Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes |
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| Authors: | Yeonhwa Jo Chang-Gi Back Kook-Hyung Kim Hyosub Chu Jeong Hun Lee Sang Hyun Moh Won Kyong Cho |
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| Affiliation: | 1.Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (Y.J.); (K.-H.K.);2.Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju 55365, Korea;3.R&D Division, BERTIS Inc., Seongnam-si 13605, Korea;4.Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Korea; |
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| Abstract: | Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study. |
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