A Transcript Perspective on Evolution

  • Yann Christinat
  • Bernard M. E. Moret
Conference paper

DOI: 10.1007/978-3-642-30191-9_5

Part of the Lecture Notes in Computer Science book series (LNCS, volume 7292)
Cite this paper as:
Christinat Y., Moret B.M.E. (2012) A Transcript Perspective on Evolution. In: Bleris L., Măndoiu I., Schwartz R., Wang J. (eds) Bioinformatics Research and Applications. ISBRA 2012. Lecture Notes in Computer Science, vol 7292. Springer, Berlin, Heidelberg

Abstract

Alternative splicing is now recognized as a major mechanism for transcriptome and proteome diversity in higher eukaryotes. Yet, its evolution is poorly understood. Most studies focus on the evolution of exons and introns at the gene level, while only few consider the evolution of transcripts.

In this paper, we present a framework for transcript phylogenies where ancestral transcripts evolve along the gene tree by gains, losses, and mutation. We demonstrate the usefulness of our method on a set of 805 genes and two different topics. First, we improve a method for transcriptome reconstruction from ESTs (ASPic), then we study the evolution of function in transcripts. The use of transcript phylogenies allows us to double the specificity of ASPic, whereas results on the functional study reveal that conserved transcripts are more likely to share protein domains than functional sites. These studies validate our framework for the study of evolution in large collections of organisms from the perspective of transcripts; we developed and provide a new tool, TrEvoR, for this purpose.

Keywords

alternative splicing transcript evolution phylogeny protein domain transcriptome reconstruction 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Yann Christinat
    • 1
  • Bernard M. E. Moret
    • 1
  1. 1.Laboratory of Computational Biology and BioinformaticsEPFLLausanneSwitzerland

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