Ten years of next-generation sequencing technology

EL Van Dijk, H Auger, Y Jaszczyszyn, C Thermes - Trends in genetics, 2014 - cell.com
Ten years ago next-generation sequencing (NGS) technologies appeared on the market.
During the past decade, tremendous progress has been made in terms of speed, read …

Bulk segregation analysis in the NGS era: a review of its teenage years

Z Li, Y Xu - The Plant Journal, 2022 - Wiley Online Library
Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme
phenotypes to conduct economical and rapidly linked marker screening or quantitative trait …

Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

ZN Kamvar, JC Brooks, NJ Grünwald - Frontiers in genetics, 2015 - frontiersin.org
To gain a detailed understanding of how plant microbes evolve and adapt to hosts,
pesticides, and other factors, knowledge of the population dynamics and evolutionary history …

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genoty** in Model and Non-Model Species

BK Peterson, JN Weber, EH Kay, HS Fisher… - PloS one, 2012 - journals.plos.org
The ability to efficiently and accurately determine genotypes is a keystone technology in
modern genetics, crucial to studies ranging from clinical diagnostics, to genotype-phenotype …

These aren't the loci you'e looking for: Principles of effective SNP filtering for molecular ecologists

SJ O'Leary, JB Puritz, SC Willis, CM Hollenbeck… - 2018 - Wiley Online Library
Sequencing reduced‐representation libraries of restriction site‐associated DNA (RAD seq)
to identify single nucleotide polymorphisms (SNP s) is quickly becoming a standard …

What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol

JJ Schenk, LE Becklund, SJ Carey… - Applications in Plant …, 2023 - Wiley Online Library
Cetyltrimethylammonium bromide (CTAB)–based methods are widely used to isolate DNA
from plant tissues, but the unique chemical composition of secondary metabolites among …

Genome-wide genetic marker discovery and genoty** using next-generation sequencing

JW Davey, PA Hohenlohe, PD Etter, JQ Boone… - Nature Reviews …, 2011 - nature.com
The advent of next-generation sequencing (NGS) has revolutionized genomic and
transcriptomic approaches to biology. These new sequencing tools are also valuable for the …

Beyond biodiversity: Can environmental DNA (eDNA) cut it as a population genetics tool?

CIM Adams, M Knapp, NJ Gemmell, GJ Jeunen… - Genes, 2019 - mdpi.com
Population genetic data underpin many studies of behavioral, ecological, and evolutionary
processes in wild populations and contribute to effective conservation management …

Ecological plant epigenetics: Evidence from model and non‐model species, and the way forward

CL Richards, C Alonso, C Becker, O Bossdorf… - Ecology …, 2017 - Wiley Online Library
Growing evidence shows that epigenetic mechanisms contribute to complex traits, with
implications across many fields of biology. In plant ecology, recent studies have attempted to …

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

DAR Eaton, RH Ree - Systematic biology, 2013 - academic.oup.com
Phylogenetic relationships among recently diverged species are often difficult to resolve due
to insufficient phylogenetic signal in available markers and/or conflict among gene trees …