Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples

Snyder‐Mackler, Noah; Yuan, Michael L.; Shaver, Amanda O.; Gordon, Jacob B.; Kopp, Gisela H.; Schlebusch, Stephen A; Wall, Jeffrey D.; Alberts, Susan C.; Mukherjee, Sayan; Zhou, Xiang; Tung, Jenny

doi:10.1534/genetics.116.187492

Cited by 85 publications

(105 citation statements)

References 67 publications

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“…One successful example was the use of custom biotin-tagged RNA baits to capture genomic DNA from fecal samples from 62 wild baboons (Papio papio). The enriched libraries were sequenced with Illumina HiSeq and provided sufficient genomic markers to undertake pedigree reconstruction (Snyder-Mackler et al, 2016). Another study, using bait captures generated from the Agilent SureSelect system, successfully sequenced more than 1.5 Mb of nuclear DNA and the entire mitochondrial genome from chimpanzee feces (Perry et al, 2010).…”

Section: Target Enrichment Methodsmentioning

confidence: 99%

Genetic and genomic monitoring with minimally invasive sampling methods

Carroll

Bruford

DeWoody

et al. 2017

Preprint

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Emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g. collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically-driven declines, which are unlikely to abate without intensive management efforts that often include MIS approaches. Here we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy datasets and recommend how to address the challenges of moving between traditional and next generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.3209v1 | CC BY 4.0 Open Access |

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Section: Target Enrichment Methodsmentioning

confidence: 99%

Genetic and genomic monitoring with minimally invasive sampling methods

Carroll

Bruford

DeWoody

et al. 2017

Preprint

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“…Capture sensitivity (CS) was defined as the proportion of target regions with an average coverage of at least one, to the total number of target regions; and capture specificity (CSp) was defined as the percentage of unique reads mapping to target sequences, determined by the number of reliable reads on‐target divided by the total number of reliable reads (Jones & Good, ). Library complexity (LC) was defined as the number of nonduplicated reads divided by the total number of reads mapped, where duplicated reads are those that have identical genomic location on both ends (Chen et al., ; Daley & Smith, ; Snyder‐Mackler et al., ).

EF = \frac{Reliable reads on - target/Total reads}{Target space (57.5 Mb) / Genome size (3000 Mb)}

CSp = \frac{Reliable reads on - target}{Reliable reads}

CS = \frac{Number target regions average coverage \geq 1}{Total number target regions (295767)}

LC = \frac{Reliable reads}{Mapped reads}

…”

Section: Methodsmentioning

confidence: 99%

“…Recent target enrichment methodologies have provided methodological advances in acquiring more information from NI samples (Perry et al., ; Snyder‐Mackler et al., ; Wall et al., ). These enrichment methods are performed with the use of biotinylated RNA baits that hybridize with the DNA from species of interest, which are subsequently isolated and sequenced.…”

Section: Introductionmentioning

confidence: 99%

The impact of endogenous content, replicates and pooling on genome capture from faecal samples

Hernández-Rodríguez

Arandjelovic

Lester

et al. 2017

Molecular Ecology Resources

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Target‐capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off‐target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.

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“…; Snyder‐Mackler et al . ). As illustrated here with the PCA, this individual‐level analysis can help detect cryptic differentiation within a population sample.…”

Section: Discussionmentioning

confidence: 97%

Practical low‐coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

Therkildsen

Palumbi

2016

Molecular Ecology Resources

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Today most population genomic studies of nonmodel organisms either sequence a subset of the genome deeply in each individual or sequence pools of unlabelled individuals. With a step-by-step workflow, we illustrate how low-coverage whole-genome sequencing of hundreds of individually barcoded samples is now a practical alternative strategy for obtaining genomewide data on a population scale. We used a highly efficient protocol to generate high-quality libraries for ~6.5 USD from each of 876 Atlantic silversides (a teleost fish with a genome size ~730 Mb) that we sequenced to 1-4× genome coverage. In the absence of a reference genome, we developed a bioinformatic pipeline for mapping the genomic reads to a de novo assembled reference transcriptome. This provides an 'in silico' method for exome capture that avoids the complexities and expenses of using wet chemistry for target isolation. Using novel tools for analysis of low-coverage data, we extracted population allele frequencies, individual genotype likelihoods and polymorphism data for 2 504 335 SNPs across the exome for the 876 fish. To illustrate the use of the resulting data, we present a preliminary analysis of geographical patterns in the exome data and a comparison of complete mitochondrial genome sequences for each individual (constructed from the low-coverage data) that show population colonization patterns along the US east coast. With a total cost per sample of less than 50 USD (including sequencing) and ability to prepare 96 libraries in only 5 h, our approach adds a viable new option to the population genomics toolbox.

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Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples

Cited by 85 publications

References 67 publications

Genetic and genomic monitoring with minimally invasive sampling methods

Genetic and genomic monitoring with minimally invasive sampling methods

The impact of endogenous content, replicates and pooling on genome capture from faecal samples

Practical low‐coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species

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