Bacterial and fungal microbiome dataset from holobionts of CP4-EPSPS–containing hybrids and wild-type Brassica juncea in South Korea

This dataset provides comprehensive profiles of bacterial and fungal communities associated with the holobionts of CP4-EPSPS-containing hybrids and wild-type <i>B. juncea</i> in a natural roadside habitat. The hybrids were genetically consistent with <i>B. napus</i> × <i>B. juncea</i> origin and possible backcrossing with <i>B. juncea</i>, though the site and mechanism of hybridization are unclear. A total of 120 holobiont samples, including flowers, leaves, dead leaves, roots, and surrounding soil, were collected from twelve wild-type and twelve hybrid individuals (60 samples per group), in a natural roadside environment. Bacterial 16S rRNA and fungal ITS genes obtained through the Illumina Miseq approach were employed to characterize the holobiont-associated microbiomes. Metadata and raw sequences collected in this study are available from the National Center for Biotechnology Information (BioProject ID: PRJNA1237916 and 1237917). Amplicon Sequence Variants (ASVs) of bacteria and fungi were processed using the DADA2 pipeline. After quality filtering, trimming, and eliminating the chimeric sequences, 15,131 bacterial and 5,353 fungal ASVs were identified in the holobiont. Proteobacteria in bacteria, and Ascomycota in fungi were the predominant groups in the holobiont. Given the reported unintended releases and hybridization of transgenic <i>B. napus</i> in South Korea, this dataset provides a comprehensive baseline of the microbial communities associated with wild-type and hybrids, offering novel insights into their holobiont structures.