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PAL ortholog nucleotide sequence > S. officinarum IK76-060 #1

PAL ortholog nucleotide sequence > S. officinarum IK76-060 #1

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PAL ortholog nucleotide sequence > S. officinarum IK76-060 #1

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  1. PAL ortholog nucleotide sequence >S. officinarum IK76-060 #1 AGGCCAGCAGCGAGTGGATCCTCGACTGCATCGCCCACGGCGGCGACATCTACGGCGTCACCACCGGCTTCGGCGGCACCTCGCACCGCCGTACCAAGGACGGGCCCGCGCTCCAGGTCGAGCTGCTCAGGTACTGTACTACATACTACCAATCTCACGAGACCACGTGTCTCTTTGCTTACTTGCTGTTGCAGTAAAGTATGCTTGTCCGCGGAGTGGTTGCAGCATCAAATGATTCATGTGAGTCACTGATGAGTGCCCACTGGCAACGACCGGCCGTCCGGCGGCCGGGTCGCTGCAGCTTGCAATTGCTGCCGATGATGCCTGTCAGCAGCTCATTAATTCTGACAGGCCGATACTAGATTCTCTGAACATTTTGCATGCTAACTCGTACAACTGACATAAGCTCGCTCGATCTGTTTTCTCCCCTGCAACCAACCACGTACAACCAGGCATCTCAATGCCGGAATCTTCGGCAATGGCTCCGACGGCCACACGCTCCCGTCAGAGGTTTCACGCGCGGCCATGCTGGTCCGCATCAACACCCTCCTCCAGGGCTACTC >S. officinarum IK76-060 #5 AGGCCAGCAGCGAGTGGATCCTCGACTGCATCGCCCACGGCGGCGACATCTACGGCGTCACCACCGGCTTCGGCGGCACCTCGCACCGCCGTACCAAGGACGGGCCCGCGCTCCAGGTCGAGCTGCTCAGGTACTGTACTACATACTACCAATCTCACGAGACCACGTGTCTCTTTGTTTACTTGCTGTTGCAGTAAAGTATGCTTGTCAGCGGAGTGGTTGCAGCGTCAAATGATTCATGTGAGTCACTGATGAGTGCCCACTGGCAGTGGCAACGACCGGCCGTCCGGCGGGTCGCTGCAACTTGCAATTGCTGCCGATGATGCCTGTCAGCAGCTCATTAATTCTGACAGGCCGATACTAGATTCTCTGAACATTTTGCATGCTAACTCGTAATGACATTATTACAAACTGACATAAGCTCGCTCGATCTGTTTTCTCCCCTGCAACCAACCACGTACAACCAGGCATCTCAATGCCGGAATCTTCGGCAATGGCTCCGACGGCCACACGCTCCCGTCCGAGGTTTCACGCGCGGCCATGCTGGTCCGCATCAACACCCTCCTCCAGGGCTACTC 4-CL ortholog nucleotide sequence >S. officinarum IK76-060 #1 CAACGCAGAGCTCAAGGTGGTGGACCCCGACACGGGCCTCTCGCTCAGCCGCAACCTCCCCGGCGAGATCTGCATCCGGGGCCCGCAGATCATGAAAGGTAATTAACCGCGCGTGACGATGCACTGTGCAAGTGACCGGTCACTGATGGACGGGCGCGTACGTGTGGTGTGGCGCAGGGTACCTGAACGACCCGGAGGCCACCGCGAGGACGATCGACGTCGACGGCTGGCTCCACACCGGCGACATCGGCTACGTCGACGACGACGAGGAGGTCTTCATCGTCGACCGCGTCAAGGAGCTCATCAAGTTCAAGGGCTTCCAGGTAACACGCTGCGCTGCCCTGAAAGCCTCTACTGTATCTATCAGTTGGTAACTCTTTCTGAGAACCGTAGCTGTCACGCCCGTGCAGGTGCCGCCGGCCGAGCTCGAGGCTCTGCTCATCGCCCACCCATCCATCGCCGACGCAGCCGTCGTCCCGTAAGACCAATCAGCTGCTTCGGAACTAGTACCAAACACCGCAGGAAAATAGCTCGTTCTGACTGTACATGTATGCGCATGGCAGGCAAAAGGATGACGCCGCCGGCGAGGTCCCTGTCGCCTTCGTGGTTCGCGCCGCCGATTCTGGCATCGCGGAGGATGCCATCAAGGACTTCATCTCCAAGCAGGTACTCAGTCACGCCGCCTTGCTAATGGTTTTTGAACGCTACAAGCCCGGCTCTTTTTTCTGACAGTTCTTGTGTGCGCGCGTGCGCCGCGCCGATTTTCAGGTGGTGTTCTACAAGAGGCTACACAAGGTGTACTTCACCCCCTCCATCCCCAAGTCGGCGTCCGGGAAGATCCTGAGGAGAGAGCTACGCGCCA >S. officinarum IK76-060 #3 