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, 11 (3), e0150273
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De Novo Transcriptome Analysis of Medicinally Important Plantago Ovata Using RNA-Seq

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De Novo Transcriptome Analysis of Medicinally Important Plantago Ovata Using RNA-Seq

Shivanjali Kotwal et al. PLoS One.

Abstract

Plantago ovata is an economically and medicinally important plant of the family Plantaginaceae. It is used extensively for the production of seed husk for its application in pharmaceutical, food and cosmetic industries. In the present study, the transcriptome of P. ovata ovary was sequenced using Illumina Genome Analyzer platform to characterize the mucilage biosynthesis pathway in the plant. De novo assembly was carried out using Oases followed by velvet. A total of 46,955 non-redundant transcripts (≥100 bp) using ~29 million high-quality paired end reads were generated. Functional categorization of these transcripts revealed the presence of several genes involved in various biological processes like metabolic pathways, mucilage biosynthesis, biosynthesis of secondary metabolites and antioxidants. In addition, simple sequence-repeat motifs, non-coding RNAs and transcription factors were also identified. Expression profiling of some genes involved in mucilage biosynthetic pathway was performed in different tissues of P. ovata using Real time PCR analysis. The study has resulted in a valuable resource for further studies on gene expression, genomics and functional genomics in P. ovata.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Plantago ovata plant at (a) vegetative and (b) reproductive phase, (c) P. ovata ovaries.
Fig 2
Fig 2. Comparison of de novo assembly of the data obtained through Velvet, Abyss, CLC genomics workbench, Oases and merged assembly of Oases programs.
The merged assembly produces less number of transcripts but the N50 transcript length and Average transcript length is much higher as compare to others.
Fig 3
Fig 3. Percentage GC content of P. ovata, A. thaliana, rice, tomato and Eucalyptus transcripts.
The percentage GC content of P. ovata and Eucalyptus falls into the range of monocots.
Fig 4
Fig 4. Gene Ontology classification of the assembled Plantago ovatatranscripts in different categories of biological process, molecular function and cellular component.
Fig 5
Fig 5. KOG functional classification of unigenes clustered into four major categories: poorly characterized, information storage and processing, cellular process and signaling and metabolism.
Fig 6
Fig 6. Distribution of Plantago ovata transcripts in different transcription factor families.
C3H, PHD and MADS transcription factor families were enriched in number however CCAAT and Tify were least in number.
Fig 7
Fig 7. Distribution of SSR repeat type and repeat motifs.
Fig (a) different repeat type SSRs and Fig (b) different repeat motifs and percentage of transcripts corresponding to them.
Fig 8
Fig 8. Different classes of non-coding RNAs (ncRNAs) as identified by the Repeat Masker software in P. ovata.

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References

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Grant support

The authors are grateful to Department of Biotechnology (DBT), Govt. of India for financial assistance in the form of a research project to MKD. Ms. Shivanjali Kotwal is grateful to the Department of Science and Technology (DST), Govt. of India for an INSPIRE fellowship.
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