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Data on large cardamom transcriptome associated with Chirke disease.

K Mary Mathew1, Ranjanan Reshma1, M Geethu1

  • 1Indian Cardamom Research Institute, Spices Board Min Commerce & Industry, Government of India, Myladumpara, Idukki, Kerala 685553, India.

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Summary

Large cardamom (Amomum subulatum) plants infected with Large Cardamom Chirke Virus (LCCV) show significant gene expression changes. This study used RNA sequencing to identify these differentially expressed genes in diseased plants.

Keywords:
Differential expressionLarge cardamomRNA sequencingTranscriptome

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Area of Science:

  • Botany
  • Plant Pathology
  • Genomics

Background:

  • Large cardamom (Amomum subulatum) is a vital spice crop native to Southeast Asia.
  • Chirke disease, caused by Large Cardamom Chirke Virus (LCCV), severely impacts large cardamom cultivation.
  • Environmental changes and poor agricultural practices contribute to aphid infestations, spreading LCCV.

Purpose of the Study:

  • To investigate the molecular mechanisms underlying LCCV infection in large cardamom.
  • To identify differentially expressed genes in large cardamom leaves due to Chirke disease.

Main Methods:

  • Transcriptome sequencing of healthy and diseased large cardamom leaf tissues using HiSeq™ 2000.
  • De novo assembly of RNA-seq data using the TRINITY assembler.
  • Analysis of raw reads and assembled contigs for gene expression profiling.

Main Results:

  • Generated over 77 million raw reads for control and 72 million for diseased samples.
  • Assembled transcriptomes yielded 156,822 contigs (control) and 148,953 contigs (diseased).
  • Identified significantly differentially expressed genes between healthy and LCCV-infected large cardamom.

Conclusions:

  • RNA sequencing provides a comprehensive view of gene expression changes in response to LCCV infection.
  • Understanding these molecular changes is crucial for developing disease management strategies for large cardamom.