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

Targeted nanopore sequencing with Cas9-guided adapter ligation

(2020) Timothy Gilpatrick et al.   NATURE BIOTECHNOLOGY

Tackling Rapid Radiations With Targeted Sequencing

(2020) Isabel Larridon et al.   Frontiers in Plant Science

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

(2020) Tobias Andermann et al.   Frontiers in Genetics

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

(2019) Laura-Jayne Gardiner et al.   GigaScience

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

(2019) NYREE J.C. ZEREGA et al.   Phytotaxa

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

(2019) Shengjun Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2019) Rafael Medina et al.   Journal of Systematics and Evolution

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

(2019) Yang Liu et al.   Nature Communications

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

(2019) Kevin Bethune et al.   Applications in Plant Sciences

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

(2019) Marybel Soto Gomez et al.   Applications in Plant Sciences

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

(2019) Dario I. Ojeda et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2019) Juan Viruel et al.   Frontiers in Plant Science

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

(2019) Grace E. Brewer et al.   Frontiers in Plant Science

Hyb-Seq for Flowering Plant Systematics

(2019) Steven Dodsworth et al.   TRENDS IN PLANT SCIENCE

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

(2019) Travis C. Glenn et al.   PeerJ

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

(2019) Laura L. Forrest et al.   Frontiers in Ecology and Evolution

A phylogenomic analysis of Nepenthes (Nepenthaceae)

(2019) Bruce Murphy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2018) David S. Gernandt et al.   AMERICAN JOURNAL OF BOTANY

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

(2018) Rebecca L. Stubbs et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2018) Tamara Villaverde et al.   NEW PHYTOLOGIST

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

(2018) Isabelle Lesur et al.   Frontiers in Plant Science

Practical considerations for plant phylogenomics

(2018) Michael R. McKain et al.   Applications in Plant Sciences

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

(2018) Paul G. Wolf et al.   Applications in Plant Sciences

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

(2018) Gillian H. Dean et al.   Applications in Plant Sciences

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

(2018) Mohammad Vatanparast et al.   Applications in Plant Sciences

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

(2018) Rui Shi et al.   PLoS One

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

(2018) Matthew G Johnson et al.   SYSTEMATIC BIOLOGY

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

(2017) Andrew A. Crowl et al.   EVOLUTION

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

(2017) Abigail J Moore et al.   SYSTEMATIC BIOLOGY

Low-Coverage, Whole-Genome Sequencing of Artocarpus camansi (Moraceae) for Phylogenetic Marker Development and Gene Discovery

(2016) Elliot M. Gardner et al.   Applications in Plant Sciences

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

(2016) Matthew G. Johnson et al.   Applications in Plant Sciences

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

(2016) Yuki Nakayama et al.   PLoS One

Comparison of DNA Quantification Methods for Next Generation Sequencing

(2016) Jérôme D. Robin et al.   Scientific Reports

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

(2014) Cédric Mariac et al.   Molecular Ecology Resources

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae

(2014) Jennifer R. Mandel et al.   Applications in Plant Sciences

DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

(2013) Michele Simbolo et al.   PLoS One

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

(2012) N. Rohland et al.   GENOME RESEARCH

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

DOES HYBRIDIZATION DRIVE THE TRANSITION TO ASEXUALITY IN DIPLOID BOECHERA?

(2011) James B. Beck et al.   EVOLUTION

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Ellen Knierim et al.   PLoS One

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

(2010) I. Ahmed et al.   JOURNAL OF APPLIED GENETICS