De novo transcriptome analysis using 454 pyrosequencing of the Himalayan Mayapple,Podophyllum hexandrum
IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata
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| Title |
De novo transcriptome analysis using 454 pyrosequencing of the Himalayan Mayapple,Podophyllum hexandrum
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| Creator |
Bhattacharyya, Dipto
Sinha, Ragini Hazra, Saptarshi Datta, Riddhi Chattopadhyay, Sharmila |
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| Subject |
Drug Development/Diagnostics & Biotechnology
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| Description |
Background: The Himalayan or Indian Mayapple (Podophyllum hexandrum Royle) produces podophyllotoxin, which
is used in the production of semisynthetic anticancer drugs. High throughput transcriptome sequences or genomic
sequence data from the Indian Mayapple are essential for further understanding of the podophyllotoxin
biosynthetic pathway.
Results: 454 pyrosequencing of a P. hexandrum cell culture normalized cDNA library generated 2,667,207 raw reads
and 1,503,232 high quality reads, with an average read length of 138 bp. The denovo assembly was performed by
Newbler using default and optimized parameters. The optimized parameter generated 40, 380 assembled
sequences, comprising 12,940 contigs and 27,440 singlets which resulted in better assembly as compared to default
parameters. BLASTX analysis resulted in the annotation of 40,380 contigs/singlet using a cut-off value of ≤1E-03.
High similarity to Medicago truncatula using optimized parameters and to Populus trichocarpa using default
parameters was noted. The Kyoto encyclopedia of genes and genomes (KEGG) analysis using KEGG Automatic
Annotation Server (KAAS) combined with domain analysis of the assembled transcripts revealed putative members
of secondary metabolism pathways that may be involved in podophyllotoxin biosynthesis. A proposed schematic
pathway for phenylpropanoids and podophyllotoxin biosynthesis was generated. Expression profiling was carried
out based on fragments per kilobase of exon per million fragments (FPKM). 1036 simple sequence repeats were
predicted in the P. hexandrum sequences. Sixty-nine transcripts were mapped to 99 mature and precursor microRNAs
from the plant microRNA database. Around 961 transcripts containing transcription factor domains were noted. High
performance liquid chromatography analysis showed the peak accumulation of podophyllotoxin in 12-day cell
suspension cultures. A comparative qRT-PCR analysis of phenylpropanoid pathway genes identified in the present data
was performed to analyze their expression patterns in 12-day cell culture, callus and rhizome.
Conclusions: The present data will help the identification of the potential genes and transcription factors involved in
podophyllotoxin biosynthesis in P. hexandrum. The assembled transcripts could serve as potential candidates for
marker discovery and conservation, which should form the foundations for future endeavors.
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| Publisher |
BioMed Central
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| Date |
2013
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| Type |
Article
PeerReviewed |
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| Format |
application/pdf
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| Identifier |
http://www.eprints.iicb.res.in/2477/1/BMC_Medical_Genomics_(2016)_9;15.pdf
Bhattacharyya, Dipto and Sinha, Ragini and Hazra, Saptarshi and Datta, Riddhi and Chattopadhyay, Sharmila (2013) De novo transcriptome analysis using 454 pyrosequencing of the Himalayan Mayapple,Podophyllum hexandrum. BMC Genomics, 14 (748). 1-`13. |
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| Relation |
http://www.eprints.iicb.res.in/2477/
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