CAACGCAGAGCTCAAGGTGGTGGACCCCGACACGGGCCTCTCGCTCAGCCGCAACCTCCCCGGCGAGATCTGCATCCGGGGCCCGCAGATCATGAAAGGTAATTAACCGCGCGTGACGATGCACTGTGCAAGTGACCGGTCACTGATGGACGGGCGCGTACGTGTGGTGTGGCGCAGGGTACCTGAACGACCCGGAGGCCACCGCGAGGACGATCGACGTCGACGGCTGGCTCCACACCGGCGACATCGGCTACGTCGACGACGACGAGGAGGTCTTCATCGTCGACCGCGTCAAGGAGCTCATCAAGTTCAAGGGCTTCCAGGTAACACGCTGCGCTGCCCTGAAAGCCTCTACTGTATCTATCAGTTGGTAACTCTTTAGCTGTCACGCCCGTGCAGGTGCCGCCGGCCGAGCTCGAGGCTCTGCTCGTCGCCCACCCATCCATCGCCGACGCAGCCGTCGTCCCGTAAGACCAATCAGCTGCTTCGGAACTAGTACCAAACACCGCAGGAAAATAGCTCGTTCTGACTGTACATGTATGCGCATGGCAGGCAAAAGGATGACGCCGCCGGCGAGGTCCCTGTCGCCTTCGTGGTTCGCGCCGCCGATTCTGACATCGCGGAGGATGCCATCAAGGACTTCATCTCCAAGCAGGTACTCAGTCACGCCGCCTTGCTAATGGTTTTTGAACGCTACAAGCCCGGCTCTTTTTCTGACAGTTCTTGTGTGCGCGCGTGCGCCGCGCCGATTTTCAGGTGGTGTTCTACAAGAGGCTACACAAGGTGTACTTCACCCCCTCCATCCCCAAGTCGGCGTCCGGGAAGATCCTGAGGAGAGAGCTACGCGCCA CCoAOMT ortholog nucleotide sequence >S. officinarum IK76-060 #1 CAGTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACTGCCAAGCACCCATGGTAAGTGTGGATCTCCCGGCGTCGATCCGTTTCGTGGATTTTAGTGGACGTGCTGGACCATCTGATCTGAAATGAAACCATGGCGGCGTCCTGTGGTGGCGTGCAGGAACCTGATGACGACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACCGCGCTCGCTCTCCCGGAGGACGGCACGGTCGGTTCTTCCCTCTCTTCCCAGATCTGCCACAACTCCCTGAAGATGAAGCAGCTAGCGCTCCACTGATAAAAGACGGATTTTTACCCTCTCTCTCTCTCTGTTGTTCGTCCCGCAGATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTGCATCGAGAAGGCCGGCGTCGCCCACAAGATCGACTTCCGCGAGGGCCCCGCGCTCCCCGTCCTCGACGACCTCATCGCAGACGTAAGAAAAAATGCCGGCTAGCTAGATCTGTCCTTGGCCTATCGATCGAGCAGTGCGTCCTGACGAAGGTTCCATCTCGAATCCGCAGGAGAAGAACCACGGGTCGTTCGACTTCGTC >S. officinarum IK76-060 #2 CAGTACATCCTGGACACGAGCGTGTACCCGCGGGAGCCGGAGAGCATGAAGGAGCTCCGCGAGATCACCGCCAAGCACCCATGGTAAGTGTCGATCTCCCGGCGTCGATCCGTTTCCTGGATTTTAGTGGACGTGCTGGACCATCTGATCTGAAACCATGGCGGCGTCCTGTGGTGGCGTGCAGGAACCTGATGACGACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCGTCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGCTACTCCCTCCTCGCCACCGCGCTCGCTCTCCCGGAGGACGGCACGGTCGGTTCTTCCCTCTCTTCCCAGATCTGCCACAACTCCCTGAAGATGAAGCAGCTAGCGCTCCACTGATAAAAGACGGATTTTTACCCTCTCTCTCTCTCTGTTGTTCGTCCCGCAGATCTTGGCCATGGACATCAACCGCGAGAACTACGAGCTGGGCCTGCCCTCCATCGAGAAGGCCGGCGTCGCCCACAAGATCGACTTCCGCGAGGGCCCCGCGCTCCCCGTCCTCGACGACCTCATCGCAGACGTAAGAAAAAATGCCGGCTAGCTAGATCTGTCCTTGGCCTATCGATCGAGCAGTGCGTCCTGACGAAGGTTCCATCTCGAATCCGCAGGAGAAGAACCACGGGTCGTTCGACTTCGTC Supplemental Fig. S1 Examples of nucleotide sequence of the cloned amplicons of PAL, 4-CL and CCoAOMT orthologs of S. officinarum IK 76-060. Two representative clones of each ortholog, showing size variation, were shown above

