A Preliminary Study on Patterns of TE-gene Associations in Oryza (Poaceae) and Adaptive Significance

doi:10.3724/SP.J.1143.2011.10183

Abstract

Abstract:

Transposable elements (TEs) have been found to be significant fractions of eukaryotic genomes. Moreover, they make great contributions to the structure, function and evolution of host genomes and associated genes in particular. Starting from bioinformatics searches, this study investigated the distribution of two TE-gene associations in 94 strains belonging to 16 Oryza species through PCR and agarose gel electrophoresis. We found that TE-insertions in the gene LOC_Os02g26349 distributed in AA-genome species while TE inserted into the gene LOC_Os02g45130 in part of AA-genome species. The result is obviously in agreement with the phylogeny of AA-genome species. The observed patterns of TE-gene associations in Oryza species and the fixation of TE-insertions within populations of different geographic origins together imply adaptive significance of TEs in the evolution of their host genes and genomes.

Key words: Transposable element, Oryza, AA-genome group, Insertion

CLC Number:

Q 78

FAN Ya-Yu-, Gao-Li-Zhi. A Preliminary Study on Patterns of TE-gene Associations in Oryza (Poaceae) and Adaptive Significance[J]. Plant Diversity, 2011, 33(2): 201-208.

References

Aminetzach YT, Macpherson JM, Petrov DA, 2005. Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila［J］. Science, 309 (5735): 764—767
Bartolome C, Maside X, Charlesworth B, 2002. On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster［J］. Molecular Biology and Evolution, 19: 926—937
Biémont C, Vieira C, 2006. Genetics: junk DNA as an evolutionary force［J］. Nature, 443: 521—524
Bureau TE, Wessler SR, 1992. Tourist: a large family of small inverted repeat elements frequently associated with maize genes［J］. The Plant Cell, 4 (10): 1283—1294
Casacuberta E, Puigdomènech JM, Monfort A, 1998. Presence of miniature inverted-repeat transposable elements (MITEs) in the genome of Arabidopsis thaliana: characterisation of the Emigrantfamily of elements［J］. The Plant Journal, 16 (1): 79—85
Charlesworth B, Charlesworth D, 2009. The population dynamics of transposable elements［J］. Genetics Research, 42 (01): 1—27
Charlesworth B, Langley CH, 1989. The population genetics of Drosophila transposable elements［J］. Annual Review of Genetics, 23 (1): 251—287
Charlesworth B, Sniegowski P, Stephan W, 1994. The evolutionary dynamics of repetitive DNA in eukaryotes［J］. Nature, 371: 215—220
Dolgin ES, Charlesworth B, 2008. The effects of recombination rate on the distribution and abundance of transposable elements［J］. Genetics, 178 (4): 2169—2177
Doyle JJ, Doyle JL, 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue［J］. Phytochemical Bulletin, 19: 11—15
Enome I, Roject SEP, 2005. The map-based sequence of the rice genome［J］. Nature, 436: 793—800
Felsenstein J, 1974. The evolutionary advantage of recombination［J］. Genetics, 78 (2): 737—756
Ge S, Sang T, Lu BR et al., 1999. Phylogeny of rice genomes with emphasis on origins of allotetraploid species［J］. Proceedings of the National Academy of Sciences, 96 (25): 14400—14405
Goff SA, Ricke D, Lan TH et al., 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica) ［J］. Science, 296 (5565): 92—100
González J, Lenkov K, Lipatov M et al., 2008. High rate of recent transposable element-Induced adaptation in Drosophila melanogaster［J］. PLoS Biology, 6 (10): 2109—2129
Gordo I, Charlesworth B, 2001. Genetic linkage and molecular evolution［J］. Current Biology, 11 (17): R684—R686
Hermisson J, Pennings PS, 2005. Soft sweeps: molecular population genetics of adaptation from standing genetic variation［J］. Genetics, 169 (4): 2335—2352
