Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome

BMC Evolutionary Biology
Jason G MezeyCorbin D Jones

Abstract

Co-expression of genes that physically cluster together is a common characteristic of eukaryotic transcriptomes. This organization of transcriptomes suggests that coordinated evolution of gene expression for clustered genes may also be common. Clusters where expression evolution of each gene is not independent of their neighbors are important units for understanding transcriptome evolution. We used a common microarray platform to measure gene expression in seven closely related species in the Drosophila melanogaster subgroup, accounting for confounding effects of sequence divergence. To summarize the correlation structure among genes in a chromosomal region, we analyzed the fraction of variation along the first principal component of the correlation matrix. We analyzed the correlation for blocks of consecutive genes to assess patterns of correlation that may be manifest at different scales of coordinated expression. We find that expression of physically clustered genes does evolve in a coordinated manner in many locations throughout the genome. Our analysis shows that relatively few of these clusters are near heterochromatin regions and that these clusters tend to be over-dispersed relative to the rest of the genome. This sugge...Continue Reading

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Citations

Aug 24, 2012·PloS One·Samina Naseeb, Daniela Delneri
Nov 22, 2013·BMC Genomics·Alan F Rubin, Phil Green
Sep 13, 2013·Cellular and Molecular Life Sciences : CMLS·Dietmar RiederZlatko Trajanoski
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Apr 24, 2012·Evolution; International Journal of Organic Evolution·Minyoung J WymanLocke Rowe
Jun 17, 2011·Briefings in Bioinformatics·Alberto FaroConcetto Spampinato
Apr 19, 2015·Genome Research·Tallulah AndrewsCaleb Webber

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Datasets Mentioned

BETA
GSE7873

Software Mentioned

Ensembl
bl2seq
Loess
BLAST
+ MAS5
DAVID
Affymetrix
Bioconductor
MAS5
MKtest

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