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Bioinformatics Advance Access published online on March 16, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp147
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome

Xiangfeng Wang 1,{dagger}, Zhihui Yu 2,{dagger}, Xiaozeng Yang 2, Xing-Wang Deng 1 and Lei Li 2,*

1Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, CT 06520, USA
2Department of Biology, University of Virginia, Charlottesville, VA 22904, USA

*To whom correspondence should be addressed. Dr. Lei Li, E-mail: ll4jn{at}virginia.edu


  Abstract

The unprecedented complexity of the transcriptomic data obtained in recent years creates opportunities for new genomic studies aimed at interpolating regulatory code of gene expression and tracing ge-nome evolution. We report here the identification and characteriza-tion of a set of 851 intergenic loci that represent transcribed gene fragments (TGFs) ectopically duplicated from 1,030 non-transposable element (non-TE) donor genes in the rice genome. We analyzed the genomic context of the TGFs and donor genes. We show that the TGFs have adopted transcriptional orientation and pattern independent of the donor genes. We further show that TGFs have undergone relaxed purifying selection, consistent with their being pseudogenized. We found that the donor genes, which are biased toward certain molecular functions, exhibit an accelerated evolution rate comparing to the genome average. Our results dem-onstrated a large number of actively transcribed gene fragments in the rice genome and shed light on the origin, mode of action and function of the TGFs.

Associate Editor: Dr. Alex Bateman

{dagger}These authors contributed equally to this work.

Received on December 18, 2008; revised on March 5, 2009; accepted on March 11, 2009

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