Single-species Microarrays and Comparative Transcriptomics

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2008 Sep 26

PMID 18815615

Citations 9

Authors

Frederic J J Chain

Dora Ilieva

Ben J Evans

Affiliations

Soon will be listed here.

Abstract

Background: Prefabricated expression microarrays are currently available for only a few species but methods have been proposed to extend their application to comparisons between divergent genomes.

Methodology/principal Findings: Here we demonstrate that the hybridization intensity of genomic DNA is a poor basis on which to select unbiased probes on Affymetrix expression arrays for studies of comparative transcriptomics, and that doing so produces spurious results. We used the Affymetrix Xenopus laevis microarray to evaluate expression divergence between X. laevis, X. borealis, and their F1 hybrids. When data are analyzed with probes that interrogate only sequences with confirmed identity in both species, we recover results that differ substantially analyses that use genomic DNA hybridizations to select probes.

Conclusions/significance: Our findings have implications for the experimental design of comparative expression studies that use single-species microarrays, and for our understanding of divergent expression in hybrid clawed frogs. These findings also highlight important limitations of single-species microarrays for studies of comparative transcriptomics of polyploid species.

Citing Articles

Comparative transcriptomics of Atlantic Salmo salar, chum Oncorhynchus keta and pink salmon O. gorbuscha during infections with salmon lice Lepeophtheirus salmonis.

Sutherland B, Koczka K, Yasuike M, Jantzen S, Yazawa R, Koop B BMC Genomics. 2014; 15:200.

PMID: 24628956 PMC: 4004277. DOI: 10.1186/1471-2164-15-200.

Expression divergence measured by transcriptome sequencing of four yeast species.

Busby M, Gray J, Costa A, Stewart C, Stromberg M, Barnett D BMC Genomics. 2011; 12:635.

PMID: 22206443 PMC: 3296765. DOI: 10.1186/1471-2164-12-635.

Toward an unbiased evolutionary platform for unraveling Xenopus developmental gene networks.

Beer R, Wagner F, Grishkevich V, Peshkin L, Yanai I Genesis. 2011; 50(3):186-91.

PMID: 21956895 PMC: 8128080. DOI: 10.1002/dvg.20811.

Comparative functional genomic analysis of Solanum glandular trichome types.

McDowell E, Kapteyn J, Schmidt A, Li C, Kang J, Descour A Plant Physiol. 2010; 155(1):524-39.

PMID: 21098679 PMC: 3075747. DOI: 10.1104/pp.110.167114.

Identification of suitable reference genes for normalization of qPCR data in comparative transcriptomics analyses in the Triticeae.

Gimenez M, Piston F, Atienza S Planta. 2010; 233(1):163-73.

PMID: 20960006 DOI: 10.1007/s00425-010-1290-y.

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