Title

A Lineage-specific Centromere Retrotransposon in Oryza brachyantha

Authors

Dongying Gao, Purdue University
Navdeep Gill, Purdue University,Follow
Hye-Ran Kim, University of Wisconsin-Madison
Jason G. Walling, University of Wisconsin-Madison
Wenli Zhang, University of Wisconsin-Madison
Chuanzhu Fan, University of Arizona
Yeisoo Yu, Arizona Genome Institute
Jianxin Ma, Purdue University
Phillip SanMiguel, Purdue University
Ning Jiang, Michigan State University
Zhukuan Cheng, Institute of Genetics and Developmental Biology
Rod A. Wing, University of Arizona
Jiming Jiang, University of Wisconsin-Madison
Scott A. Jackson, Purdue University

Document Type

Article

Publication Date

12-2009

Publication Title

The Plant Journal

Keywords

centromere, evolution, LTR retrotransposon, genomics, Oryza

ISSN

1365-313X

Volume

60

Issue/No.

5

First Page

820

Last Page

831

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.

Comments

© 2009 Purdue University. Journal compilation © 2009 Blackwell Publishing Ltd

NSUWorks Citation

Gao, Dongying; Navdeep Gill; Hye-Ran Kim; Jason G. Walling; Wenli Zhang; Chuanzhu Fan; Yeisoo Yu; Jianxin Ma; Phillip SanMiguel; Ning Jiang; Zhukuan Cheng; Rod A. Wing; Jiming Jiang; and Scott A. Jackson. 2009. "A Lineage-specific Centromere Retrotransposon in Oryza brachyantha." The Plant Journal 60, (5): 820-831. doi:https://doi.org/10.1111/j.1365-313X.2009.04005.x.

ORCID ID

http://orcid.org/0000-0003-3746-1866

DOI

https://doi.org/10.1111/j.1365-313X.2009.04005.x