Open Access Highly Accessed Research article

Genome sequencing and analysis of the paclitaxel-producing endophytic fungus Penicillium aurantiogriseum NRRL 62431

Yanfang Yang1, Hainan Zhao2, Roberto A Barrero3, Baohong Zhang4, Guiling Sun56, Iain W Wilson7, Fuliang Xie4, Kevin D Walker8, Joshua W Parks9, Robert Bruce9, Guangwu Guo10, Li Chen10, Yong Zhang11, Xin Huang12, Qi Tang13, Hongwei Liu1, Matthew I Bellgard3, Deyou Qiu1*, Jinsheng Lai2* and Angela Hoffman9*

Author Affiliations

1 State Key Laboratory of Tree Genetics and Breeding, The Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China

2 College of Agricultural Biotechnology, China Agriculture University, Beijing 100094, China

3 Centre for Comparative Genomics, Murdoch University, Perth, WA 6150, Australia

4 Department of Biology, East Carolina University, Greenville, NC 27858, USA

5 School of Life Sciences, Southwest Forestry University, Kunming 650224, China

6 Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China

7 CSIRO Plant Industry, Canberra ACT 2001, Australia

8 Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA

9 Department of Chemistry, University of Portland, Portland, OR 97203, USA

10 BGI-Shenzhen, Shenzhen 518000, China

11 Department of Plant Pathology, China Agricultural University, Beijing 100094, China

12 Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100029, China

13 Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and National Chinese Medicinal Herbs (hunan) Technology Center, Hunan Agricultural University, Changsha 410128, China

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BMC Genomics 2014, 15:69  doi:10.1186/1471-2164-15-69

Published: 25 January 2014

Additional files

Additional file 1:

Figure S1. Overview of paclitaxel biosynthetic pathway in Taxus sp. Abbreviations: BAPT: baccatin III: 3-animo-3-phenylpropanoyltransferase; DBAT: 10-deacetylbaccatin III-10-O-acetyltransferase; DBTNBT: 3′-N-debenzoyl-2′-deoxytaxol N-benzoyltransferase; GGPPS: geranylgeranyl diphosphate synthase; PAM: phenylalanine aminomutase; TAT: taxadien-5α-ol-O-acetyl transferase; TBT: taxane 2α-O-benzoyltransferase; TS: taxa-4(5),11(12)-diene synthase; T1OH: Taxane 1β-hydroxylase; T2OH: taxane 2α-hydroxylase; T5OH: cytochrome P450 taxadiene 5α-hydroxylase;T7OH: taxane 7β-hydroxylase; T10OH:taxane 10β-hydroxylase; T13OH: taxane 13α-hydroxylase. Genes responsible for C1 hydroxylation, oxetane formation, C9 oxidation, β-phenylalanoyl CoA formation and C2′hydroxylation of paclitaxel biosynthetic pathway in Taxus sp. remains to be elucidated (marked with red colour). Figure S2 HPLC-MS analysis of paclitaxel from the extracts of P. aurantiogriseum culture. (a) Total ion current (TIC) for the purified fungal extract. HPLC chromatogram showing the retention times and relative peak areas of the taxanes extracted from the P. aurantiogriseum culture medium. (b) Mass spectrum of paclitaxel extracted from total ion current. Figure S3 Sequence alignments of GGPPS in the endophytic P. aurantiogriseum NRRL 62431 and in the host Taxus. Figure S4 Sequence alignments of acyltransferases in the endophytic P. aurantiogriseum NRRL 62431 and in the host Taxus. Figure S5 Sequence alignments of P450 in the endophytic P. aurantiogriseum NRRL 62431 and in the host Taxus. Figure S6 Sequence alignments of PAM in the endophytic P. aurantiogriseum NRRL 62431 and in the host Taxus.

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Additional file 2:

Table S1. List of the 13 reported paclitaxel biosynthetic enzymes in Taxus sp. Table S2 Gene ontology classification of P. aurantiogriseum NRRL 62431 genes.

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Additional file 3:

Data S1. Transcription factors in the genome of Penicillium aurantiogriseum NRRL 62431. Data S2 Transporters in the genome of Penicillium aurantiogriseum NRRL 62431. Data S3 Blast result of the 13 reported paclitaxel biosynthetic genes in Taxus sp. against the genome of Penicillium aurantiogriseum NRRL 62431. Data S4 Blast result of the 13 reported paclitaxel biosynthetic genes in Taxus sp. against the unigenes in the transcriptome of Hazel (Corylus avellana L.). Data S5 DNA sequences of paclitaxel biosynthetic gene candidates in Hazel (Corylus avellana L.). Data S6 Blast results of Hazel paclitaxel biosynthetic gene candidates against Penicillium aurantiogriseum NRRL 62431 proteins. Data S7 DNA sequences of paclitaxel biosynthetic genes in Taxus baccata. Data S8 Blast result of paclitaxel biosynthetic genes of Taxus baccata against Penicillium aurantiogriseum NRRL 62431 proteins. Data S9 Blast result of the paclitaxel biosynthetic genes candidates in Penicillium aurantiogriseum NRRL 62431 against the genome of EF0021.

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