A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

Frontiers in Genetics
Tobias AndermannAlexandre Antonelli

Abstract

High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phyloge...Continue Reading

References

Nov 26, 2002·Trends in Genetics : TIG·Erik L L Sonnhammer, Eugene V Koonin
Feb 17, 2005·BMC Bioinformatics·Guy St C Slater, Ewan Birney
Sep 3, 2005·Nature Reviews. Microbiology·Dirk GeversJean Swings
Oct 11, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Mehrdad HajibabaeiPaul D N Hebert
Dec 21, 2005·Genome Research·Paul BertoneMark Gerstein
Oct 16, 2007·Nature Methods·Thomas J AlbertRichard A Gibbs
Oct 16, 2007·Nature Methods·David T OkouMichael E Zwick
Nov 9, 2007·Trends in Ecology & Evolution·Peter WandelerLukas F Keller
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Oct 15, 2008·PloS One·Nathan A BairdEric A Johnson
Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Dec 24, 2009·Nucleic Acids Research·Adrian W BriggsSvante Pääbo
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
Jan 30, 2010·Nature Methods·Lira MamanovaDaniel J Turner
May 8, 2010·Science·Richard E GreenSvante Pääbo
Jun 3, 2010·Cold Spring Harbor Protocols·Matthias Meyer, Martin Kircher
Oct 23, 2010·Methods in Molecular Biology·Hege VestheimSimon N Jarman
Oct 26, 2010·Nucleic Acids Research·Rasko LeinonenGuy Cochrane
Nov 9, 2010·Molecular Ecology·George H PerryYoav Gilad
Nov 11, 2010·Nucleic Acids Research·Rasko LeinonenUNKNOWN International Nucleotide Sequence Database Collaboration
Jan 11, 2011·Bioinformatics·Eric Dugat-BonyPierre Peyret
Feb 23, 2011·Genome Biology·Daniel AirdAndreas Gnirke
Mar 3, 2011·European Journal of Human Genetics : EJHG·Alison J CoffeyAarno Palotie
May 14, 2011·Molecular Ecology Resources·Nadin RohlandMichael Hofreiter
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
May 17, 2011·PloS One·Robert J ElshireSharon E Mitchell
Jun 18, 2011·Nature Reviews. Genetics·John W DaveyMark L Blaxter
Oct 25, 2011·Nucleic Acids Research·Martin KircherMatthias Meyer
Jan 24, 2012·American Journal of Botany·Corrinne E GroverJonathan F Wendel
Mar 17, 2012·Molecular Biology and Evolution·David BryantArindam RoyChoudhury
Apr 12, 2012·PloS One·Benjamin E R RubinCorrie S Moreau
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
May 19, 2012·Systematic Biology·Alan R LemmonEmily Moriarty Lemmon
Sep 1, 2012·Science·Matthias MeyerSvante Pääbo
Oct 11, 2012·Bioinformatics·Nicolas ParisotEric Peyretaillade
Jun 14, 2013·BioTechniques·Chenhong LiGavin J P Naylor
Sep 10, 2013·Methods in Enzymology·Juliane C Lessard

❮ Previous
Next ❯

Citations

Sep 5, 2020·Plant Methods·Elena López-GironaDavid Chagné
Aug 17, 2020·Systematic Biology·Daniel M Portik, John J Wiens
Nov 13, 2020·Molecular Ecology Resources·Mads Reinholdt JensenPhilip Francis Thomsen
Mar 7, 2021·Genes·Ruwani DissanayakeSukhjiwan Kaur
Jul 1, 2021·BMC Bioinformatics·Luna L Sánchez-ReyesEmily Jane McTavish
Aug 3, 2021·Applications in Plant Sciences·Lars NauheimerKatharina Nargar
Sep 4, 2021·Cladistics : the International Journal of the Willi Hennig Society·Miquel A Arnedo, Gustavo Hormiga
Oct 27, 2021·Cladistics : the International Journal of the Willi Hennig Society·David OrtizMalahat Dianat

❮ Previous
Next ❯

Methods Mentioned

BETA
electrophoresis
Illumina sequencing
PCR
pool-seq

Software Mentioned

BaitSTR
Illumina coverage calculator
Trinity
Burrows Aligner BWA
HiSpOD
Nanopolish
Trimmomatic
Minimap
aTRAM
HYBPIPER

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.