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Transcriptomics of developing embryos and organs: A raising tool for evo–devo
Author(s) -
Pantalacci Sophie,
Sémon Marie
Publication year - 2015
Publication title -
journal of experimental zoology part b: molecular and developmental evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.823
H-Index - 63
eISSN - 1552-5015
pISSN - 1552-5007
DOI - 10.1002/jez.b.22595
Subject(s) - evolutionary developmental biology , transcriptome , biology , expression (computer science) , rna seq , evolutionary biology , computational biology , genetics , computer science , gene , gene expression , programming language
Comparative transcriptomics has become an important tool for revisiting many evo–devo questions and exploring new ones, and its importance is likely to increase in the near future, partly because RNA‐seq data open many new possibilities. The aim of this opinion piece is twofold. In the first section, we discuss the particularities of transcriptomic studies in evo–devo, focusing mainly on RNA‐seq data. The preliminary processing steps (getting coding sequences as well as expression levels) are challenging, because many studied species do not have a sequenced genome. The next step (interpreting expression differences) is also challenging, due to several issues with interpreting expression levels in complex tissues, managing developmental stages and species heterochronies, and the problem of conceptualizing expression differences. In the second section, we discuss some past and possible future applications of transcriptomic approaches (using microarray or RNA‐seq) to three major themes in evo–devo: the evolution of the developmental toolkit, the genetic and developmental basis for phenotypic changes, and the general rules of the evolution of development. We believe that conceptual and technical tools are necessary in order to fully exploit the richness of multispecies transcriptomic time–series data. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 363–371, 2015 . © 2014 Wiley Periodicals, Inc.