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Supplementary data

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    Dotplot

    Word size 10 (By default)

    dotplot-10.png

    It was increased the word size to 15 in order to reduce the number of dots, smooths the plot and eliminate background noise.

    dotplot-15.png

    The main diagonal is the sequence's alignment versus itself. The lines off the main diagonal show repetitive patterns within the sequence. There are a few repetitions but there are not observed tandem repetitions.

     

    BLAST

    Blastn

    Round 1: Megablast, no specific organism

    blastn-overall.bmp

    Result: most of the matched alignments come from Zea mays, which is the highly possible sequence origin. The pattern shows that ...

     

    Round 2: Megablast, with Zea mays

    blastn-Z.Mays.bmp

    Result: (THIS ALIGNMENT IS EXACTLY THE SAME AS THE LAST ONE) significant alignments include cultivar W22 bz gene locus, alcohol dehydrogenease 1, B73 pathogenesis-related protein 2 and GASA-like genes, rust resistance protein rp3-1 gene, and a lot of BAC clones. 

    The alignment obtained are significant since present high scores and E-value of 0.0 (meaning that in not probable to find a random match at that level) and include cultivar W22 bz gene locus, alcohol dehydrogenease 1, B73 pathogenesis-related protein 2 and GASA-like genes, rust resistance protein rp3-1 gene, and a lot of BAC clones. In general terms, these alignments show query coverage less than 40%, which may indicate that the differences between them could be in the intron sequences, if codifying for the same protein. To answer this is necessary to carry out a Blastx.

     

     

    Round 3: megablast excluding Zea mays

    blastn-exclude Z.Mays.bmp

    Result: potential homologies come from Gossypium raimondii, Zea diploperennis, Zea luxurians

     

    Round 4: Blastx with Zea mays (significant alignments)

    blastx.bmp

    Main hits: copia-type pol polyprotein

                    Ji1 putative pol protein

                    putative gag-pol protein

                    putative Opie4 pol protein

                    Opie3 pol protein

                    Opie2 pol protein

                    Ji4 gag protein

     

    Round 5: Blastx excluding Zea Mays (significant alignments)   

    blastx-exclude Z.Mays.bmp        

    THE SCORES ARE MUCH LOWER. THERE ARE AT LEAST 13 EXONS. LONG INTRONS.

     

    AUGUSTUS

    Augustus.png

    According to the %GC there are 3 potential gene-rich regions: 30K-60K, 80K-11K, 12K-15K

     

    Gramene

    Gramene-blastx.png

    Gramene-blastx-2.png

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