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Conserved developmental transcriptomes in evolutionarily divergent species

Anup Parikh12, Edward Roshan Miranda13, Mariko Katoh-Kurasawa1, Danny Fuller4, Gregor Rot5, Lan Zagar5, Tomaz Curk5, Richard Sucgang6, Rui Chen1, Blaz Zupan15, William F Loomis4, Adam Kuspa136 and Gad Shaulsky123*

  • * Corresponding author: Gad Shaulsky gadi@bcm.edu

  • † Equal contributors

Author Affiliations

1 Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA

2 Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA

3 Graduate Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA

4 Section of Cell and Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA

5 Faculty of Computer and Information Science, University of Ljubljana, Trzaska cesta 25, SI-1001 Ljubljana, Slovenia

6 Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA

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Genome Biology 2010, 11:R35  doi:10.1186/gb-2010-11-3-r35

Published: 17 March 2010

Abstract

Background

Evolutionarily divergent organisms often share developmental anatomies despite vast differences between their genome sequences. The social amoebae Dictyostelium discoideum and Dictyostelium purpureum have similar developmental morphologies although their genomes are as divergent as those of man and jawed fish.

Results

Here we show that the anatomical similarities are accompanied by extensive transcriptome conservation. Using RNA sequencing we compared the abundance and developmental regulation of all the transcripts in the two species. In both species, most genes are developmentally regulated and the greatest expression changes occur during the transition from unicellularity to multicellularity. The developmental regulation of transcription is highly conserved between orthologs in the two species. In addition to timing of expression, the level of mRNA production is also conserved between orthologs and is consistent with the intuitive notion that transcript abundance correlates with the amount of protein required. Furthermore, the conservation of transcriptomes extends to cell-type specific expression.

Conclusions

These findings suggest that developmental programs are remarkably conserved at the transcriptome level, considering the great evolutionary distance between the genomes. Moreover, this transcriptional conservation may be responsible for the similar developmental anatomies of Dictyostelium discoideum and Dictyostelium purpureum.