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The evolution of duplicate gene expression in mammalian organs
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance.
Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance.
2017 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 9, p. 1461-1474Article in journal (Refereed) Published
Abstract [en]

Gene duplications generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptive evolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes in mammals were until recently limited by the lack of appropriate comparative data. Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe dynamic changes in tissue expression preference of paralogs with different duplication ages, suggesting differential contribution of paralogs to specific organ functions during vertebrate evolution. Specifically, we show that paralogs that emerged in the common ancestor of bony vertebrates are enriched for genes with brain-specific expression and provide evidence for differential forces underlying the preferential emergence of young testis-and liver-specific expressed genes. Further analyses uncovered that the overall spatial expression profiles of gene families tend to be conserved, with several exceptions of pronounced tissue specificity shifts among lineage-specific gene family expansions. Finally, we trace new lineage-specific genes that may have contributed to the specific biology of mammalian organs, including the little-studied placenta. Overall, our study provides novel and taxonomically broad evidence for the differential contribution of duplicate genes to tissue-specific transcriptomes and for their importance for the phenotypic evolution of vertebrates.

Place, publisher, year, edition, pages
2017. Vol. 27, no 9, p. 1461-1474
National Category
Biochemistry and Molecular Biology Agricultural Biotechnology Microbiology Genetics and Breeding in Agricultural Sciences
Identifiers
URN: urn:nbn:se:uu:diva-334918DOI: 10.1101/gr.215566.116ISI: 000408790600001OAI: oai:DiVA.org:uu-334918DiVA, id: diva2:1161198
Funder
EU, European Research Council, 242597
Available from: 2017-11-29 Created: 2017-11-29 Last updated: 2017-11-29Bibliographically approved

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Guschanski, Katerina

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