What to compare and how: Comparative transcriptomics for Evo-Devo
Julien Roux 1,2,3, Marta Rosikiewicz 1,2 and Marc Robinson-Rechavi 1,2,*
Article first published online: 10 APR 2015
© 2015 Wiley Periodicals, Inc.
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
Special Issue: Genomics and Evo-Devo
Volume 324, Issue 4, pages 372–382, June 15, 2015
Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of modern transcriptomics brings promising improvements, allowing us to estimate the overall impact and molecular mechanisms of convergence, constraint or innovation in anatomy and development. But it also presents major challenges, including the computational definitions of anatomical homology and of organ function, the criteria for the comparison of developmental stages, the annotation of transcriptomics data to proper anatomical and developmental terms, and the statistical methods to compare transcriptomic data between species to highlight significant conservation or changes. In this article, we review these challenges, and the ongoing efforts to address them, which are emerging from bioinformatics work on ontologies, evolutionary statistics, and data curation, with a focus on their implementation in the context of the development of our database Bgee (http://bgee.org). J. Exp. Zool. (Mol. Dev. Evol.) 324B: 372–382, 2015. © 2015 Wiley Periodicals, Inc.
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