Comparative physical mapping between O. sativa (AA genome type) and O. punctata (BB genome type)
HyeRan Kim 1, Phillip San Miguel 2, William Nelson 1, Kristi Collura 1, Marina Wissotski 1, Jason G Walling 2, Jun Pyo Kim 1, Scott A Jackson 2, Carol Soderlund 1 and Rod A. Wing 1*
1 University of Arizona
2 Purdue University
* To whom correspondence should be addressed. E-mail: rwing{at}ag.arizona.edu.
Submitted on November 22, 2006
Revised on January 16, 2007
Accepted on 9 February 2007
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Abstract |
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A comparative physical map of the AA genome (O. sativa) and the BB genome (O. punctata) was constructed by aligning a physical map 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 two species was determined by calculating a ratio of BES alignments. The alignment result suggests more divergence of intergenic and repeat regions in comparison to gene rich regions. Further, this characteristic enabled localization of heterochromatic and 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 map covered 98% of O. sativa genome sequence. The genome size of 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 larger than 500 Kb were similar, suggesting that most of contractions/expansions contributing to the genome size difference between the two species are small, thus preserving the macro-colinearity between these species which diverged approximately two million years ago.
Key Words:
BES alignment, Oryza. punctata, SNaPshot fingerprinting, SyMAP, comparative physical map
