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Next-generation sequencing (NGS) transcriptomes reveal association of multiple genes and pathways contributing to secondary metabolites accumulation in tuberous roots of Aconitum heterophyllum Wall.

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Abstract

Main conclusion

The transcriptomes of Aconitum heterophyllum were assembled and characterized for the first time to decipher molecular components contributing to biosynthesis and accumulation of metabolites in tuberous roots.

Aconitum heterophyllum Wall., popularly known as Atis, is a high-value medicinal herb of North-Western Himalayas. No information exists as of today on genetic factors contributing to the biosynthesis of secondary metabolites accumulating in tuberous roots, thereby, limiting genetic interventions towards genetic improvement of A. heterophyllum. Illumina paired-end sequencing followed by de novo assembly yielded 75,548 transcripts for root transcriptome and 39,100 transcripts for shoot transcriptome with minimum length of 200 bp. Biological role analysis of root versus shoot transcriptomes assigned 27,596 and 16,604 root transcripts; 12,340 and 9398 shoot transcripts into gene ontology and clusters of orthologous group, respectively. KEGG pathway mapping assigned 37 and 31 transcripts onto starch–sucrose metabolism while 329 and 341 KEGG orthologies associated with transcripts were found to be involved in biosynthesis of various secondary metabolites for root and shoot transcriptomes, respectively. In silico expression profiling of the mevalonate/2-C-methyl-d-erythritol 4-phosphate (non-mevalonate) pathway genes for aconites biosynthesis revealed 4 genes HMGR (3-hydroxy-3-methylglutaryl-CoA reductase), MVK (mevalonate kinase), MVDD (mevalonate diphosphate decarboxylase) and HDS (1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase) with higher expression in root transcriptome compared to shoot transcriptome suggesting their key role in biosynthesis of aconite alkaloids. Five genes, GMPase (geranyl diphosphate mannose pyrophosphorylase), SHAGGY, RBX1 (RING-box protein 1), SRF receptor kinases and β-amylase, implicated in tuberous root formation in other plant species showed higher levels of expression in tuberous roots compared to shoots. A total of 15,487 transcription factors belonging to bHLH, MYB, bZIP families and 399 ABC transporters which regulate biosynthesis and accumulation of bioactive compounds were identified in root and shoot transcriptomes. The expression of 5 ABC transporters involved in tuberous root development was validated by quantitative PCR analysis. Network connectivity diagrams were drawn for starch–sucrose metabolism and isoquinoline alkaloid biosynthesis associated with tuberous root growth and secondary metabolism, respectively, in root transcriptome of A. heterophyllum. The current endeavor will be of practical importance in planning a suitable genetic intervention strategy for the improvement of A. heterophyllum.

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Abbreviations

AHSR:

Root transcriptome

AHSS:

Shoot transcriptome

COG:

Cluster of orthologous group

GO:

Gene ontology

KO:

KEGG orthology

MEP:

2-C-Methyl-d-erythritol 4-phosphate

MVA:

Mevalonate

NGS:

Next-generation sequencing

FPKM:

Fragments per kilobase of transcript per million fragments mapped

SSR:

Simple sequence repeat

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Acknowledgments

The authors are thankful to the Department of Biotechnology, Ministry of Science and Technology, Government of India, for providing funds to RSC in the form of a program support on high-value medicinal plants. The authentic plant material provided by Dr. Sandeep Sharma, HFRI, Panthaghati, Shimla (HP), is also acknowledged.

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The authors declare that they have no conflict of interest.

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    Authors and Affiliations

    1. Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234, Himachal Pradesh, India

      Tarun Pal, Nikhil Malhotra, Sree Krishna Chanumolu & Rajinder Singh Chauhan

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    1. Tarun Pal
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    2. Nikhil Malhotra
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    3. Sree Krishna Chanumolu
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    4. Rajinder Singh Chauhan
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    Correspondence to Rajinder Singh Chauhan .

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    Tarun Pal and Nikhil Malhotra contributed equally to this work.

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    Pal, T., Malhotra, N., Chanumolu, S.K. et al. Next-generation sequencing (NGS) transcriptomes reveal association of multiple genes and pathways contributing to secondary metabolites accumulation in tuberous roots of Aconitum heterophyllum Wall.. Planta 242, 239–258 (2015). https://doi.org/10.1007/s00425-015-2304-6

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