Sequence analysis of a 24-kb contiguous genomic region at the Arabidopsis thaliana PFL locus on chromosome 1

Classification of Arabidopsis thaliana gene sequences: clustering of coding sequences into two groups according to codon usage improves gene prediction

While genomic sequences are accumulating, finding the location of the genes remains a major issue that can be solved only for about a half of them by homology searches. Prediction methods are thus required, but unfortunately are not fully satisfying. Most prediction methods implicitly assume a unique model for genes. This is an oversimplification as demonstrated by the possibility to group coding sequences into several classes in Escherichia coli and other genomes. As no classification existed for Arabidopsis thaliana, we classified genes according to the statistical features of their coding sequences. A clustering algorithm using a codon usage model was developed and applied to coding sequences from A. thaliana, E. coli, and a mixture of both. By using it, Arabidopsis sequences were clustered into two classes. The CU1 and CU2 classes differed essentially by the choice of pyrimidine bases at the codon silent sites: CU2 genes often use C whereas CU1 genes prefer T. This classification discriminated the Arabidopsis genes according to their expressiveness, highly expressed genes being clustered in CU2 and genes expected to have a lower expression, such as the regulatory genes, in CU1. The algorithm separated the sequences of the Escherichia-Arabidopsis mixed data set into five classes according to the species, except for one class. This mixed class contained 89 % Arabidopsis genes from CU1 and 11 % E. coli genes, mostly horizontally transferred. Interestingly, most genes encoding organelle-targeted proteins, except the photosynthetic and photoassimilatory ones, were clustered in CU1. By tailoring the GeneMark CDS prediction algorithm to the observed coding sequence classes, its quality of prediction was greatly improved. Similar improvement can be expected with other prediction systems.

Distribution of genes in the genome of Arabidopsis thaliana and its implications for the genome organization of plants

Previous work has shown that, in the large genomes of three Gramineae [rice, maize, and barley: 415, 2,500, and 5,300 megabases (Mb), respectively] most genes are clustered in long DNA segments (collectively called the "gene space") that represent a small fraction (12-24%) of nuclear DNA, cover a very narrow (0.8-1.6%) GC range, and are separated by vast expanses of gene-empty sequences. In the present work, we have analyzed the small (ca. 120 Mb) nuclear genome of Arabidopsis thaliana and shown that its organization is drastically different from that of the genomes of Gramineae. Indeed, (i) genes are distributed over about 85% of the main band of DNA in CsCl and cover an 8% GC range; (ii) ORFs are fairly evenly distributed in long (>50 kb) sequences from GenBank that amount to about 10 Mb; and (iii) the GC levels of protein-coding sequences (and of their third codon positions) are correlated with the GC levels of their flanking sequences. The different pattern of gene distribution of Arabidopsis compared with Gramineae appears to be because the genomes of the latter comprise (i) many large gene-empty regions separating gene clusters and (ii) abundant transposons in the intergenic sequences of gene clusters. Both sequences are absent or very scarce in the Arabidopsis genome. These observations provide a comparative view of angiosperm genome organization.