Phylogenomics using low-depth whole genome sequencing: a case study with the olive tribe.

08:00 EDT 1st April 2019 | BioPortfolio

Summary of "Phylogenomics using low-depth whole genome sequencing: a case study with the olive tribe."

Species trees have traditionally been inferred from a few selected markers, and genome-wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historic species diversity. The genomes of an increasing number of species, including specimens extracted from natural history collections, are being sequenced at low depth. While these datasets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored. Here we evaluate different reference-based methods to infer phylogenies of large taxonomic groups from such datasets. Using the example of the Oleeae tribe, a worldwide-distributed group, we build phylogenies based on single-nucleotide polymorphisms (SNPs) obtained using two reference genomes (the olive and ash trees). The inferred phylogenies are overall congruent, yet present differences that might reflect the effect of the distance to the reference on the amount of missing data. To limit this issue, the genome complexity was reduced by using pairs of orthologous coding sequences as the reference, thus allowing combining SNPs obtained using two distinct references. Concatenated and coalescence trees based on these combined SNPs suggest events of incomplete lineage sorting and/or hybridization during the diversification of this large phylogenetic group. Our results show that genome-wide phylogenetic trees can be inferred from low-depth sequence datasets for eukaryote groups with complex genomes, and histories of reticulate evolution. This opens new avenues for large-scale phylogenomics and biogeographic analyses covering both the extant and historic diversity stored in museum collections. This article is protected by copyright. All rights reserved.


Journal Details

This article was published in the following journal.

Name: Molecular ecology resources
ISSN: 1755-0998


DeepDyve research library

PubMed Articles [24711 Associated PubMed Articles listed on BioPortfolio]

Genomic epidemiological investigation of a Streptococcus suis outbreak in Guangxi, China, 2016.

In June 2016, a Streptococcus suis outbreak occurred in Guangxi, China. We determined the genetic characteristics of six clinically isolated strains by serotyping, PCR, and whole-genome sequencing, pe...

Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes.

Phylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing...

Imputation accuracy of wheat genotyping-by-sequencing (GBS) data using barley and wheat genome references.

Genotyping-by-sequencing (GBS) provides high SNP coverage and has recently emerged as a popular technology for genetic and breeding applications in bread wheat (Triticum aestivum L.) and many other pl...

The Status and Impact of Clinical Tumor Genome Sequencing.

Since the discovery that DNA alterations initiate tumorigenesis, scientists and clinicians have been exploring ways to counter these changes with targeted therapeutics. The sequencing of tumor DNA was...

SRG Extractor: A Skinny Reference Genome Approach for Reduced-Representation Sequencing.

Reduced-representation sequencing (RRS) is a genome-wide scanning method for simultaneous discovery and genotyping of thousands to millions of SNPs that is used across a wide range of species. However...

Clinical Trials [2964 Associated Clinical Trials listed on BioPortfolio]

The VetSeq Study: a Pilot Study of Genome Sequencing in Veteran Care

The VetSeq Study is a pilot intervention study exploring the feasibility of integrating genome sequencing into clinical care at the VA Boston Healthcare System.

Investigating the Feasibility and Implementation of Whole Genome Sequencing in Patients With Suspected Genetic Disorder

The study "Investigating the Feasibility and Implementation of Whole Genome Sequencing in Patients With Suspected Genetic Disorder" is a research study that aims to explore the use of whol...

Rapid Whole Genome Sequencing Study

Rapid Whole Genome Sequencing (rWGS) has proven to provide much faster diagnoses than traditional clinical testing, including clinical Whole Exome Sequencing (WES) and standard Whole Genom...

Whole Genome Sequencing in the Detection of Rare Undiagnosed Genetic Diseases in Children in China

To assess the indications and diagnostic efficiency of whole genome sequencing (WGS) in pediatric patients with unexplained intellectual disability/developmental delay, multiple congenital...

Utility of Rapid Whole Genome Sequencing in the NICU: A Pilot Study

This is a pilot study involving a prospective group of 15 evaluable patients who will undergo rapid whole genome sequencing in addition to standard of care testing. Subjects will be drawn ...

Medical and Biotech [MESH] Definitions

Techniques to determine the entire sequence of the GENOME of an organism or individual.

An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.

The systematic study of the complete DNA sequences (GENOME) of organisms.

Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.

Component of the NATIONAL INSTITUTES OF HEALTH. It conducts and supports research into the mapping of the human genome and other organism genomes. The National Center for Human Genome Research was established in 1989 and re-named the National Human Genome Research Institute in 1997.

Quick Search


DeepDyve research library

Relevant Topics

Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

DNA sequencing
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...

Searches Linking to this Article