Article Figures & Data
Figures
- Figure 1.
Base Preferences of Tos17 Insertion Sites.
Average base preferences at each position were calculated based on flanking sequences at 20,458 loci. From position 1 to position 5 is the TSD sequence. Numbers with minus and plus signs are base numbers upstream and downstream, respectively, from the TSD. The percentages of A (green), C (blue), G (black), and T (red) at each position were plotted.
- Figure 2.
Frequency Distribution of the GC Content of Tos17-Inserted Regions and Published Rice Genomic Sequences.
The percentages of GC for 1-kb windows centered on 20,458 insertion points were calculated, and the frequency distribution was plotted in red. For continuous rice genomic sequences, derived from PAC or BAC clones with at least 70 kb of sequence, GC contents were calculated with a 1-kb sliding window, and the frequency distribution was plotted in blue. To determine the GC content distribution of CDS, all annotated CDS sequences were first joined into one large sequence. This sequence then was split into 1-kb pieces to determine the percentage of GC and the frequency distribution (green line). To generate a frequency distribution for protein kinase and defense-related genes (pink line), each 1-kb fragment of the rice genomic sequences was searched by BLASTX against an amino acid data set containing records of protein kinase and disease resistance genes. Fragments showing matches with E values of <e-10 were included in the frequency distribution. Each frequency distribution of GC content is plotted using 1% intervals.
- Figure 3.
Tos17 Insertion Map on Contigs of Rice Chromosome 1.
Contigs were assembled through a combination of BLASTN searches and the EMBOSS megamerger program. Seven remaining gaps between the contigs were joined simply. The x axes represent the position on chromosome 1. The y axes show the frequency of Tos17 insertions, retrotransposons, and genes.
(A) Tos17 insertions.
(B) Protein kinase genes.
(C) Disease resistance–related genes.
(D) Retrotransposons.
(E) Rice ESTs.
Frequencies were calculated at 100-kb intervals along chromosome 1. The position of the centromere is shown with a box. For (B), (C), and (D), the joined sequence of chromosome 1 was split into 1-kb fragments. Each fragment was searched with BLASTX against an amino acid data set of protein kinase genes, disease resistance genes, and retrotransposons, respectively. Gene frequencies represent the number of 1-kb fragments that have matches with E values of <e-10 for BLASTX or <e-100 for BLASTN.
- Figure 4.
Estimation of the Window Sizes of Tos17 Hot Spots.
All insertion points were mapped onto public PAC and BAC sequences. The distances between adjacent Tos17 insertion points on the rice genomic sequences were obtained, and the frequency distribution of the distances was plotted in 100-bp increments. Each distance was calculated from continuous genomic sequences of at least 70 kb. Red, green, and blue bars indicate Tos17 insertions in coding, intergenic, and unknown regions, respectively.
Tables
Category Number (<e-4) Number (<e-25) Percent Cell growth/division 396 141 4.7 Cell structure 289 121 3.4 Disease/defense 1,175 661 13.8 Energy 36 12 0.4 Intracellular trafficking 32 9 0.4 Metabolism 598 231 7.0 Protein synthesis 69 35 0.8 Protein targeting and storage 138 36 1.6 Secondary metabolism 88 28 1.0 Signal transduction 768 357 9.0 Transcription 364 203 4.3 Transporters 364 180 4.3 Transposons 704 450 8.3 Unclear classification 3,474 1,072 40.9 Total hits 8,495 3,536 Total independent insertions 16,784 A total of 42,292 sequences (from 4316 lines) were analyzed. The hit ratio in independent flanking sequences was 50.6%.
