This Article Full Text Full Text (PDF) Supplemental Data All Versions of this Article: 138/2/935    most recent pp.105.060244v1 Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Web of Science (12) Citing Articles via Google Scholar Google Scholar Articles by Zhang, Y. Articles by Han, B. Search for Related Content PubMed PubMed Citation Articles by Zhang, Y. Articles by Han, B. Agricola Articles by Zhang, Y. Articles by Han, B.

GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

Computational Identification of 69 Retroposons in Arabidopsis^1,[w]

National Center for Gene Research (Y.Z., Y.W., Y.L., B.H.), and Shanghai Institute of Plant Physiology and Ecology (Y.Z., B.H.), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China

Retroposition is a shot-gun strategy of the genome to achieve evolutionary diversities by mixing and matching coding sequences with novel regulatory elements. We have identified 69 retroposons in the Arabidopsis (Arabidopsis thaliana) genome by a computational approach. Most of them were derivatives of mature mRNAs, and 20 genes contained relics of the reverse transcription process, such as truncations, deletions, and extra sequence additions. Of them, 22 are processed pseudogenes, and 52 genes are likely to be actively transcribed, especially in tissues from apical meristems (roots and flowers). Functional compositions of these retroposon parental genes imply that not the mRNA itself but its expression in gamete cells defines a suitable template for retroposition. The presence/absence patterns of retroposons can be used as cladistic markers for biogeographic research. Effects of human and the Mediterranean Pleistocene refugia in Arabidopsis biogeographic distributions were revealed based on two recent retroposons (At1g61410 and At5g52090). An evolutionary rate of new gene creation by retroposition was calculated as 0.6 genes per million years. Retroposons can also be used as molecular fossils of the parental gene expressions in ancient time. Extensions of 3' untranslated regions for those expressed parental genes are revealed as a possible trend of plant transcriptome evolution. In addition, we reported the first plant functional chimeric gene that adapts to intercompartmental transport by capturing two additional exons after retroposition.

² These authors contributed equally to the paper.

^[w] The online version of this article contains Web-only data.

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.105.060244.

^* Corresponding author; e-mail bhan{at}ncgr.ac.cn; fax 86–21–64825775.

Received January 26, 2005; returned for revision March 14, 2005; accepted March 17, 2005.

This article has been cited by other articles:

				C. Zou, M. D. Lehti-Shiu, F. Thibaud-Nissen, T. Prakash, C. R. Buell, and S.-H. Shiu Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice Plant Physiology, September 1, 2009; 151(1): 3 - 15. [Abstract] [Full Text] [PDF]

				M. Freeling, E. Lyons, B. Pedersen, M. Alam, R. Ming, and D. Lisch Many or most genes in Arabidopsis transposed after the origin of the order Brassicales Genome Res., December 1, 2008; 18(12): 1924 - 1937. [Abstract] [Full Text] [PDF]

				C. Fan, Y. Zhang, Y. Yu, S. Rounsley, M. Long, and R. A. Wing The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice Mol Plant, September 1, 2008; 1(5): 839 - 850. [Abstract] [Full Text] [PDF]

				Q. Zhou, G. Zhang, Y. Zhang, S. Xu, R. Zhao, Z. Zhan, X. Li, Y. Ding, S. Yang, and W. Wang On the origin of new genes in Drosophila Genome Res., September 1, 2008; 18(9): 1446 - 1455. [Abstract] [Full Text] [PDF]

				W. Wang, H. Zheng, C. Fan, J. Li, J. Shi, Z. Cai, G. Zhang, D. Liu, J. Zhang, S. Vang, et al. High Rate of Chimeric Gene Origination by Retroposition in Plant Genomes PLANT CELL, August 1, 2006; 18(8): 1791 - 1802. [Abstract] [Full Text] [PDF]