Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba

PLoS Genetics
Rebekah L RogersKevin R Thornton

Abstract

One common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes. Here, we use genome wide RNA-seq data from a population sample of Drosophila yakuba to test this 'gene dosage' hypothesis. We observe little evidence of expression changes in response to whole transcript duplication capturing 5' and 3' UTRs. Among whole gene duplications, we observe evidence that dosage sharing across copies is likely to be common. The lack of expression changes after whole gene duplication suggests that the majority of genes are subject to tight regulatory control and therefore not sensitive to changes in gene copy number. Rather, we observe changes in expression level due to both shuffling of regulatory elements and the creation of chimeric structures via tandem duplication. Additionally, we observe 30 de novo gene structures arising from tandem duplications, 23 of which form with expression in the testes. Thus, the value of tandem duplications is likely to be more intricate than simple changes in gene dosage. The common regulatory effects from chimeric gene formation after tandem duplication may explain their contribution to genom...Continue Reading

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Citations

Sep 30, 2017·Molecular Biology and Evolution·Luís Baudouin-GonzalezKohtaro Tanaka
Jan 29, 2019·Genome Biology and Evolution·Juan LiChau-Ti Ting
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Jun 23, 2021·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Duck-Hyun KimJae-Seong Lee
Jan 1, 2022·Nature Ecology & Evolution·Ben-Yang Liao

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Datasets Mentioned

BETA
PRJNA269314
PRJNA196536
GE24588

Methods Mentioned

BETA
RNA-seq
RNA seq
Illumina sequencing
transgenic
RNAseq
dissection
PCR
Assay

Software Mentioned

PacBio
Cufflinks suite
bcftools
ExpressionHMM
Cufflinks
HMM
Bowtie2
Cuffdiff
Tophat

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