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Phylostratigraphic analyses of mouse tissue transcriptomes and comparative genomics of orphan genes


Neme Garrido,  Rafik Tarek
Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Neme Garrido, R. T. (2011). Phylostratigraphic analyses of mouse tissue transcriptomes and comparative genomics of orphan genes. Master Thesis, Georg August University, Göttingen.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0010-0C27-B
Assuming that the genomes of the modern organisms keep record of their evolutionary history, genomic phylostratigraphy was used to estimate the period of emergence of the genes in an organism, depending only on a phylogenetic tree and genomic information from the organisms constituting the tree. A mouse phylostratigraphic map was constructed and associated with expression data from oligonucleotide arrays of 55 tissues and organs as an approach to understand the functional shifts related to processes of gene emergence across the evolutionary history. Tissue specific genes appear to increase after the emergence and specialization of the tissues and organ system. Ubiquitously expressed genes show dynamics almost opposite to the diversification of functions in tissues. The testes are the tissue with the highest number of tissue specific genes, and show enhanced rates of gene acquisition over time, confirming a central role from this tissue in gene emergence. Mouse orphan genes were analyzed at the transcript level according to different models of gene emergence. A large number of long noncoding RNAs was found to be part of this orphan gene repertoire, and an important number of orphans were found to be near regions of high transcription. The transcriptional activity of specific regions of the genome might play an important role in future models of gene emergence.