We compared the diversity of endophytes in buckwheat (Fagopyrum esculentum Moench.) seeds collected from the Dingxi, Datong, and Xizang autonomous region in China. The ITS and 16S rRNA gene sequences of endophytic fungi and bacteria were obtained, respectively. The obtained raw reads were subjected to quality control and then classified to microbial genomes. All effective tags were clustered into operational taxonomic units (OTUs) and the representative sequences were selected for the annotation of taxonomic information. Afterwards, alpha and beta diversity analyses, a taxonomic composition, and differential analyses were performed. A total of 316854 and 942202 clean reads were obtained from all samples for bacteria and fungi, respectively. The diversity of endophytes varied at the three different locations. At the genus level, the top 5 dominant bacteria were Fraxinus excelsior, Escherichia shigella, Pseudomonas, Hymenobacter, and Sphingomonas, while the top 5 dominant fungi belonged to Cryptococcus, Aureobasidium, Botrytis, Acremonium, and Didymella. Pseudomonas, Aureimonas, and Beauveria were also found in the seeds from Xizang, Datong, and Dingxi. The present study for the first time investigated the microbiome from different environments of buckwheat using sequencing technology. The data will help to excavate the potential of biological control of diseases and pests and inoculation of beneficial microbiome to promote crop growth.
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