Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes

G3 : Genes - Genomes - Genetics
Yong-Bi FuYibo Dong

Abstract

Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for exploring genome-wide genetic variation. However, GBS commonly samples a genome unevenly and can generate a substantial amount of missing data. These technical features would limit the power of various GBS-based genetic and genomic analyses. Here we present software called IgCoverage for in silico evaluation of genomic coverage through GBS with an individual or pair of restriction enzymes on one sequenced genome, and report a new set of 21 restriction enzyme combinations that can be applied to enhance GBS applications. These enzyme combinations were developed through an application of IgCoverage on 22 plant, animal, and fungus species with sequenced genomes, and some of them were empirically evaluated with different runs of Illumina MiSeq sequencing in 12 plant species. The in silico analysis of 22 organisms revealed up to eight times more genome coverage for the new combinations consisted of pairing four- or five-cutter restriction enzymes than the commonly used enzyme combination PstI + MspI. The empirical evaluation of the new enzyme combination (HinfI + HpyCH4IV) in 12 plant species showed 1.7-6 times more genome coverage than PstI + MspI, and 2.3 t...Continue Reading

References

Nov 11, 1995·Nucleic Acids Research·P VosM Kuiper
Jun 8, 2001·Bioinformatics·O TroyanskayaR B Altman
Dec 13, 2005·Plant Physiology·Georg HabererJoachim Messing
Jun 24, 2006·Bulletin of Mathematical Biology·Michael C Wendl
Mar 9, 2007·Bioinformatics·Wolfram StackliesJoachim Selbig
May 8, 2009·Genome Research·Xuehui HuangBin Han
Dec 10, 2009·Nature Reviews. Genetics·Michael L Metzker
Jan 14, 2010·Genome Research·John E PoolRasmus Nielsen
Jun 3, 2010·Nature Reviews. Genetics·Jonathan Marchini, Bryan Howie
May 17, 2011·PloS One·Robert J ElshireSharon E Mitchell
May 19, 2011·Nature Reviews. Genetics·Rasmus NielsenYun S Song
Jun 18, 2011·Nature Reviews. Genetics·John W DaveyMark L Blaxter
Nov 1, 2011·Bioinformatics·Daniel J Stekhoven, Peter Bühlmann
Dec 20, 2011·Molecular Ecology Resources·Yong-Bi Fu, Gregory W Peterson
Feb 16, 2013·Genetics·Timothy M BeissingerNatalia de Leon
Mar 2, 2013·G3 : Genes - Genomes - Genetics·Jessica E RutkoskiMark E Sorrells
Jan 18, 2014·Nature Reviews. Genetics·David SimsChris P Ponting
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Sep 17, 2014·Proceedings of the National Academy of Sciences of the United States of America·Petr ŠmardaOlga Rotreklová
Oct 17, 2014·Molecular Ecology·Kimberly R AndrewsGordon Luikart
Oct 17, 2014·Molecular Ecology·Jonathan B PuritzChristopher E Bird
Nov 20, 2014·BMC Genomics·Christopher HeffelfingerStephen L Dellaporta

❮ Previous
Next ❯

Citations

Mar 1, 2017·Biology of the Cell·Charlotte AlibertJean-Baptiste Manneville
Aug 2, 2018·Frontiers in Plant Science·Anne-Frédérique Gendron St-MarseilleBenjamin Mimee
Jun 8, 2019·Bioinformatics·Davoud TorkamanehFrançois Belzile
Sep 12, 2018·International Journal of Molecular Sciences·Kiran BaralYong-Bi Fu
Dec 22, 2020·Frontiers in Plant Science·Paula Arielle Mendes Ribeiro ValdisserRosana Pereira Vianello

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRP066269

Methods Mentioned

BETA
genotyping
flow cytometry

Software Mentioned

Trimommatic
npGeno
Miseq
custom Perl script
FastX
GBS
IgCoverage
rar
IgCoverage1RE
Minia

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.