Supplementary information
From the following article:
Pack-MULE transposable elements mediate gene evolution in plants
Ning Jiang, Zhirong Bao, Xiaoyu Zhang, Sean R. Eddy & Susan R. Wessler
Nature 431, 569-573(30 September 2004)
doi:10.1038/nature02953
Supplementary Methods
Detailed description of methods including identification of MULEs from rice genomic sequence, the PCR amplification of Pack-MULE fragments from Nipponbare genomic DNA, and control experiment for Ka/Ks analysis.
Supplementary Table 1
TIR sequences of 62 MULE families that were involved in the formation of Pack-MULEs. Sequences in fasta format were also provided.
Supplementary Table 2
The TSDs of 100 randomly chosen Pack-MULEs from the genome-wide search.
Supplementary Table 3
The 320 Pack-MULEs on rice chromosome 1. Their position in relevant genomic sequence, the TSD sequences, their size, and a short description of the relevant protein hit for each Pack-MULE.
Supplementary Table 4
The 156 Pack-MULEs on rice chromosome 10. See Supplementary Table 3.
Supplementary Table 5
Multi-copy Pack-MULEs and their TSDs on rice chromosomes 1 and 10.
Supplementary Table 6
Pack-MULEs and their genomic homologs. The 100 randomly chosen Pack-MULEs and the gene structure of their genomic homologs. The size of the acquired fragment and the similarity between Pack-MULE and their genomic counterparts.
Supplementary Table 7
PCR primers and amplified fragments for 13 Pack-MULEs. The detailed information about primers and PCR conditions used to amplify Pack-MULE fragments (3 Pack-MULEs described in Figure 3, and 10 randomly selected Pack-MULEs from the 100 Pack-MULEs on chromosomes 1 and 10). The expected and observed fragment sizes were also provided.
Supplementary Table 8
25 Pack-MULEs with cDNA matches from chromosomes 1 and 10. The 34 full cDNA clones that correspond to 25 Pack-MULEs from chromosomes 1 and 10, and their transcription initiation sites inside Pack-MULEs.
Supplementary Table 9
Pack-MULEs with peptide matches. The genomic position of the relevant Pack-MULEs, the sequence of the peptides involved, and the tissue where each peptide was detected.
Supplementary Table 10
Ka/Ks analysis for Pack-MULEs and their genomic copies. The gene structure of the genomic copy, the regions involved in the analysis, the Ka and Ks value and the p value of purifying selection test.
Supplementary Figure 1
Genomic origin of Pack-MULE gene fragments.
Supplementary Figure 2
Amplification of Pack-MULE fragments using Nipponbare genomic DNA.
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