Comparative Performance of Two Whole Genome Capture Methodologies on Ancient DNA Illumina Libraries

1. The application of whole genome capture (WGC) methods to ancient DNA (aDNA) promises to increase the efficiency of ancient genome sequencing. 2. We compared the performance of two recently developed WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded (DSL) and single-stranded (SSL) build protocols. Although both methods effectively enriched aDNA, one consistently produced marginally better results, giving us the opportunity to further explore the parameters influencing WGC experiments. 3. Our results suggest that bait length has an important influence on library enrichment. Moreover, we show that WGC biases against the shorter molecules that are enriched in SSL preparation protocols. Therefore application of WGC to such samples is not recommended without future optimization. Lastly, we document the effect of WGC on other features including clonality, GC composition and repetitive DNA content of captured libraries. 4. Our findings provide insights for researchers planning to perform WGC on aDNA, and suggest future tests and optimization to improve WGC efficiency.

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Challenges and Approaches to Genotyping Repetitive DNA

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400771 ◽

2019 ◽

Vol 10 (1) ◽

pp. 417-430 ◽

Cited By ~ 2

Author(s):

Elizabeth A. Morton ◽

Ashley N. Hall ◽

Elizabeth Kwan ◽

Calvin Mok ◽

Konstantin Queitsch ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Repetitive Dna ◽

Complex Traits ◽

Copy Number ◽

Model Organisms ◽

Whole Genome ◽

Copy Number Estimation ◽

Rdna Copy ◽

Rdna Copy Number

Individuals within a species can exhibit vast variation in copy number of repetitive DNA elements. This variation may contribute to complex traits such as lifespan and disease, yet it is only infrequently considered in genotype-phenotype associations. Although the possible importance of copy number variation is widely recognized, accurate copy number quantification remains challenging. Here, we assess the technical reproducibility of several major methods for copy number estimation as they apply to the large repetitive ribosomal DNA array (rDNA). rDNA encodes the ribosomal RNAs and exists as a tandem gene array in all eukaryotes. Repeat units of rDNA are kilobases in size, often with several hundred units comprising the array, making rDNA particularly intractable to common quantification techniques. We evaluate pulsed-field gel electrophoresis, droplet digital PCR, and Nextera-based whole genome sequencing as approaches to copy number estimation, comparing techniques across model organisms and spanning wide ranges of copy numbers. Nextera-based whole genome sequencing, though commonly used in recent literature, produced high error. We explore possible causes for this error and provide recommendations for best practices in rDNA copy number estimation. We present a resource of high-confidence rDNA copy number estimates for a set of S. cerevisiae and C. elegans strains for future use. We furthermore explore the possibility for FISH-based copy number estimation, an alternative that could potentially characterize copy number on a cellular level.

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An Efficient Pipeline for Ancient DNA Mapping and Recovery of Endogenous Ancient DNA from Whole-Genome Sequencing Data

Authorea ◽

10.22541/au.158714091.12520027 ◽

2020 ◽

Author(s):

Wenhao Xu ◽

Yu Lin ◽

Ke Zhao ◽

Hai Li ◽

Yin Tian ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Ancient Dna ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Dna Mapping

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Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data

Genome Biology ◽

10.1186/gb-2012-13-12-r113 ◽

2012 ◽

Vol 13 (12) ◽

pp. R113 ◽

Cited By ~ 25

Author(s):

Matthew Parker ◽

Xiang Chen ◽

Armita Bahrami ◽

James Dalton ◽

Michael Rusch ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Dna Content ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Telomeric Dna ◽

Pediatric Cancers

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Whole genome sequencing improves estimation of nuclear DNA content of Chinese hamster ovary cells

Cytometry Part A ◽

10.1002/cyto.a.22331 ◽

2013 ◽

pp. n/a-n/a

Author(s):

Andreas Maccani ◽

Wolfgang Ernst ◽

Reingard Grabherr

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Dna Content ◽

Chinese Hamster Ovary ◽

Nuclear Dna ◽

Chinese Hamster Ovary Cells ◽

Chinese Hamster ◽

Nuclear Dna Content ◽

Whole Genome ◽

Ovary Cells

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An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole‐genome sequencing data

Ecology and Evolution ◽

10.1002/ece3.7056 ◽

2020 ◽

Author(s):

Wenhao Xu ◽

Yu Lin ◽

Keliang Zhao ◽

Haimeng Li ◽

Yinping Tian ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Ancient Dna ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Dna Mapping

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

Frontiers in Genetics ◽

10.3389/fgene.2021.639355 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sixin Liu ◽

Guangtu Gao ◽

Ryan M. Layer ◽

Gary H. Thorgaard ◽

Gregory D. Wiens ◽

...

Keyword(s):

Rainbow Trout ◽

Repetitive Dna ◽

Dna Content ◽

Repetitive Sequences ◽

Principal Component ◽

Whole Genome ◽

Structural Variants ◽

High Confidence ◽

Breeding Populations ◽

Or Gene

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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