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

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.

Establishment and Validation of a New Analysis Strategy for the Study of Plant Endophytic Microorganisms

“…Generally, the relative content was bacteria > fungi > protozoa > viruses, but in maize kernels and roots, the relative content of fungi exceeded that of bacteria. In general, numerous studies have shown that bacteria are the predominant of all microorganisms [45][46][47], but the results of the new analysis strategy showed the composition of various types of microorganisms, from which it can be seen that eukaryotic microorganisms, including fungi and protozoa, sometimes dominate in specific tissues. In addition, protozoa are generally not a hot spot for research on plant endophytic microorganisms; however, in this study, we note that the relative content of protozoa should not be neglected, as they may also play an important role in promoting plant growth and other aspects.…”

Uncovering the special microbiota associated with occurrence and progression of gastric cancer by using RNA-sequencing

“…These new techniques provides more information about the composition of the bacterial community than traditional cloning and sequencing methods. Among them, Kraken2 has been found to be very reliable in microbial identification in a large number of studies, especially in microbiome studies based on RNA sequencing data 19 . Poore has been provided a valuable and feasible approach to discovering unique microbial information by analyzing genome-wide and transcriptomic data from blood and tissues of cancer patients 20 .…”

Meta’omics: Challenges and Applications

“…Jo and colleagues [ 6 ] instead exploited existing RNA-seq data to carry out an extensive characterization of the garlic microbiome. Their approach highlights that reanalysis of existing datasets on different premises is a valid approach to metagenomics.…”