| Increasing studies reported the occurrence of transposable element activation when plants were subjected to environmental stresses, such as tissue culture, radiation or pathogen infection. Transposition of transposable element increases its copy number and thus restructures the genome. The rice Rim2 is a novel element transcriptionally activated by the infection of rice blast pathogen Magnaporthe grisea and its elicitors. The Rim2 protein deduced from its cDNA shares some identity with transposases encoded by plant CACTA TEs. This result implies the probable lurk of CACTA-like elements in rice genome.To disclose its genomic DNA structure, Rim2 cDNA was employed as probe to screen rice bacterial artificial chromosome (BAG) library and many positive BACs were therefore obtained. Among them, 6C9, 7118, 2JC8, 22H17and 22N5 were digested with Hindlll for subcloning using the vector pBluescript SK(-). As a result, more than 20 positive fragments were obtained such as Rim2-228, Rim2-248, Rim2-553, Rim2-569, Rim2-411. Sequence analysis and data mining revealed that Rim2 elements belong to a novel transposon family different from CACTA elements. The relevant conclusions are listed as follows:1. Rim2 elements possess the fundamental structure of Class II elements, but belong to a novel DNA TE familyBy using Blast program in NCBI for data searching in GeneBank, abundant sequences homologous to cloned positive fragments were identified, emerging from all rice chromosomes. After searching the upstream and downstream of these sequences, 16-bp perfect terminal inverted repeats CACTGGTGGAGAAACC was recognized, flanked by 3-bp target site duplication. Different from the previously described En/Spm, Taml and Tgml, its end sequence of terminal inverted repeats is CACTG instead of CACTA, a structural hallmark distinguishes Rim2 from CACTA elements. Besides, 16-bp subterminal repeats ATCTTTAGTCCGGTT was found to reside in subterminal regions. And several tandem repeats were also found. Additionally, Rim2 elements harbor undisrupted open reading frame and the putative proteins share low homology with TNPD/TNP2 and other plant Tpases. No open reading frames in Rim2 elements were detected to encode TNPA/TNPl-like DNA binding proteins.2. Abundant Rim2 elements constitute a super family and unevenly distribute onchromosomes.By using conserved Rim2 end sequences as a query to blast in GenBank, 344 elements were mined from available 230Mb rice sequences. It was therefore reckoned that whole rice genome of 430~460Mb size might contain 600-700 Rim2 elements. FISH assay was carried out and the result displayed the wide distribution ofRim2 elements in all rice chromosomes, consistent with the conclusion of data mining. In order to view the detailed distribution pattern, a map was plotted to locate all mined Rim2 elements on rice chromosome. The map shows uneven distribution ofRim2 elements on chromosomes. Attractively, they are obviously enriched within centromeric regions. All above results attest the abundance of Rim2 elements in rice genome.The observation that Rim2 elements unequally distributed on chromosomes aroused a concern of Rim2 insertion preference. To address this issue, a survey of AT/GC contents of the regions adjacent to all Rim2 inserts was conducted, the result indicated that Rim2 elements appear to have an AT-rich insertion preference with average 58.2-59.4% and 60.9-62.0% AT contents in 5' and 3' flanking regions within different distance of lOObp to SOObp from target site duplication (TSD) respectively, compared to the average 56.3% AT contents in randomly picked rice sequences. Besides, a probable preference of insertion into genie regions was observed for this family. Of mined 344 elements, 204 elements have been anotated in sequences. We surveyed the distribution patterns of the 204 elements. There are 44 elements (21.6%) inserting into coding regions of predicted genes, 101 (49.5%) into non-coding regions including introns and immediately 5' and 3' noncoding termini of predicted genes, b...
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