  2. aPAL b 4-CL c CCoAOMT (i) S. officinarum subgroup Saccharum-Narenga Saccharum-Narenga Saccharum-Narenga (ii) S. spontaneum subgroup Miscanthus Erianthus-Imperata Erianthus-Imperata Erianthus-Imperata Miscanthus Miscanthus Supplemental Fig. S2 Phylogenetic analysis of the orthologs of (a) PAL, (b) 4-CL and (c) CCoAOMT. Phylogenetic tree was generated using the neighbor-joining and p-distance methods. The names of species and accessions were indicated on the tree. The clone numbers used for phylogenetic analysis were indicated at the end of each accession. The clone No. 4 of S. spontaneum Djantoer II and the clone No. 3 of S. officinarum Bourbonriet Surinam, are highlighted with ● and ▲, respectively

  3. a b S. officinarum S. officinarum Before digestion M M Before digestion M M (kb) (kb) 1.0 1.0 0.5 0.5 After digestion M M After digestion M M (kb) * * (kb) 1.0 1.0 0.5 0.5 0.1 Miscanthus Miscanthus Before digestion Before digestion Fiji hybrids M M Fiji hybrids M M (kb) (kb) 1.0 1.0 0.5 0.5 After digestion After digestion M M M M (kb) (kb) 1.0 1.0 0.5 0.5 0.1 Suppremental Fig. S3 PCR-RFLP of 4-CL and CCoAOMT orthologs of S. officinarum, Miscanthus and Saccharum Fiji hybrids. (a) 4-CL PCR-RFLP of S. officinarum (top), and Miscanthus and Saccharum Fiji hybrids (bottom) after BfaI digestion. (b) CCoAOMT PCR-RFLP of S. officinarum (top), and Miscanthus and Saccharum Fiji hybrids (bottom) after HaeII digestion. Lane designation from left to right: S. officinarum - Black Cheribon, Black Innes, Bourbonriet Surinam, Guam A, Hawaiian Original 52, Hinahina 18, IJ76-521 and IK76-060, Miscanthus sp. - M. floridulus US56-0022-03 and M. floridulus 2x, M. sinensis Gracillimus, US64-0004-02 and US64-0007-01, Miscanthus sp. M75-062 and NG77-022, M. sinensis US47-0011 and Miscanthus sp. US64-0016-03, Saccharum hybrid - Fiji 17, 54, 57 and 55. M denotes the DNA size marker

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