scholarly journals ERVcaller: Identify polymorphic endogenous retrovirus (ERV) and other transposable element (TE) insertions using whole-genome sequencing data

2018 ◽  
Author(s):  
Xun Chen ◽  
Dawei Li
Keyword(s):  
Transposable Element ◽  
Whole Genome Sequencing ◽  
Human Genome ◽  
Genome Sequencing ◽  
Small Sample ◽  
Endogenous Retroviruses ◽  
Detection Sensitivity ◽  
Supplementary Information ◽  
Whole Genome Sequencing Data ◽  
Whole Genome

AbstractMotivationApproximately 8% of the human genome is derived from endogenous retroviruses (ERVs). In recent years, an increasing number of human diseases have been found to be associated with ERVs. However, it remains challenging to accurately detect the full spectrum of polymorphic (unfixed) ERVs using next-generation sequencing (NGS) data.ResultsWe designed a new tool, ERVcaller, to detect and genotype transposable element (TE) insertions, including ERVs, in the human genome. We evaluated ERVcaller using both simulated and real benchmark whole-genome sequencing (WGS) datasets. By comparing with existing tools, ERVcaller consistently obtained both the highest sensitivity and precision for detecting simulated ERV and other TE insertions derived from real polymorphic TE sequences. For the WGS data from the 1000 Genomes Project, ERVcaller detected the largest number of TE insertions per sample based on consensus TE loci. By analyzing the experimentally verified TE insertions, ERVcaller had 94.0% TE detection sensitivity and 96.6% genotyping accuracy. PCR and Sanger sequencing in a small sample set verified 86.7% of examined insertion statuses and 100% of examined genotypes. In conclusion, ERVcaller is capable of detecting and genotyping TE insertions using WGS data with both high sensitivity and precision. This tool can be applied broadly to other species.Availabilitywww.uvm.edu/genomics/software/[email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data

2019 ◽  
Vol 35 (20) ◽  
pp. 3913-3922 ◽  
Author(s):  
Xun Chen ◽  
Dawei Li
Keyword(s):  
Transposable Element ◽  
Whole Genome Sequencing ◽  
Human Genome ◽  
Genome Sequencing ◽  
Small Sample ◽  
Endogenous Retroviruses ◽  
Detection Sensitivity ◽  
Supplementary Information ◽  
Whole Genome Sequencing Data ◽  
Whole Genome

Abstract Motivation Approximately 8% of the human genome is derived from endogenous retroviruses (ERVs). In recent years, an increasing number of human diseases have been found to be associated with ERVs. However, it remains challenging to accurately detect the full spectrum of polymorphic (unfixed) ERVs using whole-genome sequencing (WGS) data. Results We designed a new tool, ERVcaller, to detect and genotype transposable element (TE) insertions, including ERVs, in the human genome. We evaluated ERVcaller using both simulated and real benchmark WGS datasets. Compared to existing tools, ERVcaller consistently obtained both the highest sensitivity and precision for detecting simulated ERV and other TE insertions derived from real polymorphic TE sequences. For the WGS data from the 1000 Genomes Project, ERVcaller detected the largest number of TE insertions per sample based on consensus TE loci. By analyzing the experimentally verified TE insertions, ERVcaller had 94.0% TE detection sensitivity and 96.6% genotyping accuracy. Polymerase chain reaction and Sanger sequencing in a small sample set verified 86.7% of examined insertion statuses and 100% of examined genotypes. In conclusion, ERVcaller is capable of detecting and genotyping TE insertions using WGS data with both high sensitivity and precision. This tool can be applied broadly to other species. Availability and implementation http://www.uvm.edu/genomics/software/ERVcaller.html. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals TranspoScope: interactive visualization of retrotransposon insertions

2020 ◽  
Vol 36 (12) ◽  
pp. 3877-3878
Author(s):  
Mark Grivainis ◽  
Zuojian Tang ◽  
David Fenyö
Keyword(s):  
Experimental Evidence ◽  
Whole Genome Sequencing ◽  
Human Genome ◽  
Genome Sequencing ◽  
Source Code ◽  
Prenatal Development ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genome Browsers

Abstract Motivation Retrotransposition is an important force in shaping the human genome and is involved in prenatal development, disease and aging. Current genome browsers are not optimized for visualizing the experimental evidence for retrotransposon insertions. Results We have developed a specialized browser to visualize the evidence for retrotransposon insertions for both targeted and whole-genome sequencing data. Availability and implementation TranspoScope’s source code, as well as installation instructions, are available at https://github.com/FenyoLab/transposcope.

scholarly journals Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽  
2021 ◽  
Author(s):  
Axel Jensen ◽  
Mette Lillie ◽  
Kristofer Bergström ◽  
Per Larsson ◽  
Jacob Höglund
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Peripheral Populations ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

scholarly journals Comprehensive identification of transposable element insertions using multiple sequencing technologies

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chong Chu ◽  
Rebeca Borges-Monroy ◽  
Vinayak V. Viswanadham ◽  
Soohyun Lee ◽  
Heng Li ◽  
...  
Keyword(s):  
Transposable Element ◽  
Structure And Function ◽  
Endogenous Retroviruses ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Short Read ◽  
Sequencing Technologies ◽  
Long Read ◽  
And Function

AbstractTransposable elements (TEs) help shape the structure and function of the human genome. When inserted into some locations, TEs may disrupt gene regulation and cause diseases. Here, we present xTea (x-Transposable element analyzer), a tool for identifying TE insertions in whole-genome sequencing data. Whereas existing methods are mostly designed for short-read data, xTea can be applied to both short-read and long-read data. Our analysis shows that xTea outperforms other short read-based methods for both germline and somatic TE insertion discovery. With long-read data, we created a catalogue of polymorphic insertions with full assembly and annotation of insertional sequences for various types of retroelements, including pseudogenes and endogenous retroviruses. Notably, we find that individual genomes have an average of nine groups of full-length L1s in centromeres, suggesting that centromeres and other highly repetitive regions such as telomeres are a significant yet unexplored source of active L1s. xTea is available at https://github.com/parklab/xTea.

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