Extensive shuffling of gene order in genomes of grass family

Jinsheng Lai¹, Zuzana Swigonova¹, Jianxin Ma², Jeffrey Bennetzen² and Joachim Messing¹

¹Waksman Institute, Rutgers University, Piscataway, NJ; ²Department of Genetics, University of Georgia, Athens, GA

To provide additional insights into the structure and evolution of plant genomes, we isolated and sequenced 24 BAC clones, representing five orthologous region from maize and sorghum and compared them with the orthologous regions from rice. In these regions (more than 4 Mb in length), we have identified putative 212 genes. However, we find that at least 25% of the genes differ in presence/absence in otherwise colinear regions. We further find that most of the non-colinear genes, identified within the five regions in maize and sorghum, are indeed present in non-orthologous positions of the rice genome. They do not cluster in any chromosomal region but appear randomly distributed throughout the rice genome. Several genes were found to be colinear only between maize and sorghum. In contrast to the non-colinear genes, the colinear genes can be determined by a comparison of any two distantly-related genomes (rice-sorghum, or rice-maize). Although there have been many gene losses during the maize diploidization processes from both subgenomes, each colinear gene can be found on at least one of the two subgenomes. We hypothesize that genes in grass genomes can move around the genome as small translocations, often involving only a single gene. Such a dynamic nature of the grass genomes could provide exceptional potential for the evolution of new genetic functions.