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New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification

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Abstract

An ∼247-kb genomic region from FF genome of wild rice Oryza brachyantha, possessing the smallest Oryza genome, was compared to the orthologous ∼450-kb region from AA genome, O. sativa L. ssp. japonica. 37 of 38 genes in the orthologous regions are shared between japonica and O. brachyantha. Analyses of nucleotide substitution in coding regions suggest the two genomes diverged ∼10 million years ago. Comparisons of transposable elements (TEs) reveal that the density of DNA TEs in O. brachyantha is comparable to O. sativa; however, the density of RNA TEs is dramatically lower. The genomic fraction of RNA TEs in japonica is two times greater than in O. brachyantha. Differences, particularly in RNA TEs, in this region and in BAC end sequences from five wild and two cultivated Oryza species explain major genome size differences between sativa and brachyantha. Gene expression analyses of three ObDREB1 genes in the sequenced region indicate orthologous genes retain similar expression patterns following cold stress. Our results demonstrate that size and number of RNA TEs play a major role in genomic differentiation and evolution in Oryza. Additionally, distantly related O. brachyantha shares colinearity with O. sativa, offering opportunities to use comparative genomics to explore the genetic diversity of wild species to improve cultivated rice.

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Abbreviations

EST:

Expressed sequence tag

mya:

Million years ago

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Acknowledgements

The authors thank Zhirong Bao (University of Washington) and Ling Meng (University of California, Berkeley) for valuable discussions and Gerald R. Lazo from USDA-ARS, Western Regional Research Center for bioinformatics assistance.

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Authors and Affiliations

  1. Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA

    Shibo Zhang, Jaswinder Singh & Peggy G. Lemaux

  2. Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, Albany, CA, 94710, USA

    Yong Qiang Gu & Devin Coleman-Derr

  3. International Rice Research Institute, P.O. Box 933, Manila, Philippines

    Darshan S. Brar

  4. Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA

    Ning Jiang

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  1. Shibo Zhang
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  2. Yong Qiang Gu
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  3. Jaswinder Singh
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  5. Darshan S. Brar
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  7. Peggy G. Lemaux
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Correspondence to Yong Qiang Gu or Peggy G. Lemaux.

Additional information

Data deposition: Sequence data from this article were deposited with GenBank Library under accession number DQ810282.

Shibo Zhang and Yong Qiang Gu contributed equally to the work

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Zhang, S., Gu, Y.Q., Singh, J. et al. New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification. Plant Mol Biol 64, 589–600 (2007). https://doi.org/10.1007/s11103-007-9178-3

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