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Identification of an active Mutator-like element (MULE) in rice (Oryza sativa)

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Abstract

Transposable elements (TEs) represent an important fraction of plant genomes and play a significant role in gene and genome evolution. Among all TE superfamilies discovered in plants, Mutator from maize (Zea mays) is the most active and mutagenic element. Mutator-like elements (MULEs) were identified in a wide range of plants. However, only few active MULEs have been reported, and the transposition mechanism of the elements is still poorly understood. In this study, an active MULE named Os3378 was discovered in rice (Oryza sativa) by a combination of computational and experimental approaches. The four newly identified Os3378 elements share more than 98% sequence identity between each other, and all of them encode transposases without any deletion derivatives, indicating their capability of autonomous transposition. Os3378 is present in the rice species with AA genome type but is absent in other non-AA genome species. A new insertion of Os3378 was identified in a rice somaclonal mutant Z418, and the element remained active in the descendants of the mutant for more than ten generations. Both germinal and somatic excision events of Os3378 were observed, and no footprint was detected after excision. Furthermore, the occurrence of somatic excision of Os3378 appeared to be associated with plant developmental stages and tissue types. Taken together, Os3378 is a unique active element in rice, which provides a valuable resource for further studying of transposition mechanism and evolution of MULEs.

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Acknowledgments

I would like to thank Dr. Ning Jiang at the Michigan State University for her guidance and support on this research. I also thank the people who have provided the rice seeds or DNAs for this study. I appreciate two anonymous reviewers for their valuable comments. This research was supported by the grants from the Scholarship for Overseas Training Program from the government of Jiangsu province in China and the National Natural Science Foundation of China (30471066).

Author information

Correspondence to Dongying Gao.

Additional information

Communicated by M.-A. Grandbastien.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Fig. 1: PCR amplifications of the genomic DNAs from Nipponbare, Z418 and C418 using three- and two-primer combinations.

Supplementary Fig. 2: Sothern blots of 11 rice cultivars. 1. Nipponbare, 2. 93-11, 3. Azucena, 4. Heijie, 5. Rexodo, 6. Jeffererson, 7. Lemont, 8. Veharpater, 9. T442-57, 10. N.A.R.B.Upland, 11. Gimbozu.

Supplementary Fig. 3: Phylogenetic analysis of MULEs from bacteria, fungi, and plants using neighbor-joining method. Bootstrap values are indicated as a percentage of 1000 replicates.

Supplementary material 1 (PPT 513 kb)

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Gao, D. Identification of an active Mutator-like element (MULE) in rice (Oryza sativa). Mol Genet Genomics 287, 261–271 (2012). https://doi.org/10.1007/s00438-012-0676-x

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Keywords

  • MULE
  • Somaclonal mutant
  • Rice
  • Excision
  • Activity