Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type)

HyeRan Kim^*^,1, Phillip San Miguel, William Nelson, Kristi Collura^*, Marina Wissotski^*, Jason G. Walling^,1, Jun Pyo Kim^*, Scott A. Jackson, Carol Soderlund and Rod A. Wing^*^,2

^* Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, Department of Horticulture, Purdue University, West Lafayette, Indiana 47907, Department of Agronomy, Purdue University, West Lafayette, Indiana 47907 and Arizona Genomics Computational Laboratory, University of Arizona, Tucson, Arizona 85721

^² Corresponding author: Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721.
E-mail: rwing{at}ag.arizona.edu

A comparative physical map of the AA genome (Oryza sativa) andthe BB genome (O. punctata) was constructed by aligning a physicalmap of O. punctata, deduced from 63,942 BAC end sequences (BESs)and 34,224 fingerprints, onto the O. sativa genome sequence.The level of conservation of each chromosome between the twospecies was determined by calculating a ratio of BES alignments.The alignment result suggests more divergence of intergenicand repeat regions in comparison to gene-rich regions. Further,this characteristic enabled localization of heterochromaticand euchromatic regions for each chromosome of both species.The alignment identified 16 locations containing expansions,contractions, inversions, and transpositions. By aligning 40%of the punctata BES on the map, 87% of the punctata FPC mapcovered 98% of the O. sativa genome sequence. The genome sizeof O. punctata was estimated to be 8% larger than that of O.sativa with individual chromosome differences of 1.5–16.5%.The sum of expansions and contractions observed in regions >500kb were similar, suggesting that most of the contractions/expansionscontributing to the genome size difference between the two speciesare small, thus preserving the macro-collinearity between thesespecies, which diverged $~$ 2 million years ago.