Journal article

Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach

Ajna S Rivera, M Sabrina Pankey, David C Plachetzki, Carlos Villacorta, Anna E Syme, Jeanne M Serb, Angela R Omilian, Todd H Oakley



BACKGROUND: Duplication and divergence of genes and genetic networks is hypothesized to be a major driver of the evolution of complexity and novel features. Here, we examine the history of genes and genetic networks in the context of eye evolution by using new approaches to understand patterns of gene duplication during the evolution of metazoan genomes. We hypothesize that 1) genes involved in eye development and phototransduction have duplicated and are retained at higher rates in animal clades that possess more distinct types of optical design; and 2) genes with functional relationships were duplicated and lost together, thereby preserving genetic networks. To test these hypotheses, we ex..

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Awarded by University of California, Lawrence Livermore National Laboratory

Awarded by Lawrence Berkeley National Laboratory

Awarded by Los Alamos National Laboratory

Funding Acknowledgements

The Capitella sp. I, Helbodella robusta, Fugu rubripes, and Lottia gigantea genome data were produced by the US Department of Energy Joint Genome Institute collaboration with the user community. The Daphnia pulex sequencing and portions of the analyses were performed at the DOE Joint Genome Institute under the auspices of the U.S. Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under Contract No. DE-AC0205CH11231, Los Alamos National Laboratory under Contract No. W-7405ENG- 36 and in collaboration with the Daphnia Genomics Consortium ( DGC) http://daphnia. cgb. indiana. edu. Additional analyses were performed by wFleaBase, developed at the Genome Informatics Lab of Indiana University with support to Don Gilbert from the National Science Foundation and the National Institutes of Health. Coordination infrastructure for the DGC is provided by The Center for Genomics and Bioinformatics at Indiana University, which is supported in part by the METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc. Our work benefits from, and contributes to the Daphnia Genomics Consortium. Thanks to Gavin Wu of the UCSB Statlab for writing the correlation script in R. Thanks also to H. Robertson and others for performing detailed annotation of opsin genes in Daphnia, which will be described elsewhere.