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Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes.

Yeonhwa Jo1, Chang-Gi Back2, Kook-Hyung Kim1

  • 1Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.

International Journal of Molecular Sciences
|July 2, 2021
PubMed
Summary

This study identified bacteria, viruses, and fungi in garlic tissues using RNA sequencing. Bacteria and viruses were most common, with specific species like Streptomyces lividans and allexiviruses dominating different tissues.

Keywords:
bacteriafruitfungimetagenomicsmetatranscriptomicsmicrobiomepepperviruses

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Area of Science:

  • Plant Pathology
  • Microbiology
  • Bioinformatics

Background:

  • Garlic (Allium sativum) is vital but susceptible to diseases due to clonal propagation.
  • Understanding the garlic microbiome is crucial for crop health and yield.

Purpose of the Study:

  • To identify bacteria, fungi, and viruses in various garlic tissues using in silico analysis.
  • To characterize the microbial community composition across different garlic tissues.

Main Methods:

  • In silico analysis of garlic RNA-sequencing data.
  • Utilized Kraken2 for microbial identification and classification.
  • Sequenced viral genomes.

Main Results:

  • Inflorescences, flowers, and bulb cloves showed the highest microbial diversity.
  • Bacteria constituted 57% and viruses 41% of microbial reads; fungi were 1%.
  • Dominant species included Streptomyces lividans (bacteria) and Fusarium pseudograminearum (fungi); allexiviruses, particularly garlic virus C, were abundant.

Conclusions:

  • Microbial communities in garlic are tissue-specific, with dominant microorganisms in each.
  • Kraken2 is effective for bacterial identification in RNA-seq data but has limitations for virome studies.
  • This research provides insights into the garlic microbiome and viral populations.