Molecular and Cytological Characterization of Centromeric Retrotransposons in a Wild Relative of Rice, Oryza granulata
- 129 Downloads
Centromeric retrotransposons (CRs) are important component of the functional centromeres of rice chromosomes. To track the evolution of the CR elements in genus Oryza, we sequenced the orthologous region of the rice centromere 8 (Cen8) in O. granulata and analyzed transposons in this region. A total of 12 bacterial artificial chromosomes (BACs) that span the centromeric region in O. granulata were sequenced. The O. granulate centromeric sequences are composed of as much as 85% of transposons, higher than any other reported eukaryotic centromeres. Ten novel LTR retrotransposon families were identified but a single retrotransposon, Gran3, constitutes nearly 43% of the centromeric sequences. Integration times of complete LTR retrotransposons indicate that the centromeric region had a massive insertion of LTR retrotransposons within 4.5 million year (Myr), which indicates a recent expansion of the centromere in O. granulata after the radiation of the Oryza genus. Two retrotransposon families, OGRetro7 and OGRetro9, show sequence similarity with the canonical CRs from rice and maize. Both OGRetro7 and OGRetro9 are highly concentrated in the centromeres of O. granulata chromosomes. Furthermore, strong hybridization signals were detected in all Oryza species but in O. brachyantha with the OGRetro7 and OGRetro9 probes. Characterization of the centromeric retrotransposons in O. granulata confirms the conservation of the CRs in the Oryza genus and provides a resource for comparative analysis of centromeres and centromere evolution among the Oryza genus and other genomes.
KeywordsCentromere 8 Evolution Centromeric retrotransposon Oryza granulata Comparative genomics
We thank Dr. Ning Jiang for providing us the unpublished rice transposon database. This research was founded by the National Science Foundation DBI 0603927 (JJ, SAJ and RAW) and 0424833 (SAJ).
- Ammiraju JS, Zuccolo A, Yu Y, Song X, Piegu B, Chevalier F, Walling JG, Ma J, Talag J, Brar DS, SanMiguel PJ, Jiang N, Jackson SA, Panaud O, Wing RA (2007) Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J 52:342–351PubMedCrossRefGoogle Scholar
- Ammiraju JS, Lu F, Sanyal A, Yu Y, Song X, Jiang N, Pontaroli AC, Rambo T, Currie J, Collura K, Talag J, Fan C, Goicoechea JL, Zuccolo A, Chen J, Bennetzen JL, Chen M, Jackson S, Wing RA (2008) Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell 20:3191–209PubMedCrossRefGoogle Scholar
- Ge S, Sang T, Lu BR, Hong DY (1999) Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc Natl Acad Sci U S A 96:14400–14405Google Scholar
- Kim H, Hurwitz B, Yu Y, Collura K, Gill N, SanMiguel P, Mullikin JC, Maher C, Nelson W, Wissotski M, Braidotti M, Kudrna D, Goicoechea JL, Stein L, Ware D, Jackson SA, Soderlund C, Wing RA (2008) Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biol 9:R45PubMedCrossRefGoogle Scholar
- Piegu B, Guyot R, Picault N, Roulin A, Saniyal A, Kim H, Collura K, Brar DS, Jackson S, Wing RA, Panaud O (2006) Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome Res 16:1262–1269PubMedCrossRefGoogle Scholar
- Sanyal A, Ammiraju JS, Lu F, Yu Y, Rambo T, Currie J, Kollura K, Kim HR, Chen J, Ma J, San Miguel P, Mingsheng C, Wing RA, Jackson SA (2010) Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum. Mol Biol Evol 27:2487–2506PubMedCrossRefGoogle Scholar
- Yan H, Ito H, Nobuta K, Ouyang S, Jin W, Tian S, Lu C, Venu RC, Wang GL, Green PJ, Wing RA, Buell CR, Meyers BC (2006) Jiang J (2006) Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell 18:2123–33PubMedCrossRefGoogle Scholar