Data from: Characterization of fungal community associated with quinoa

The uploaded files correspond to fungal DNA sequences. These data were used for identification of quinoa stem endophyte isolates. Fungal communities are central elements of phytobiomes, yet their roles in mediating plant-insect interactions remain poorly understood. We used culture-based isolation from stems and amplicon-based profiling of rhizosphere soils to characterize quinoa-associated fungi across six site-year combinations in Colorado and to relate community patterns to abundance of stem-boring fly <i>Amauromyza karli</i> Hendel (Diptera: Agromyzidae). Eighteen stem endophytes dominated by Ascomycota were isolated. Soil sequencing resolved 23 core amplicon sequence variants detected across all site-years; the core was primarily Ascomycota, with <i>Fusarium</i> spp. <i>Alternaria</i> spp., and <i>Plectosphaerella</i> spp. comprising over half of relative abundance of the entire community. Alpha diversity (richness, Shannon, inverse Simpson) differed significantly among site-years, and beta-diversity analyses revealed clustering by site and year. Abundance of adult <i>A. karli</i> was correlated positively with soil fungal richness and Shannon diversity and was also significantly associated with differences in community composition. Indicator and differential-abundance analyses identified taxa linked to low fly abundance (e.g., <i>Cladosporium herbarum</i>, <i>Alternaria </i>spp.) versus high abundance (e.g., <i>Fusarium </i><i>solani</i>, <i>Microdochium </i>spp.). <i>Fusarium</i> spp., and <i>Alternaria</i> spp. were more prevalent in fields with high larval abundance, whereas antagonistic endophytes such as <i>Gibellulopsis piscis</i><i> </i>and <i>Heydenia</i> spp. dominated in low-abundance fields. These results indicated that community composition impacted pest pressure, with pathogenic fungi coinciding with higher fly abundance and entomopathogenic fungi enriched where larval pressure was lower. These findings identify candidate taxa for microbiome-informed integrated pest management and underscore the potential of site-specific practices (e.g., intercrops, organic amendments) to foster fungal communities that enhance quinoa resilience.