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Comparative transcriptome profiling of healthy and diseased Chowghat Green Dwarf coconut palms from root (wilt) disease hot spots

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Abstract

Understanding the molecular basis of host-pathogen interactions is imperative for devising disease management strategies. The root (wilt) disease is the foremost debilitating disease threatening coconut production in India. To explore the molecular mechanisms involved in compatible and incompatible interactions, global transcriptome profiling of leaves of healthy and diseased Chowghat Green Dwarf (CGD) palms was conducted. RNA-Seq analysis generated more than 190 million 100 bp reads from both healthy and diseased samples. Assembled transcriptome yielded 59,282 transcripts with a median length of 987 bp. BLASTX annotation of transcriptome resulted in 39,665 transcripts getting annotated from Uniprot and date palm proteome database. Differential gene expression profiling analysis revealed 2718 transcripts to be up- or down- regulated in the diseased palms in comparison to healthy control at a fold change of 2 and above with a p value <=0.05. The differentially expressed transcripts could be categorized into pathways which included cell wall biogenesis, primary and secondary metabolism, plant-pathogen interaction, cellular transport, hormone biosynthesis and signaling. Validation by quantitative real time PCR (RT-qPCR) of a set of arbitrarily selected genes, both up-regulated and down-regulated, established a comparable pattern as observed by RNA-Seq analysis. Overall, the resources generated in this study provide an in-depth analysis and new insights into the interaction of coconut palms with the root (wilt) disease pathogen.

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Acknowledgements

The authors wish to thank Indian Council of Agricultural Research (ICAR) for funding.

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Authors and Affiliations

  1. ICAR-Central Plantation Crops Research Institute, Kasaragod, Kerala, 671124, India

    M. K. Rajesh, K. E. Rachana & A. Karun

  2. Bionivid Technology Private Limited, Bengaluru, Karnataka, 560043, India

    K. Kulkarni

  3. National Institute of Technology, Rourkela, Odisha, 769008, India

    B. B. Sahu

  4. ICAR-CPCRI (RS), Kayamkulam, Kerala, 690533, India

    R. J. Thomas

Authors
  1. M. K. Rajesh
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  2. K. E. Rachana
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  3. K. Kulkarni
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  4. B. B. Sahu
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  5. R. J. Thomas
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  6. A. Karun
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Contributions

MKR and AK conceived and designed this research. MKR, KER, RJT and AK conducted the experiments. MKR, KK, KER and BBS analyzed the data. MKR and BBS wrote the manuscript. All authors read and approved the manuscript.

Corresponding author

Correspondence to M. K. Rajesh.

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Conflict of interest

The authors declare that they have no conflict of interest.

Human studies and participants

There was no involvement of human participants and/or animals in the present study.

Informed consent

The research does not involve informed consent.

Electronic supplementary material

Suppl. Fig. 1

Transcript length distribution in the assembled coconut leaf transcriptome (JPEG 50 kb)

Suppl. Fig. 2

a. Pie chart showing key enriched biological processes in coconut leaf transcriptome based on GO annotations obtained from date palm genome database (JPEG 54 kb)

Suppl. Fig. 2

b. Pie chart showing key enriched sub cellular localization in coconut leaf transcriptome based on GO annotations obtained from date palm genome database (JPEG 45 kb)

Suppl. Fig. 2

c. Pie chart showing key enriched molecular functions in coconut leaf transcriptome based on GO annotations obtained from date palm genome database (JPEG 49 kb)

Suppl. Table 1

(DOC 52 kb)

Suppl. Table 2

(DOC 52 kb)

Suppl. Table 3

List of non-redundant transcripts obtained (XLS 19390 kb)

Suppl. Table 4

(DOC 36 kb)

Suppl. Table 5

Annotation of coconut transcripts with date palm proteome (XLS 22372 kb)

Suppl. Table 6

Transcripts specifically expressed in diseased palms (XLS 64 kb)

Suppl. Table 7

Transcripts specifically expressed in healthy palms (XLS 163 kb)

Suppl. Table 8

Transcripts up-regulated in diseased palms (XLS 578 kb)

Suppl. Table 9

Transcripts down-regulated in diseased palms (XLS 453 kb)

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Rajesh, M.K., Rachana, K.E., Kulkarni, K. et al. Comparative transcriptome profiling of healthy and diseased Chowghat Green Dwarf coconut palms from root (wilt) disease hot spots. Eur J Plant Pathol 151, 173–193 (2018). https://doi.org/10.1007/s10658-017-1365-8

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  • DOI: https://doi.org/10.1007/s10658-017-1365-8

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