Accuracy of allele frequency estimation using pooled RNA-Seq

Molecular Ecology Resources
M KonczalWiesław Babik

Abstract

For nonmodel organisms, genome-wide information that describes functionally relevant variation may be obtained by RNA-Seq following de novo transcriptome assembly. While sequencing has become relatively inexpensive, the preparation of a large number of sequencing libraries remains prohibitively expensive for population genetic analyses of nonmodel species. Pooling samples may be then an attractive alternative. To test whether pooled RNA-Seq accurately predicts true allele frequencies, we analysed the liver transcriptomes of 10 bank voles. Each sample was sequenced both as an individually barcoded library and as a part of a pool. Equal amounts of total RNA from each vole were pooled prior to mRNA selection and library construction. Reads were mapped onto the de novo assembled reference transcriptome. High-quality genotypes for individual voles, determined for 23,682 SNPs, provided information on 'true' allele frequencies; allele frequencies estimated from the pool were then compared with these values. 'True' frequencies and those estimated from the pool were highly correlated. Mean relative estimation error was 21% and did not depend on expression level. However, we also observed a minor effect of interindividual variation in ge...Continue Reading

Associated Datasets

References

Oct 6, 1999·Genome Research·X Huang, A Madan
Sep 27, 2000·Proceedings of the National Academy of Sciences of the United States of America·R SandbergC Barlow
Nov 5, 2002·Nature Reviews. Genetics·Pak ShamMichael Owen
Jul 23, 2004·Nature·Michael MorleyVivian G Cheung
Nov 30, 2004·Nature Genetics·Marjorie F OleksiakDouglas L Crawford
Apr 29, 2005·Evolution; International Journal of Organic Evolution·Edyta T SadowskaPaweł Koteja
Mar 29, 2006·Proceedings of the National Academy of Sciences of the United States of America·Andrew Whitehead, Douglas L Crawford
Feb 13, 2008·Molecular Ecology·J Cristobal VeraJames H Marden
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Jun 20, 2008·Evolution; International Journal of Organic Evolution·Vincent J Lynch, Günter P Wagner
Sep 11, 2008·Physiological and Biochemical Zoology : PBZ·Edyta T SadowskaPaweł Koteja
Mar 3, 2009·Nature Methods·Todd E DruleyRobi D Mitra
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Oct 6, 2009·Trends in Genetics : TIG·Yoav GiladKevin Thornton
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
Jun 17, 2010·Genetic Epidemiology·Su Yeon KimRasmus Nielsen
Jul 14, 2010·Current Biology : CB·Deborah Charlesworth, Brian Charlesworth
Sep 30, 2010·BMC Bioinformatics·Murray P CoxPatrick J Biggs
Oct 14, 2010·Nature Reviews. Genetics·Vikas BansalNicholas J Schork
Nov 13, 2010·Ecology Letters·Amber M RiceAnna Qvarnström
Jan 8, 2011·Genetics·Zachariah Gompert, C Alex Buerkle
Apr 29, 2011·Journal of Human Genetics·Suying BaoYou-Qiang Song
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Jun 21, 2011·Bioinformatics·Andre AltmannBertram Müller-Myhsok
Jun 28, 2011·Bioinformatics·Robert C EdgarRob Knight
Sep 8, 2011·Nature Reviews. Genetics·Jeffrey A Martin, Zhong Wang
Sep 20, 2011·Genome Research·Dent EarlBenedict Paten
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Apr 7, 2012·Nature·Felicity C JonesDavid M Kingsley
May 11, 2012·PloS One·Mohamed SalemJianbo Yao

❮ Previous
Next ❯

Citations

May 3, 2014·Genome Biology and Evolution·Michael LynchScott Harrison
Sep 24, 2014·Nature Reviews. Genetics·Christian SchlöttererViola Nolte
Nov 1, 2015·The Journal of Heredity·Melissa B DeBiasse, Morgan W Kelly
Jul 13, 2016·Molecular Biology and Evolution·Mateusz KonczalWiesław Babik
Jun 26, 2018·Journal of Experimental Zoology. Part A, Ecological and Integrative Physiology·Danielle Roush, Turk Rhen
Nov 20, 2018·Bioinformatics·Carine ReyMarie Sémon
Oct 24, 2019·Ecology and Evolution·Jóhannes GuðbrandssonArnar Pálsson
Jun 7, 2019·BMC Genomics·Michael SabehBenjamin Mimee
Apr 26, 2015·G3 : Genes - Genomes - Genetics·Katharine M H TomaltyMelinda R Baerwald
Sep 30, 2015·The Journal of Experimental Biology·Crista B Wadsworth, Erik B Dopman

❮ Previous
Next ❯

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.