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Comparative analysis of Cassandra TRIMs in three Brassicaceae genomes

Published online by Cambridge University Press:  16 July 2014

Perumal Sampath  and
Tae-Jin Yang
Perumal Sampath
Affiliation:
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul151-921, Republic of Korea
Tae-Jin Yang*
Affiliation:
Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul151-921, Republic of Korea
*
* Corresponding author. E-mail: [email protected]
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Abstract

Terminal-repeat retrotransposon in miniature (TRIM) elements are a miniature form of retrotransposons and play an important role in genome organization. The Cassandra TRIM family has been identified in over 50 plant species, including both monocots and dicots. Cassandra elements carry an independently transcribed 5S RNA sequence in their terminal repeat regions, which is unique compared with other TRIM families. Although the existence of Cassandra elements has been documented in many plants, much work remains to characterize Cassandra family members and elucidate their distribution. In this study, we comparatively analysed the Cassandra family members in the Brassica oleracea, B. rapa and Arabidopsis thaliana genomes. A total of 602, 451 and 173 members, of which 130, 60 and 9 were relatively intact, were identified from the B. oleracea, B. rapa and A. thaliana genomes, respectively. Most of the Cassandra elements (1120/1226) were found in intergenic spaces, but 106 elements were inserted in genic regions such as introns, exons and untranslated regions. Our comparative analysis of the Cassandra family members in A. thaliana, B. rapa and B. oleracea reveals that some Cassandra elements have been commonly retained during the last 20 million years in three species and some elements have been uniquely evolved in Brassica species. This study promotes our understanding of the role and utility of Cassandra elements in the evolution of the Brassicaceae family.

Keywords

Arabidopsis thalianaBrassicaBrassica oleraceaBrassica rapaCassandraTRIMs
Type
Research Article
Information
Plant Genetic Resources , Volume 12 , Issue S1: Special issue on the 3rd International Symposium on “Genomics of Plant Genetic Resources” , July 2014 , pp. S146 - S150
Copyright
Copyright © NIAB 2014 

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