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Vol. 12, Issue 6, 851-856, June 2002

Compositional Gradients in Gramineae Genes

Gane Ka-Shu Wong,1,2,3,5 Jun Wang,1,2,4 Lin Tao,1,2 Jun Tan,1,2 JianGuo Zhang,2 Douglas A. Passey,3 and Jun Yu1,2,3

1 Hangzhou Genomics Institute, Institute of Bioinformatics of Zhejiang University, Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China; 2 Beijing Genomics Institute, Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China; 3 University of Washington Genome Center, Department of Medicine, Seattle, Washington 98195, USA 4 College of Life Sciences, Peking University, Beijing 100871, China.

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.

5 Corresponding author.

12:851-856 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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