Arabidopsis - Rice: Will colinearity allow gene prediction across the eudicot-monocot divide?

With the genomic sequencing of Arabidopsis nearing completion and rice sequ encing very much in its infancy, a key question is whether we can exploit t he Arabidopsis sequence to identify candidate genes for traits in cereal cr ops using a map-based approach. This requires the existence of colinearity between the Arabidopsis and cereal genomes, represented by rice, which is r eadily detectable using currently available resources, that is, Arabidopsis genomic sequence, rice ESTs, and genetic and physical maps. A detailed stu dy of the colinearity remaining between two small regions of Arabidopsis ch romosome 1 and rice suggests that at least in these regions of the Arabidop sis genome, conservation of gene orders with rice has been eroded to the po int that it is no longer identifiable using comparative mapping. Although o ur analysis does not preclude that tracts of colinear gene orders may be id entified using sequence comparisons or may exist in other regions of the ri ce and Arabidopsis genomes, it is unlikely that the extent of colinearity w ill be sufficient to allow map-based cross-species gene prediction and isol ation. Our research also highlights the difficulties encountered in identif ying orthologs using BLAST searches in incomplete sequence databases. This complicates the interpretation of comparative data among highly divergent s pecies and limits the exploitation of Arabidopsis sequence in monocot studi es.