10.5061/DRYAD.3K8V9
Fuentes-Pardo, Angela P.
Dalhousie University
Ruzzante, Daniel E.
Dalhousie University
Data from: Whole-genome sequencing approaches for conservation biology:
advantages, limitations, and practical recommendations
Dryad
dataset
2017
whole genome sequencing
Low-coverage sequencing
Pool-Seq
2017-08-07T13:59:38Z
2017-08-07T13:59:38Z
en
https://doi.org/10.1111/mec.14264
22023415 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Whole-genome resequencing (WGR) is a powerful method for addressing
fundamental evolutionary biology questions that have not been fully
resolved using traditional methods. WGR includes four approaches: the
sequencing of individuals to a high depth of coverage with either
unresolved (huWGR) or resolved haplotypes (hrWGR), the sequencing of
population genomes to a high depth by mixing equimolar amounts of
unlabelled-individual DNA (Pool-seq), and the sequencing of multiple
individuals from a population to a low depth (lcWGR). These techniques
require the availability of a reference genome. This, along with the still
high cost of shotgun sequencing and the large demand for computing
resources and storage, has limited their implementation in non-model
species with scarce genomic resources and in fields such as conservation
biology. Our goal here is to describe the various WGR methods, their pros
and cons, and potential applications in conservation biology. WGR offers
an unprecedented marker density and surveys a wide diversity of genetic
variations not limited to single nucleotide polymorphisms (e.g. structural
variants and mutations in regulatory elements), increasing their power for
the detection of signatures of selection and local adaptation as well as
for the identification of the genetic basis of phenotypic traits and
diseases. Currently though, no single WGR approach fulfills all
requirements of conservation genetics, and each method has its own
limitations and sources of potential bias. We discuss proposed ways to
minimize such biases. We envision a not distant future where the analysis
of whole genomes becomes a routine task in many non-model species and
fields including conservation biology.
data_Genbank_june2017Each file contains the metadata of genomes available
in GenBank for a given taxonomic group up to June 2017
(https://www.ncbi.nlm.nih.gov/genome/browse/#). Four levels of assembly
were considered: contigs, scaffolds, chromosomes, and complete genome
(https://www.ncbi.nlm.nih.gov/assembly/help/#definition).