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Comparative NGS Transcriptomics Unravels Molecular Components Associated with Mosaic Virus Infection in a Bioenergy Plant Species, Jatropha curcas L.

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Abstract

Jatropha curcas, a promising bioenergy crop is becoming vulnerable to various biotic stresses due to large-scale cultivation of selected genotypes, thereby affecting its yield potential. Virus causing mosaic disease is prevalent in Jatropha plantations and causing significant reduction in seed yield and quality. To better understand the molecular mechanisms associated with virus infection response, we performed RNA-seq-based comprehensive transcriptome sequencing of symptomatic virus-infected (JV) and healthy (JH) leaf tissues of J. curcas. Through reference genome-based mapping approach, 55,755 genes expressed in both samples were identified. Differential expression analysis identified genes linked to various pathways, upregulated and downregulated during mosaic virus infection. Upon KEGG-based functional annotation, it was observed that various metabolism-associated processes along with oxidative phosphorylation, endocytosis, terpenoid biosynthesis, and hormone signal transduction were upregulated whereas photosynthesis, anthocyanin biosynthesis, plant-pathogen interaction, and calcium signaling were downregulated in response to virus infection. Significantly, genes associated with hormone signal transduction were upregulated as physiological symptoms induced upon mosaic virus infection is due to the interplay of various phytohormones regulating general growth and development of plant. Also, many genes regulating photosynthesis which were downregulated during virus infection showed repressed rate of photosynthesis and also reduction in seed yield and oil content upon mosaic virus infection in J. curcas. RT-qPCR-based experimental validation approach was supplemented to confirm the computational identification. The study provides a repertoire of molecular components which have been affected in response to virus infection, and their precise role can be further functionally validated.

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Abbreviations

ABA:

Abscisic acid

CDS:

Coding sequence

CML:

Calcium-binding protein

CMV:

Cucumber mosaic virus

CNGCs:

Cyclic nucleotide-gated ion channels

FPKM:

Fragments per kilobase of transcripts per million mapped reads

GO:

Gene ontology

JA:

Jasmonic acid

JcMD:

Jatropha curcas mosaic disease

JH:

Healthy

JV:

Virus infected

KEGG:

Kyoto Encyclopedia of Genes and Genomes

NGS:

Next-generation sequencing

RNA-seq:

Ribose nucleic acid sequencing

RPM1:

Resistance to Pseudomonas syringae PV Maculicola 1

RPS2:

Resistance to Pseudomonas syringae 2

RT-qPCR:

Reverse transcription-quantitative polymerase chain reaction

SA:

Salicylic acid

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Acknowledgments

The authors are thankful to Mr. Ankush Bansal (Jaypee University of Information Technology) for assisting in the coexpression network analysis and Mr. Tarun Pal (Jaypee University of Information Technology) for assisting in maintaining transcriptome data in the in-house web server. Financial support from the Department of Biotechnology (DBT), Govt. of India, to RSC in the form of a R&D project on Jatropha curcas is also acknowledged. The authors are also thankful to Dr. Sandeep Sharma, Scientist, Himalayan Forest Research Institute (HFRI), Shimla, India, for providing experimental farm facilities.

Availability of Transcriptome Data

The raw reads and annotated data, i.e., CDSs for JH and JV are available at http://14.139.240.55/NGS/download.php.

Author Contribution

AS and RSC defined the research theme and designed experiments. AS performed experiments and in silico analysis. AS and RSC wrote the manuscript and discussed analysis. Both authors read and approved the final manuscript.

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  1. Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, H P, 173 215, India

    Archit Sood & Rajinder Singh Chauhan

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  1. Archit Sood
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Correspondence to Rajinder Singh Chauhan.

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Sood, A., Chauhan, R.S. Comparative NGS Transcriptomics Unravels Molecular Components Associated with Mosaic Virus Infection in a Bioenergy Plant Species, Jatropha curcas L.. Bioenerg. Res. 10, 129–145 (2017). https://doi.org/10.1007/s12155-016-9783-6

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