Reference health

Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants

59/59 checkable references clean · checked 2026-07-22

Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.

6 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.

The 59 checked references that resolve

resolves10.1007/BF03195661

High-quality plant DNA extraction for PCR: an easy approach

resolves10.1007/PL00013971

Paraphyly of Veronica (Veroniceae; Scrophulariaceae): Evidence from the Internal Transcribed Spacer (ITS) Sequences of Nuclear Ribosomal DNA

resolves10.1111/j.1471-8286.2006.01549.x

Recovery of plant DNA using a reciprocating saw and silica‐based columns

resolves10.3389/fgene.2019.01407

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

resolves10.1111/j.1558-5646.2011.01507.x

DOES HYBRIDIZATION DRIVE THE TRANSITION TO ASEXUALITY IN DIPLOID BOECHERA?

resolves10.1002/aps3.1243

Long‐fragment targeted capture for long‐read sequencing of plastomes

resolves10.3389/fpls.2019.01102

Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms

resolves10.1111/evo.13203

Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a MediterraneanCampanula(Campanulaceae) clade

resolves10.1002/aps3.1167

Generating <scp>DNA</scp> sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia

resolves10.1016/j.tplants.2019.07.011

Hyb-Seq for Flowering Plant Systematics

resolves10.1007/s10592-005-9073-x

Development and characterization of polymorphic microsatellite loci in endangered fern Adiantum reniforme var. sinense

resolves10.1007/BF02799431

Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of juncaceae

resolves10.1093/sysbio/sys004

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

resolves10.3389/fevo.2019.00439

The Limits of Hyb-Seq for Herbarium Specimens: Impact of Preservation Techniques

resolves10.1093/gigascience/giz018

Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat

resolves10.3732/apps.1600017

Low‐coverage, whole‐genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery

resolves10.1002/ajb2.1052

Multi‐locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes

resolves10.1038/s41587-020-0407-5

Targeted nanopore sequencing with Cas9-guided adapter ligation

resolves10.7717/peerj.7755

Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

resolves10.15407/ukrbotj75.06.564

DNA extraction from old herbarium material of Veronica subgen. Pseudolysimachium (Plantaginaceae)

resolves10.3732/apps.1600016

HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment

resolves10.1093/sysbio/syy086

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering

resolves10.1093/nar/gkr771

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

resolves10.1371/journal.pone.0028240

Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing

resolves10.3389/fpls.2019.01655

Tackling Rapid Radiations With Targeted Sequencing

resolves10.1093/sysbio/sys049

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

resolves10.1021/bi00034a013

Relative Thermodynamic Stability of DNA, RNA, and DNA:RNA Hybrid Duplexes: Relationship with Base Composition and Structure

resolves10.3389/fpls.2018.00996

Development of Target Sequence Capture and Estimation of Genomic Relatedness in a Mixed Oak Stand

resolves10.1093/jxb/erz202

Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy

resolves10.1038/s41467-019-09454-w

Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

resolves10.1016/j.ab.2003.10.026

Improved plant RNA stability in storage

resolves10.3732/apps.1300085

A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae

resolves10.1111/1755-0998.12258

Cost‐effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies

resolves10.1002/aps3.1038

Practical considerations for plant phylogenomics

resolves10.1111/jse.12516

Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma

resolves10.1101/pdb.prot5448

Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing

resolves10.1016/S0003-2697(02)00665-6

Extraction of high-quality genomic DNA from latex-containing plants

resolves10.1093/sysbio/syx078

Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales)

resolves10.1016/j.ympev.2019.106668

A phylogenomic analysis of Nepenthes (Nepenthaceae)

resolves10.1371/journal.pone.0150528

Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions

resolves10.1016/j.ympev.2019.05.002

Phylogenomic analyses reveal an exceptionally high number of evolutionary shifts in a florally diverse clade of African legumes

resolves10.1038/srep24067

Comparison of DNA Quantification Methods for Next Generation Sequencing

resolves10.1007/978-94-017-5294-7_6

Extraction of DNA from plant tissues

resolves10.1101/gr.128124.111

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

resolves10.5402/2012/205049

DNA Extraction Protocol for Plants with High Levels of Secondary Metabolites and Polysaccharides without Using Liquid Nitrogen and Phenol

resolves10.1007/978-1-4939-9176-1

Ancient DNA

resolves10.1371/journal.pone.0203011

Filter paper-based spin column method for cost-efficient DNA or RNA purification

resolves10.1371/journal.pone.0062692

DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

resolves10.1002/aps3.11254

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

resolves10.2307/1223934

An improved method of DNA isolation from plants collected in the field and conserved in saturated NaCl/CTAB solution

resolves10.1016/j.ympev.2018.02.016

Pseudo-parallel patterns of disjunctions in an Arctic-alpine plant lineage

resolves10.1023/A:1007656315275

Modified CTAB Procedure for DNA Isolation from Epiphytic Cacti of the Genera Hylocereus and Selenicereus (Cactaceae)

resolves10.1002/aps3.1036

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

resolves10.1111/nph.15312

Bridging the micro‐ and macroevolutionary levels in phylogenomics: Hyb‐Seq solves relationships from populations to species and above

resolves10.3389/fpls.2019.00937

A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens

resolves10.1007/978-1-4939-9176-1_6

Extraction of Ancient DNA from Plant Remains

resolves10.3732/apps.1400042

Hyb‐Seq: Combining target enrichment and genome skimming for plant phylogenomics

resolves10.1002/aps3.1148

Target sequence capture of nuclear‐encoded genes for phylogenetic analysis in ferns

resolves10.11646/phytotaxa.388.4.1

Delimitation of the new tribe Parartocarpeae (Moraceae) is supported by a 333-gene phylogeny and resolves tribal level Moraceae taxonomy

The 6 references without a DOI — listed, not checked

no DOI — not checkedData from: Does hybridization drive the transition to asexuality in diploid Boechera?

no DOI — not checkedAnchored phylogenomics of angiosperms I: Assessing the robustness of phylogenetic estimates

no DOI — not checkedTargeted nanopore sequencing by real‐time mapping of raw electrical signal with UNCALLED

no DOI — not checkedNanopore adaptive sequencing for mixed samples, whole exome capture and targeted panels

no DOI — not checkedReconstructing the complex evolutionary history of the Papuasian Schefflera radiation through herbariomics

no DOI — not checkedIndex hopping on the Illumina HiseqX Platform and its consequences for ancient DNA studies

What this badge says. CiteStamped means the CHECKABLE references of this work were clean at the dated check: each resolved to a known work in a public registry, and none carried a retraction notice at that time. It says nothing about the quality, findings, or importance of the work itself, and nothing about references deposited without a DOI.

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