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Bioinformatics Advance Access originally published online on March 16, 2009
Bioinformatics 2009 25(10):1215-1218; 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 and 2Department of Biology, University of Virginia, Charlottesville, VA 22904, USA

*To whom correspondence should be addressed.


  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 genome evolution. We report here the identification and characterization of a set of 851 intergenic loci that represent transcribed gene fragments (TGFs) ectopically duplicated from 1030 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 demonstrated a large number of actively TGFs in the rice genome and shed light on the origin, mode of action and function of the TGFs.

Contact: 114jn{at}virginia.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Alex Bateman

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

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