• Corpus ID: 13829893

Functional annotation of expressed sequence tags of Papaver somniferum.

@article{Priya2012FunctionalAO,
  title={Functional annotation of expressed sequence tags of Papaver somniferum.},
  author={Avantika Priya and Himanshu Tripathi and Dharmendra Kumar Yadav and Feroz Khan and Vikrant Gupta and Rakesh Kumar Shukla and Mahendra Pandurang Darokar},
  journal={Plant Omics},
  year={2012},
  volume={5},
  pages={223-230}
}

• A. Priya, Himanshu Tripathi, +4 authors M. Darokar
• Published 2012
• Biology
• Plant Omics

Papaver somniferum (opium poppy) is the source for several pharmaceutical benzylisoquinoline alkaloids (BIA) including morphine, codeine and sanguinarine. In an attempt to identify additional biosynthetic steps at the molecular level, a large expressed sequence tag (EST) dataset with a total of 20,532 sequences from opium poppy were assembled and functionally annotated. Sequence cleaning filter showed 20,445 (709 trimmed) valid sequences and 87 trashed sequences at 96% minimum identity parameter for an alignment with a contaminant. Repeat masking filter showed length of valid sequences 1,69,60,151 bp, GC level 41.12% and masked bases 5,01,768 bp (2.96%) by using RepBase (update 8.12) repeats library of Arabidopsis. Elements observed in EST sequences were 1017 retroelements, 55 LINEs, 55 L1/CIN4, 962 LTR elements, 412 Ty1/Copia, 550 Gypsy/DIRS1, 56 DNA transposons, 15 hoboActivator, 7 Tc1-IS630-Pogo, 7 En-Spm, 11 MuDR-IS905, 6 Tourist/Harbinger, 1 satellite, 920 simple repeats and 1697 low complexity elements. NCBI's vector library UniVec (core) and plastids library of Arabidopsis were used for masking vector and organelle sequences, respectively. For EST sequence assembly, the cutoff for overlap sequence identity was kept 80%. A total of 15,279 assembled unique transcripts were identified, which include 1,408 contigs and 13,871 singletons. Functional annotation was performed through BLASTX using UniProtKB/Swiss-Prot database. EST sequences were retrieved from dbEST (NCBI) and processed, cleaned, clustered and assembled through Gencheck, EGassembler, Phred, RepeatMasker, Cross-Match, Phrap and Cap3 softwares. Mostly hypothetical genes were observed apart from important genes related to secondary metabolism such as enzymes of BIA biosynthesis e.g ., stylopine synthase , S-norcoclaurine synthase 1, salutaridine synthase, salutaridine reductase, (S)-coclaurine Nmethyltransferase, S-adenosyl-L-methionine:3'-hydroxy-N-methylcoclaurine 4'-O-methyltransferase and salutaridinol 7-Oacetyltransferase. This functionally annotated EST dataset will be a useful resource for further studies such as taxonomy, molecular breeding, genetics, genomics and secondary metabolism.