Abstract
Transposable elements (TEs) are distributed throughout the genome and play an important role in genome variation of the rice blast fungus, Magnaporthe oryzae. TE-associated molecular markers have been developed and used extensively for diversity analysis in natural populations. Here, we investigated the genomic distribution of a selected group of TEs that are dispersed as singletons, and each is of a size feasible for PCR validation, designated as SSTEs, in the genome of the reference laboratory strain, 70-15. The 75 SSTEs identified were distributed evenly on seven chromosomes of the M. oryzae genome. Approximately 40 % of SSTEs were located either in the coding or promoter regions of the predicted genes. The presence or absence of each SSTE at the respective locus was assessed, resolving significant presence/absence polymorphism among 11 rice blast strains collected from different locations worldwide. The presence/absence (P/A) polymorphism of SSTEs in different strains suggests that they may be useful for developing map-based land PATE markers for genetic analysis in M. oryzae.
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Acknowledgments
We are grateful to Drs. Jong-Seong Jeon at the Kyung Hee University, Korea, Guo-Liang Wang at the Ohio State University, USA, Yulin Jia at USDA-ARS Dale Bumpers National Rice Research Center, USA, and Chenyun Li at Yunnan Agriculture University, China, for providing the strains listed in Tables 1 and S4. We thank Mr. Neal Rasmi for a grammatical review of this manuscript. This project was supported by grants from Natural Science Foundation in China (30971878), Open Project of State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control (2010DS700124-KF1108) and partial funding from the Faculty of Science and the Graduate School, Kasetsart University.
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10327_2013_428_MOESM5_ESM.ppt
Fig. S1. Chromosomal distribution of SSTEs. The supercontigs indicated in grey bars were aligned on each chromosome in the same order as the one in the integrated map of M. grisea (http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/maps/ViewMap.html?sp=0http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/maps/ViewMap.html?sp=0). The SSTEs corresponding to the PATE loci are indicated by lines with different abbreviated names. Abbreviated name for each SSTE family: Mg-SINE = MS; Pot2-A = P2A; Pot2-B = P2B; Pot3 = P3; MINE = MN; solo-LTR = SR; Occan = ON; MGL = ML. The location of SSTE in each supercontig is listed in Table 2. The expected size of PCR product at each PATE locus is listed in Table 4. The map was drawn to scale. (PPT 672 kb)
10327_2013_428_MOESM6_ESM.ppt
Fig. S2. Cladistic analyses of Mg-SINE (A) and Pot2 (B) elements used in this study. The nucleotide sequences of TEs were used for multiple sequence alignments in the program Clustal_X 1.81 (Thompson et al. 1997). The derived phylogenetic tree was viewed with the program Njplot (Perrière and Gouy 1996). (PPT 116 kb)
10327_2013_428_MOESM7_ESM.ppt
Fig. S3. Multiple sequence alignments of Pot2 elements. Two loci, 6-194-M10 and 3-191-M1, were used as representatives for Pot2-A and Pot2-B elements, respectively. Locus 6-169-M3 is a chimera of Pot2-A and -B. (A). Nucleotide sequences of these three Pot2 elements were used for the multiple sequence alignment. The terminal inverted repeat (TIR) sequences are indicated by the upper lines at both termini. (B). Amino-acid sequences of these three Pot2 elements used for the multiple sequence alignment. The central DDE domain is indicated by line above sequences. (PPT 265 kb)
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Zhang, Hy., He, Dy., Kasetsomboon, T. et al. Analysis of selected singleton transposable elements (SSTEs) and their application for the development of land PATE markers in Magnaporthe oryzae . J Gen Plant Pathol 79, 96–104 (2013). https://doi.org/10.1007/s10327-013-0428-8
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DOI: https://doi.org/10.1007/s10327-013-0428-8