Comparative Metagenomic Analysis of Endophytic Fungal Communities in Shoot and Corm Tissues of Gladiolus spp.
cycle without causing apparent harm to the host plant. These microorganisms include bacteria, fungi, actinomycetes, and mycoplasma-like organisms, among which fungal endophytes are particularly diverse and ecologically significant. Endophytic fungi are known to enhance plant fitness by producing bioactive compounds, improving nutrient acquisition, and conferring resistance to biotic and abiotic stresses. Many endophytes also synthesize antimicrobial metabolites that have been exploited for pharmaceutical and agricultural applications.Fungal endophytes have been documented across a wide range of plant species, with the majority belonging to the phylum Ascomycota, followed by Basidiomycota and other minor fungal lineages. Advances in next-generation sequencing (NGS) technologies have revolutionized the study of endophytic microbial communities by enabling culture-independent profiling of taxonomic diversity and community structure. Metagenomics is a novel approach which integrates genomics, microbial ecology, and bioinformatics, allows direct analysis of nucleic acids from environmental samples, facilitating comprehensive insights into microbial diversity and functional potential.NGS platforms such as Roche 454 pyrosequencing, Illumina MiSeq, and Ion Torrent PGM have been widely employed to characterize fungal communities in diverse ecological niches, including the phyllosphere, rhizosphere, and internal plant tissues. Despite these advances, metagenomic studies focusing on endophytic fungal communities in horticultural crops remain limited.Gladiolus is an economically important ornamental crop, severely affected by Fusarium wilt caused by Fusarium spp. Among the cultivated germplasms, Pusa Rajat is highly susceptible, whereas Pusa Manmohak exhibits comparatively greater resistance reported in field trails in ICAR-IARI, New Delhi. Differences in disease susceptibility may be partly attributed to variation in associated endophytic fungal communities. Therefore, the objectives of the present study were to (i) compare the richness and diversity of endophytic fungal communities between Pusa Rajat and Pusa Manmohak, and (ii) characterize tissue-specific and genotype-dependent taxonomic patterns of endophytic fungi using Illumina MiSeq-based ITS metabarcoding.