Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents

Gill, N., SanMiguel, P., Dhillon, B. D. S., Abernathy, B., Kim, H., Stein, L. D., Ware, D. H., Wing, R., Jackson, S. A. (December 2010) Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents. Rice, 3 (4). pp. 251-269.

URL: http://link.springer.com/article/10.1007/s12284-01...
DOI: 10.1007/s12284-010-9054-7

Abstract

Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. However, little is known about how these sequences originate, evolve and function in context of a genome. In an attempt to address this question, we performed a comparative analysis of repetitive DNA sequences in the genus Oryza, representing ~15 million years of evolution. Both Class I and Class II transposable elements, through their expansion, loss and movement in the genome, were found to influence genome size variation in this genus. We identified 38 LTRretrotransposon families that are present in 1,500 or more copies throughout Oryza, and many are preferentially amplified in specific lineages. The data presented here, besides furthering our understanding of genome organization in the genus Oryza, will aid in the assembly, annotation and analysis of genomic data, as part of the future genome sequencing projects of O. sativa wild relatives. © 2010 Springer Science + Business Media, LLC.

Item Type: Paper
Uncontrolled Keywords: Genome size variation LTR-retrotransposons Oryza Repetitive sequences Transposable elements
Subjects: organism description > plant > Oryza
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transposons
CSHL Authors:
Communities: CSHL labs > Jackson lab
CSHL labs > Stein lab
CSHL labs > Ware lab
Depositing User: CSHL Librarian
Date: December 2010
Date Deposited: 30 Sep 2011 14:42
Last Modified: 23 Feb 2017 16:46
URI: http://repository.cshl.edu/id/eprint/15421

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