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A lineage-specific centromere retrotransposon in Oryza brachyantha.
Plant J. 2009 Dec; 60(5):820-31.PJ

Abstract

Most eukaryotic centromeres contain large quantities of repetitive DNA, such as satellite repeats and retrotransposons. Unlike most transposons in plant genomes, the centromeric retrotransposon (CR) family is conserved over long evolutionary periods among a majority of the grass species. CR elements are highly concentrated in centromeres, and are likely to play a role in centromere function. In order to study centromere evolution in the Oryza (rice) genus, we sequenced the orthologous region to centromere 8 of Oryza sativa from a related species, Oryza brachyantha. We found that O. brachyantha does not have the canonical CRR (CR of rice) found in the centromeres of all other Oryza species. Instead, a new Ty3-gypsy (Metaviridae) retroelement (FRetro3) was found to colonize the centromeres of this species. This retroelement is found in high copy numbers in the O. brachyantha genome, but not in other Oryza genomes, and based on the dating of long terminal repeats (LTRs) of FRetro3 it was amplified in the genome in the last few million years. Interestingly, there is a high level of removal of FRetro3 based on solo-LTRs to full-length elements, and this rapid turnover may have played a role in the replacement of the canonical CRR with the new element by active deletion. Comparison with previously described ChIP cloning data revealed that FRetro3 is found in CENH3-associated chromatin sequences. Thus, within a single lineage of the Oryza genus, the canonical component of grass centromeres has been replaced with a new retrotransposon that has all the hallmarks of a centromeric retroelement.

Authors+Show Affiliations

Molecular and Evolutionary Genetics, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

19702667

Citation

Gao, Dongying, et al. "A Lineage-specific Centromere Retrotransposon in Oryza Brachyantha." The Plant Journal : for Cell and Molecular Biology, vol. 60, no. 5, 2009, pp. 820-31.
Gao D, Gill N, Kim HR, et al. A lineage-specific centromere retrotransposon in Oryza brachyantha. Plant J. 2009;60(5):820-31.
Gao, D., Gill, N., Kim, H. R., Walling, J. G., Zhang, W., Fan, C., Yu, Y., Ma, J., SanMiguel, P., Jiang, N., Cheng, Z., Wing, R. A., Jiang, J., & Jackson, S. A. (2009). A lineage-specific centromere retrotransposon in Oryza brachyantha. The Plant Journal : for Cell and Molecular Biology, 60(5), 820-31. https://doi.org/10.1111/j.1365-313X.2009.04005.x
Gao D, et al. A Lineage-specific Centromere Retrotransposon in Oryza Brachyantha. Plant J. 2009;60(5):820-31. PubMed PMID: 19702667.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A lineage-specific centromere retrotransposon in Oryza brachyantha. AU - Gao,Dongying, AU - Gill,Navdeep, AU - Kim,Hye-Ran, AU - Walling,Jason G, AU - Zhang,Wenli, AU - Fan,Chuanzhu, AU - Yu,Yeisoo, AU - Ma,Jianxin, AU - SanMiguel,Phillip, AU - Jiang,Ning, AU - Cheng,Zhukuan, AU - Wing,Rod A, AU - Jiang,Jiming, AU - Jackson,Scott A, Y1 - 2009/08/21/ PY - 2009/8/26/entrez PY - 2009/8/26/pubmed PY - 2010/2/25/medline SP - 820 EP - 31 JF - The Plant journal : for cell and molecular biology JO - Plant J VL - 60 IS - 5 N2 - Most eukaryotic centromeres contain large quantities of repetitive DNA, such as satellite repeats and retrotransposons. Unlike most transposons in plant genomes, the centromeric retrotransposon (CR) family is conserved over long evolutionary periods among a majority of the grass species. CR elements are highly concentrated in centromeres, and are likely to play a role in centromere function. In order to study centromere evolution in the Oryza (rice) genus, we sequenced the orthologous region to centromere 8 of Oryza sativa from a related species, Oryza brachyantha. We found that O. brachyantha does not have the canonical CRR (CR of rice) found in the centromeres of all other Oryza species. Instead, a new Ty3-gypsy (Metaviridae) retroelement (FRetro3) was found to colonize the centromeres of this species. This retroelement is found in high copy numbers in the O. brachyantha genome, but not in other Oryza genomes, and based on the dating of long terminal repeats (LTRs) of FRetro3 it was amplified in the genome in the last few million years. Interestingly, there is a high level of removal of FRetro3 based on solo-LTRs to full-length elements, and this rapid turnover may have played a role in the replacement of the canonical CRR with the new element by active deletion. Comparison with previously described ChIP cloning data revealed that FRetro3 is found in CENH3-associated chromatin sequences. Thus, within a single lineage of the Oryza genus, the canonical component of grass centromeres has been replaced with a new retrotransposon that has all the hallmarks of a centromeric retroelement. SN - 1365-313X UR - https://www.unboundmedicine.com/medline/citation/19702667/A_lineage_specific_centromere_retrotransposon_in_Oryza_brachyantha_ L2 - https://doi.org/10.1111/j.1365-313X.2009.04005.x DB - PRIME DP - Unbound Medicine ER -