Hey J, 1989. The transposable portion of the genome of Drosophila algonquin is very different from that in D.melanogaster［J］. Molecular Biology and Evolution, 6 (1): 66—79
Hughes JF, Coffin JM, 2001. Evidence for genomic rearrangements mediated by human endogenous retroviruses during primate evolution［J］. Nature Genetics, 29 (4): 487—489
Kaminker JS, Bergman CM, Kronmiller B et al., 2002. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective［J］. Genome Biology, 3 (12): 1—84
Kapitonov VV, Jurka J, 2003. Molecular paleontology of transposable elements in the Drosophila melanogaster genome［J］. Proceedings of the National Academy of Sciences, 100 (11): 6569—6574
Kaplan NL, Brookfield JFY, 1983. The effect on homozygosity of selective differences between sites of transposable elements［J］. Theoretical Population Biology, 23 (3): 273—280
Kazazian HH Jr, 2004. Mobile elements: drivers of genome evolution［J］. Science, 303 (5664): 1626—1632
Khush GS, 1997. Origin, dispersal, cultivation and variation of rice［J］. Plant Molecular Biology, 35 (1): 25—34
Kidwell MG, Lisch D, 1997. Transposable elements as sources of variation in animals and plants［J］. Proceedings of the National Academy of Sciences, 94 (15): 7704—7711
Kidwell MG, Lisch DR, 2001. Perspective: transposable elements, parasitic DNA, and genome evolution［J］. Evolution, 55 (1): 1—24
Kumar A, Bennetzen JL, 1999. Plant retrotransposons［J］. Annual Review of Genetics, 33 (1): 479—532
Lipatov M, Lenkov K, Petrov D et al., 2005. Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome［J］. BMC Biology, 3 (1): 24—36
Montgomery E, Charlesworth B, Langley CH et al., 2009. A test for the role of natural selection in the stabilization of transposable element copy number in a population of Drosophila melanogaster［J］. Genetics Research, 49 (01): 31—41
Montgomery EA, Huang SM, Langley CH et al., 1991. Chromosome rearrangement by ectopic recombination in Drosophila melanogaster: genome structure and evolution［J］. Genetics, 129 (4): 1085—1098
Naito K, Zhang F, Tsukiyama T et al., 2009. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression［J］. Nature, 461: 1130—1134
Nekrutenko A, Li WH, 2001. Transposable elements are found in a large number of human protein-coding genes［J］. Trends Genet, 17 (11): 619—621
Nishikawa T, Vaughan DA, Kadowaki K, 2005. Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes［J］. Theoretical and Applied Genetics, 110 (4): 696—705
Oka HI, 1988. Origin of Cultivated Rice［M］. Tokyo: Japan Scientific Societies Press
Park KC, Kim NH, Cho YS et al., 2003. Genetic variations of AA genome Oryza species measured by MITE-AFLP［J］. Theoretical and Applied Genetics, 107 (2): 203—209
Przeworski M, Coop G, Wall JD, 2005. The signature of positive selection on standing genetic variation［J］. Evolution, 59 (11): 2312—2323
SanMiguel P, Tikhonov A, Jin YK et al., 1996. Nested retrotransposons in the intergenic regions of the maize genome［J］. Science, 274 (5288): 765—768
Teshima KM, Coop G, Przeworski M, 2006. How reliable are empirical genomic scans for selective sweeps?［J］. Genome Research, 16 (6): 702—712
Walser JC, Chen B, Feder ME, 2006. Heat-shock promoters: targets for evolution by P transposable elements in Drosophila［J］. PLoS Genet, 2 (10): 1541—1555
Wang Y, Liu K, Liao H et al., 2008. The plant WNK gene family and regulation of flowering time in Arabidopsis［J］. Plant Biology, 10 (5): 548—562
Xiao H, Jiang N, Schaffner E et al., 2008. A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit［J］. Science, 319(5869): 1527—1530
Xu Z, Ramakrishna W, 2008. Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history［J］. Gene, 412(1-2): 50—58
Yu J, Hu S, Wang J et al., 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica)［J］. Science, 296 (5565): 79—92

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