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Almost all enzymes involved in BIA biosynthesis were identified by LC-MS/MS peptide analysis (Additional File 5; Figure 6).
Potential gene candidates involved in paclitaxel biosynthesis were identified by homology with existing paclitaxel biosynthetic genes from Taxus.
The genome of Penicillium aurantiogriseum NRRL 62431 was sequenced and gene candidates that may be involved in paclitaxel biosynthesis were identified by comparison with the 13 known paclitaxel biosynthetic genes in Taxus.
Homologous proteins involved in (bacterio chlorophyll biosynthesis were identified by Basic Local Alignment Search Tool (BLAST) (Altschul et al. 1997) within the data set of downloaded genomes (17 eukaryotes and 87 prokaryotes, supplementary table S1, Supplementary Material online) using the proteins shown in supplementary table S2, Supplementary Material online, as queries.
Specifically, nine pigment synthesis genes related to fungal melanin biosynthesis were identified by data mining analysis (DMA) as up-regulated in the MS + library vs. NoMS library (Additional file 4, #s 1 9), whereas only two of these genes were detected with the first GWA (Additional file 1, #s 1 2).
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A remarkable influence of IEF2 signaling on the protein biosynthesis was identified by merging both network and pathway analysis.
Genes involved in melanin biosynthesis were identified in V. dahliae by homology searches, including polyketide synthase (VDAG_00190), scytalone dehydratase (VDAG_03393) and hydroxynaphthalene reductase (VDAG_03665).
Also, various genes involved in podophyllotoxin biosynthesis were identified and their expression both by FPKM and the qRT-PCR showed up-regulation of eight out of twelve genes at 15°C.
Key genes associated with cell-wall biogenesis/modification, xylem identity, auxin regulation and fatty acid biosynthesis were identified among our candidate genes potentially affected by divergent selection in flax (Additional file 4: Table S2).
Enzymes from thiamine biosynthesis, protein biosynthesis, and folate biosynthesis were identified as attractive candidates for drug development.
Enzymes from peptidoglycan biosynthesis, folate biosynthesis were identified as candidates for drug development.
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