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

item ZHANG, S
item Gu, Yong
item SINGH, J
item BRAR, D
item NING, J
item LEMAUX, P

Submitted to: Plant Molecular Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/26/2007
Publication Date: 5/30/2007
Citation: Zhang, S., Gu, Y., Singh, J., Coleman-Derr, D., Brar, D., Jiang, N., Lemaux, P. 2007. New Insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification. Plant Molecular Biology. 64:589-600.

Interpretive Summary: Rice is one of the most important cereal crops and feeds over half the world’s population. To increase yield and quality of rice production, it is of importance to exploit the genetic diversity of Oryza species. The Oryza genus includes 21 wild species and encompasses ten different genome types. Comparative sequence analysis of genomic regions from different genomes will not only provides new means to explore allelic variation in Oryza species, but also offer insights into evolution of the Oryza genomes. In this study, the authors sequenced a large genomic region from a wild rice species, O. brachyantha, which has smallest genome in Oryza genus and grows mainly in Central Africa. The sequenced region contained three DREB1 genes, representing one of the most important genetic loci that are known to play a critical role in stress tolerance. The results indicate that size difference between the two rice genomes are mainly due to the differential amplification of transposable elements. In addition, expression analysis revealed that the DREB1 genes identified in O. brachyantha likely play the same roles in stress tolerance as those found in cultivated rice.

Technical Abstract: A genomic region (~247kb) from an FF genome, wild Oryza species, O. brachyantha L., was sequenced and compared to the orthologous region (~450 kb) from AA genome rice, O. sativa L. ssp japonica ¬ the first such comparison reported between cultivated Oryza and a distantly related wild species. Among the 38 genes identified in this region in O. brachyantha, 37 are colinear with orthologous genes in japonica; with eight inverted due to a single large inversion event. Nucleotide sequence identities of orthologous genes range from 60¬90%; analyses of nucleotide substitutions in coding regions suggest the two genomes diverged ~10 mya. Although intergenic regions are generally more diverged, conserved segments of uncharacterized functionality are present in some regions. Comparison of transposable elements (TEs) in this region revealed that in O. brachyantha insertion density of DNA TEs (Class II) is comparable to that of japonica; however, density of RNA TEs (Class I) is dramatically lower (47%) and there are markedly fewer TEs that are > 1 kb. These differences in TEs, particularly RNA TEs, explain the major size variation between the genomes of sativa and brachyantha, the Oryza species with the smallest genome. Comparative analyses of TEs present in BAC end sequences from six wild and one cultivated Oryza species were consistent with these results. The genomic fraction represented by RNA TEs in O. sativa is more than two times that of O. brachyantha; there is a four-fold variation in the genomic fraction of RNA TEs among the species studied. RT-PCR analyses of three DREB1 genes, ObDREB1a, ObDREB1b, and ObDREB1m, in the sequenced region showed that orthologous genes from O. brachyantha and O. sativa share a similar pattern of expression in response to cold stress. Demonstration of expression of ObDREB1m from O. brachyantha implies potential function for this pseudogene.