals. Among the reported insertions, only 17 to 28% could be discovered with short-read based tools. Results In this work, we performed an in-depth analysis of these unprecedented insertion callsets in order to investigate the causes of such failures. We have first established a precise classification of insertion variants according to four layers of characterization: the nature and size of the inserted sequence, the genomic context of the insertion site and the breakpoint junction complexity. Because these levels are intertwined, we then used simulations to characterize the impact of each complexity factor on the recall of several structural variant callers. We showed that most reported insertions exhibited characteristics that may interfere with their discovery: 63% were tandem repeat expansions, 38% contained homology larger than 10 bp within their breakpoint junctions and 70% were located in simple repeats. Consequently, the recall of short-read based variant callers was significantly lower for such insertions (6% for tandem repeats vs 56% for mobile element insertions). Simulations showed that the most impacting factor was the insertion type rather than the genomic context, with various difficulties being handled differently among the tested structural variant callers, and they highlighted the lack of sequence resolution for most insertion calls. Conclusions Our results explain the low recall by pointing out several difficulty factors among the observed insertion features and provide avenues for improving SV caller algorithms and their combinations.

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sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data

Cited by 18 publications

References 41 publications

Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant PathogenVerticillium dahliae

Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant PathogenVerticillium dahliae

Transposable elements contribute to genome dynamics and gene expression variation in the fungal plant pathogenVerticillium dahliae

Towards a better understanding of the low recall of insertion variants with short-read based variant callers

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