Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type)

Hye Ran Kim, Phillip San Miguel, William Nelson, Kristi Collura, Marina Wissotski, Jason G. Walling, Pyo Kim Jun, Scott A. Jackson, Carol Soderlund, Rod A. Wing

Research output: Contribution to journalArticle

37 Scopus citations

Abstract

A comparative physical map of the AA genome (Oryza 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 the 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 >500 kb were similar, suggesting that most of the contractions/expansions contributing to the genome size difference between the two species are small, thus preserving the macro-collinearity between these species, which diverged ∼2 million years ago.

Original languageEnglish (US)
Pages (from-to)379-390
Number of pages12
JournalGenetics
Volume176
Issue number1
DOIs
StatePublished - May 2007

ASJC Scopus subject areas

  • Genetics

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    Kim, H. R., San Miguel, P., Nelson, W., Collura, K., Wissotski, M., Walling, J. G., Jun, P. K., Jackson, S. A., Soderlund, C., & Wing, R. A. (2007). Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type). Genetics, 176(1), 379-390. https://doi.org/10.1534/genetics.106.068783