Targeted DNA Region Re-sequencing

Heyduk, Karolina; Stephens, Jessica D.; Faircloth, Brant C.; Glenn, Travis C.

doi:10.1007/978-3-319-31350-4_3

Cited by 10 publications

(14 citation statements)

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“…However, many questions can be addressed with a small fraction of the genome (DeWoody & DeWoody, 2005; Cariou, Duret, & Charlat, 2013; Pante et al, 2015; Andrews et al, 2016). Thus, researchers have created a variety of strategies to sample a consistent portion of the genome from large numbers of individuals at low cost (Harvey et al, 2016; Heyduk et al, 2016; Glenn & Faircloth, 2016). One of the most popular genome sampling strategies uses restriction enzymes (REs) to reduce genome complexity and sequence a set of orthologous loci across individuals (Restriction site Associated DNA sequencing, RADseq; Miller et al, 2007; Baird et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…Many variants of the general RADseq approach have been developed (Andrews et al 2016; Salas-Linaza & Oono, 2018), including but not limited to: the original method (RAD; Miller et al, 2007; Baird et al, 2008), genotype-by-sequencing (GBS; Elshire et al, 2011), 2-enzyme GBS (Poland & Rife, 2012), dual-digest RADseq (ddRAD; Peterson et al, 2012), 2bRAD (Wang et al, 2012), ezRAD (Toonen et al, 2013), and PCR duplicate removal (quaddRAD; Franchini et al, 2017). Although some of these RADseq approaches are in widespread use, they also have well-documented limitations (Davey et al, 2011; Andrews et al, 2014) which have been thoroughly reviewed in other publications (Andrews et al, 2016; Harvey et al, 2016; Heyduk et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

Bayona‐Vásquez

Glenn

Pierson

et al. 2017

Preprint

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Keywords: 3RAD, dual digest RADseq, ddRAD, DNA libraries, multiplexing, NGS. Bldg., University of Georgia, Athens, GA 30602, USA; 3 2 E-mail: njbayona@uga.edu . CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/205799 doi: bioRxiv preprint first posted online Oct. 19, 2017; 2 Running Title: 3RAD -triple-enzyme RADseq digestion of genomic DNA to sample consistent portions of the genome from individuals being 4 0 studied (e.g., RADseq, GBS). However, researchers often find the existing methods expensive 4 1 to initiate and/or difficult to implement consistently. Here, we present a low-cost and highly integrating adapter designs that can be used interchangeably; 6) incorporating variable-length 4 9 internal tags within the adapters to increase the scope of sample tagging and facilitate pooling 5 0 while also increasing sequence diversity; 7) maintaining compatibility with universal dual- discover thousands of variable loci in each species.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

Bayona‐Vásquez

Glenn

Pierson

et al. 2017

Preprint

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“…With the advancement of next‐generation sequencing technologies, obtaining genomic‐scale data is increasingly affordable. Multiple approaches have been introduced to survey genome content and collect hundreds to thousands of nuclear loci or single‐nucleotide polymorphisms for phylogenetics and population genetic studies (Egan et al., ; Wen et al., ; Heyduk et al., ). Target enrichment or hybridization‐based methods are some of the known “reduced representation” genome sequencing approaches (Mamanova et al., ; Faircloth, ) that have been developed and used in animals (Faircloth et al., ; Lemmon et al., ) and plants (Mandel et al., ; Nicholls et al., ; Uribe‐Convers et al., ) for phylogenomic studies.…”

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confidence: 99%

“…single-nucleotide polymorphisms for phylogenetics and population genetic studies (Egan et al, 2012;Wen et al, 2015;Heyduk et al, 2016). Target enrichment or hybridization-based methods are some of the known "reduced representation" genome sequencing approaches (Mamanova et al, 2010;Faircloth, 2017) that have been developed and used in animals (Faircloth et al, 2012;Lemmon et al, 2012) and plants Nicholls et al, 2015;Uribe-Convers et al, 2016) for phylogenomic studies.…”

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confidence: 99%

Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics

et al. 2018

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Premise of the StudyThe development of pipelines for locus discovery has spurred the use of target enrichment for plant phylogenomics. However, few studies have compared pipelines from locus discovery and bait design, through validation, to tree inference. We compared three methods within Leguminosae (Fabaceae) and present a workflow for future efforts.MethodsUsing 30 transcriptomes, we compared Hyb‐Seq, MarkerMiner, and the Yang and Smith (Y&S) pipelines for locus discovery, validated 7501 baits targeting 507 loci across 25 genera via Illumina sequencing, and inferred gene and species trees via concatenation‐ and coalescent‐based methods.ResultsHyb‐Seq discovered loci with the longest mean length. MarkerMiner discovered the most conserved loci with the least flagged as paralogous. Y&S offered the most parsimony‐informative sites and putative orthologs. Target recovery averaged 93% across taxa. We optimized our targeted locus set based on a workflow designed to minimize paralog/ortholog conflation and thus present 423 loci for legume phylogenomics.ConclusionsMethods differed across criteria important for phylogenetic marker development. We recommend Hyb‐Seq as a method that may be useful for most phylogenomic projects. Our targeted locus set is a resource for future, community‐driven efforts to reconstruct the legume tree of life.

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“…Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics (in plants see, for example, the works by Mandel et al, Weitemier et al, and Nicholls et al 1 – 3 ; see also the works by Lemmon and Lemmon, Heyduk et al 4 , 5 for a general overview of genome subsampling methods). Up to now, two well-documented data analysis pipelines have been published: PHYLUCE 6 and HybPiper 7 .…”

Section: Introductionmentioning

confidence: 99%

HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees

Fér

Schmickl

2018

Evol Bioinform Online

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Summary:Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMaker is written in BASH and integrates common bioinformatics tools. It can be launched both locally and on a high-performance computer cluster. Compared with existing target enrichment data analysis pipelines, HybPhyloMaker offers the following main advantages: implementation of all steps of data analysis from raw reads to species tree reconstruction, calculation and summary of alignment and gene tree properties that assist the user in the selection of “quality-filtered” genes, implementation of several species tree reconstruction methods, and analysis of the coding regions of organellar genomes.Availability:The HybPhyloMaker scripts, manual as well as a test data set, are available in https://github.com/tomas-fer/HybPhyloMaker/. HybPhyloMaker is licensed under open-source license GPL v.3 allowing further modifications.

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Targeted DNA Region Re-sequencing

Cited by 10 publications

References 70 publications

Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics

HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees

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