Predictions based on the rat–mouse comparative map provide mapping information on over 6000 new rat genes

Abstract

For identification of ECS ("evolutionarily conserved segments") between rat and mouse, 893 rat-mouse orthologous gene-pairs were brought together with zoo-FISH analysis. In total, 59 autosomal ECS and 4 X-chromosomal ones were detected. Combining FISH and zoo-FISH data, the segments were anchored on the rat chromosomes, providing an improved comparative map between the two species. Since chromosomal evolution is a slow process, it is reasonable to assume that the genome organization, including gene order, is essentially conserved within the ECS. In this way we assigned tentative subchromosomal map positions to 303 rat genes, for which no regional mapping information was available. Furthermore, the concept of prediction mapping was extended to unmapped rat homologs of genes, which in the mouse are situated inside or in the vicinity of an ECS. For a total of 6669 genes, we predicted a single rat chromosomal position, whereas for another 448 genes we could predict that they were located in one of two possible positions. Thus, our study has increased the number of genes for which there is positional mapping information in the rat almost fivefold.

Integration of the Rat Recombination and EST Maps in the Rat Genomic Sequence and Comparative Mapping Analysis With the Mouse Genome

“…The present study was limited to sequence homology searches between rat and mouse ESTs, as it is anticipated that the construction of mouse-human comparative maps, which is well under way (Waterston et al 2002), will provide essential links for rat-human genome relationships. With our approach, we could define 39 groups of synteny conservation between the rat and mouse genomes, and 45 contiguous conserved regions as compared to 51, 59, 49, or 39 resulting from the RH mapping of ESTs , the RH mapping of gene markers (Watanabe et al 1999), the mouse-on-rat zoo-FISH analysis of orthologous rat-mouse gene pairs (Gomez-Fabre et al 2002), and the linkage mapping of microsatellites associated to genes (Bihoreau et al 2001), respectively. The combination of these data gives a consensus of 33 segments of synteny conservation between rat and mouse.…”

RatMap--rat genome tools and data

“…This mouse–rat prediction map, called mouseGAPP, is also integrated into the RatMap database and can, optionally, be retrieved through the general RatMap query form. Since the mouse map contains about five times as many chromosomally localized genes as that of the rat, the position of more than 6000 genes could be predicted in the rat based on this study with accuracy estimated to exceed 95% (16). …”

“…Based on 893 orthologous gene pairs, a detailed comparative map between rat and mouse was put together and made available as a separate tool (16). This mouse–rat prediction map, called mouseGAPP, is also integrated into the RatMap database and can, optionally, be retrieved through the general RatMap query form.…”

Evolutionary aspects of the genomic organization of rat chromosome 10

“…Genomic cross-species comparative mapping and sequencing of vertebrates can be powerful methods in providing insight into evolutionary genome rearrangements as well as in paving the way for functional analysis and interpretation of the human genomic sequence data (Miller, 2000;Summers et al, 2001). Furthermore, the refinement of comparative maps across mammalian genomes will specify where chromosome breakage and rearrangements have taken place between species (Summers et al, 2001), and will provide the basis for exchanging genetic data between different mammalian species, including humans (Gó mez- Fabre et al, 2002). Such data exchange will lead to rapid development of the gene maps in map-poor species, and can be extended to reveal historical karyotype events, permitting the visualization of the organization of chromosome complements in extinct ancestors to present-day species.…”