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Properties of Sequence Conservation in Upstream Regulatory and Protein Coding Sequences among Paralogs in Arabidopsis thaliana

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Comparative Genomics (RECOMB-CG 2009)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5817))

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Abstract

Whole genome duplication (WGD) has catalyzed the formation of new species, genes with novel functions, altered expression patterns, complexified signaling pathways and has provided organisms a level of genetic robustness. We studied the long-term evolution and interrelationships of 5’ upstream regulatory sequences (URSs), protein coding sequences (CDSs) and expression correlations (EC) of duplicated gene pairs in Arabidopsis. Three distinct methods revealed significant evolutionary conservation between paralogous URSs and were highly correlated with microarray-based expression correlation of the respective gene pairs. Positional information on exact matches between sequences unveiled the contribution of micro-chromosomal rearrangements on expression divergence. A three-way rank analysis of URS similarity, CDS divergence and EC uncovered specific gene functional biases. Transcription factor activity was associated with gene pairs exhibiting conserved URSs and divergent CDSs, whereas a broad array of metabolic enzymes was found to be associated with gene pairs showing diverged URSs but conserved CDSs.

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Authors and Affiliations

  1. Institute for Genetics, University of Cologne, Zülpicher Str. 47, 50674, Cologne, Germany

    Dale N. Richardson & Thomas Wiehe

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  1. Dale N. Richardson
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  2. Thomas Wiehe
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Editors and Affiliations

  1. European Institute of oncology, IFOM-IEO Campus,, Via Adamello, 16, 20139, Milan, Italy

    Francesca D. Ciccarelli

  2. Rényi Institute, Hungarian Academy of Sciences, Reáltanoda utca 13-15, 1053, Budapest, Hungary

    István Miklós

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Richardson, D.N., Wiehe, T. (2009). Properties of Sequence Conservation in Upstream Regulatory and Protein Coding Sequences among Paralogs in Arabidopsis thaliana . In: Ciccarelli, F.D., Miklós, I. (eds) Comparative Genomics. RECOMB-CG 2009. Lecture Notes in Computer Science(), vol 5817. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04744-2_18

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  • DOI: https://doi.org/10.1007/978-3-642-04744-2_18

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-04743-5

  • Online ISBN: 978-3-642-04744-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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