Compositional Gradients in Gramineae Genes
- Gane Ka-Shu Wong1,2,3,5,
- Jun Wang1,2,4,
- Lin Tao1,2,
- Jun Tan1,2,
- JianGuo Zhang2,
- Douglas A. Passey3, and
- Jun Yu1,2,3
- 1Hangzhou Genomics Institute, Institute of Bioinformatics of Zhejiang University, Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China; 2Beijing Genomics Institute, Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China; 3University of Washington Genome Center, Department of Medicine, Seattle, Washington 98195, USA 4College of Life Sciences, Peking University, Beijing 100871, China.
Abstract
In this study, we describe a property of Gramineae genes, and perhaps all monocot genes, that is not observed in eudicot genes. Along the direction of transcription, beginning at the junction of the 5′-UTR and the coding region, there are gradients in GC content, codon usage, and amino-acid usage. The magnitudes of these gradients are large enough to hinder the annotation of the rice genome and to confound the detection of protein homologies across the monocot–eudicot divide.
Footnotes
-
↵5 Corresponding author.
-
E-MAIL gksw{at}u.washington.edu; FAX (206) 685-7344.
-
Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.189102.
-
- Received February 14, 2002.
- Accepted April 3, 2002.
- Cold Spring Harbor Laboratory Press
