Abstract
Amplicon sequencing of bacterial or fungal marker sequences is currently the main method for the study of endophytic microorganisms in plants. However, it cannot obtain all types of microorganisms, including bacteria, fungi, protozoa, etc., in samples, nor compare the relative content between endophytic microorganisms and plants and between different types of endophytes. Therefore, it is necessary to develop a better analysis strategy for endophytic microorganism investigation. In this study, a new analysis strategy was developed to obtain endophytic microbiome information from plant transcriptome data. Results showed that the new strategy can obtain the composition of microbial communities and the relative content between plants and endophytic microorganisms, and between different types of endophytic microorganisms from the plant transcriptome data. Compared with the amplicon sequencing method, more endophytic microorganisms and relative content information can be obtained with the new strategy, which can greatly broaden the research scope and save the experimental cost. Furthermore, the advantages and effectiveness of the new strategy were verified with different analysis of the microbial composition, correlation analysis, inoculant content test, and repeatability test.