Accession Numbera Entryb Putative Identification Organismc Score E Value AG020730 BAA24449.1 6-4 photolyase Arabidopsis thaliana 89.7 4e-31 AG020828 CAB41466.1 Inositol 1,4,5-trisphosphate 5-phosphatase Arabidopsis thaliana 69.1 4e-11 AG020899 CAB88264.1 Callose synthase catalytic subunit–like Arabidopsis thaliana 205 5e-53 AG020942 AAF74563.1 Heat stress transcription factor A3 Lycopersicon peruvianum 119 3e-26 AG020963 AAF31730.1 Phosphoribosylformylglycinamidine synthase–like Arabidopsis thaliana 159 1e-50 AG020968 BAA94795.1 S-Adenosyl-l-Met:l-Met S-methyltransferase Hordeum vulgare 90.5 1e-27 AG021106 AAD37810.1 NADP-specific isocitrate dehydrogenase Oryza sativa 77.6 5e-14 AG021182 BAB11335.1 Eukaryotic release factor 1 Arabidopsis thaliana 181 2e-45 AG021242 JDMU1 DNA-directed RNA polymerase II largest chain Arabidopsis thaliana 357 6e-98 AG021377 AAF23509.1 Fructose-1,6-bisphosphatase Porteresia coarctata 101 2e-26 AG021380 BAA94509.1 Protein kinase 1 Populus nigra 184 5e-46 AG021400 BAB08003.1 Adenine phosphoribosyltransferase Hordeum vulgare 93.6 8e-19 AG021445 T03846 Plasma membrane H+-ATPase Oryza sativa 102 3e-45 AG021473 T00020 Bacterial blight resistance protein Xa1 Oryza sativa 289 1e-77 AG021543 T01661 DNA (cytosine-5-)-methyltransferase Zea mays 90.1 2e-53 AG021593 CAA65053.1 Pro transporter 2 Arabidopsis thaliana 116 2e-25 AG021694 BAA35120.1 NADH-dependent glutamate synthase Oryza sativa 266 1e-70 AG021741 S64721 Protoporphyrin IX magnesium chelatase precursor Hordeum vulgare 433 e-121 AG021763 BAB10513.1 NAM (no apical meristem)–like Arabidopsis thaliana 114 8e-25 AG021795 CAA94437.1 PDR5-like ABC transporter Spirodela polyrrhiza 136 6e-52 AG021958 AAC39369.1 Trehalose-6-phosphate phosphatase Arabidopsis thaliana 65.2 1e-24 AG021996 BAB03631.1 Putative protein kinase Xa21 Oryza sativa 229 1e-59 AG022284 S47582 High-affinity potassium uptake transporter Triticum aestivum 162 3e-39 AG022440 O23755 Elongation factor 2 Beta vulgaris 161 2e-39 AG022521 P30298 Sucrose synthase 1 Oryza sativa 85.8 6e-17 AG022936 P17801 Putative receptor protein kinase zmpk1 precursor Zea mays 162 4e-61 AG023034 AAF26975.1 Stelar K+ outward rectifying channel Arabidopsis thaliana 98.3 1e-25 AG023207 T09999 Cytochrome P450 Catharanthus roseus 120 8e-40 AG023219 P10931 Phytochrome A Oryza sativa 258 2e-68 AG023602 BAB08867.1 DNA-3-methyladenine glycosylase Arabidopsis thaliana 65.2 6e-26 AG023738 AAD40979.1 Peroxisomal copper-containing amine oxidase Glycine max 196 1e-49 AG023869 BAA34861.1 Importin-β1 Oryza sativa 132 3e-30 AG023905 BAB10038.1 Dihydropyrimidinase Arabidopsis thaliana 88.5 2e-25 AG023996 BAA90462.1 Chlorophyll a oxygenase Arabidopsis thaliana 100 9e-31 AG024163 P52421 Phosphoribosylamine-Gly ligase Vigna unguiculata 244 9e-64 AG024164 T04103 Sucrose phosphate synthase Oryza sativa 311 4e-84 AG024224 AAC18440.1 Argonaute protein Arabidopsis thaliana 68.7 1e-21 AG024327 AAC49302.1 Erecta Arabidopsis thaliana 157 4e-38 AG024330 P52711 Ser carboxypeptidase II-3 Hordeum vulgare 117 2e-25 Location Number of Insertions Percent Total Target Length (bp) Percent Average Interval (bp) Exon 2,260 11.0 25,780,287 4.9 11,407 Intron 1,837 9.0 29,727,948 5.7 16,182 Intergenic 1,950 9.5 78,227,314 15.0 40,116 Unknown 14,412 70.4 387,279,814 74.3 26,872 Total 20,458 521,015,363 25,467
