Hostname: page-component-8448b6f56d-cfpbc Total loading time: 0 Render date: 2024-04-16T16:23:20.622Z Has data issue: false hasContentIssue false
  • English
  • Français

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: tjyang@snu.ac.kr
Get access Rights & Permissions [Opens in a new window]

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 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Cheng, F, Liu, S, Wu, J, Fang, L, Sun, S, Liu, B, Li, P, Hua, W and Wang, X (2011) BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biology 11: 136.Google Scholar
Johnston, JS, Pepper, AE, Hall, AE, Chen, ZJ, Hodnett, G, Drabek, J, Lopez, R and Price, HJ (2005) Evolution of genome size in Brassicaceae. Annals of Botany 95: 229–235.Google Scholar
Kalendar, R, Tanskanen, J, Chang, W, Antonius, K, Sela, H, Peleg, O and Schulman, AH (2008) Cassandra retrotransposons carry independently transcribed 5S RNA. Proceedings of the National Academy of Sciences of the United States of America 105: 5833–5838.Google Scholar
Kwon, SJ, Kim, DH, Lim, MH, Long, Y, Meng, JL, Lim, KB, Kim, JA, Kim, JS, Jin, M, Kim, HI, Ahn, SN, Wessler, SR, Yang, TJ and Park, BS (2007) Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives. Molecular Genetics and Genomics 278: 361–370.CrossRefGoogle ScholarPubMed
Lamesch, P, Berardini, TZ, Li, D, Swarbreck, D, Wilks, C, Sasidharan, R, Muller, R, Dreher, K, Alexander, DL, Garcia-Hernandez, M, Karthikeyan, AS, Lee, CH, Nelson, WD, Ploetz, L, Singh, S, Wensel, A and Huala, E (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research 40: D1202–D1210.Google Scholar
Mun, JH, Kwon, SJ, Yang, TJ, Seol, YJ, Jin, M, Kim, JA, Lim, MH, Kim, JS, Baek, S, Choi, BS, Yu, HJ, Kim, DS, Kim, N, Lim, KB, Lee, SI, Hahn, JH, Lim, YP, Bancroft, I and Park, BS (2009) Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biology 10: R111.Google Scholar
Sampath, P, Lee, S-C, Lee, J, Izzah, NK, Choi, B-S, Jin, M, Park, B-S and Yang, T-J (2013) Characterization of a new high copy Stowaway family MITE, BRAMI-1 in Brassica genome. BMC Plant Biology 13: 56.CrossRefGoogle ScholarPubMed
Tamura, K, Peterson, D, Peterson, N, Stecher, G, Nei, M and Kumar, S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731–2739.Google Scholar
Town, CD, Cheung, F, Maiti, R, Crabtree, J, Haas, BJ, Wortman, JR, Hine, EE, Althoff, R, Arbogast, TS, Tallon, LJ, Vigouroux, M, Trick, M and Bancroft, I (2006) Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. The Plant Cell 18: 1348–1359.CrossRefGoogle ScholarPubMed
Wang, X, Wang, H, Wang, J, Sun, R, Wu, J, Liu, S, Bai, Y, Mun, JH, Bancroft, I, Cheng, F, Huang, S, Li, X, Hua, W, Freeling, M, Pires, JC, Paterson, AH, Chalhoub, B, Wang, B, Hayward, A, Sharpe, AG, Park, BS, Weisshaar, B, Liu, B, Li, B, Tong, C, Song, C, Duran, C, Peng, C, Geng, C, Koh, C, Lin, C, Edwards, D, Mu, D, Shen, D, Soumpourou, E, Li, F, Fraser, F, Conant, G, Lassalle, G, King, GJ, Bonnema, G, Tang, H, Belcram, H, Zhou, H, Hirakawa, H, Abe, H, Guo, H, Jin, H, Parkin, IA, Batley, J, Kim, JS, Just, J, Li, J, Xu, J, Deng, J, Kim, JA, Yu, J, Meng, J, Min, J, Poulain, J, Hatakeyama, K, Wu, K, Wang, L, Fang, L, Trick, M, Links, MG, Zhao, M, Jin, M, Ramchiary, N, Drou, N, Berkman, PJ, Cai, Q, Huang, Q, Li, R, Tabata, S, Cheng, S, Zhang, S, Sato, S, Sun, S, Kwon, SJ, Choi, SR, Lee, TH, Fan, W, Zhao, X, Tan, X, Xu, X, Wang, Y, Qiu, Y, Yin, Y, Li, Y, Du, Y, Liao, Y, Lim, Y, Narusaka, Y, Wang, Z, Li, Z, Xiong, Z and Zhang, Z (2011) The genome of the mesopolyploid crop species Brassica rapa . Nature Genetics 43: 1035–1039.Google Scholar
Wicker, T, Sabot, F, Hua-Van, A, Bennetzen, JL, Capy, P, Chalhoub, B, Flavell, A, Leroy, P, Morgante, M, Panaud, O, Paux, E, SanMiguel, P and Schulman, AH (2007) A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics 8: 973–982.Google Scholar
Witte, C-P, Le, QH, Bureau, T and Kumar, A (2001) Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proceedings of the National Academy of Sciences of the United States of America 98: 13778–13783.Google Scholar
Yang, TJ, Kwon, SJ, Choi, BS, Kim, JS, Jin, M, Lim, KB, Park, JY, Kim, JA, Lim, MH, Kim, HI, Lee, HJ, Lim, YP, Paterson, AH and Park, BS (2007) Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives. Theoretical and Applied Genetics 114: 627–636.Google Scholar
Yang, Y-W, Lai, K-N, Tai, P-Y and Li, W-H (1999) Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. Journal of Molecular Evolution 48: 597–604.Google Scholar
Yu, J, Zhao, M, Wang, X, Tong, C, Huang, S, Tehrim, S, Liu, Y, Hua, W and Liu, S (2013) Bolbase: a comprehensive genomics database for Brassica oleracea . BMC Genomics 14: 664.Google Scholar
Zhou, Y and Cahan, SH (2012) A novel family of terminal-repeat retrotransposon in miniature (TRIM) in the genome of the red harvester ant, Pogonomyrmex barbatus . PLoS One 7: e53401.CrossRefGoogle ScholarPubMed
Zou, J, Gong, H, Yang, T-J and Meng, J (2009) Retrotransposons – a major driving force in plant genome evolution and a useful tool for genome analysis. Journal of Crop Science and Biotechnology 12: 1–8.Google Scholar
Supplementary material: File

Sampath and Yang Supplementary Material

Figures S1-S3 and Table S1-S6

Download Sampath and Yang Supplementary Material(File)
File 1.1 MB