Supplementary file 1_Biological characteristics and genetics differentiation of smut fungi in Coix L..docx

Adlay is one of the most important crops of subtropical regions, and it can be affected by several fungal pathogens, with adlay smut being one of the most devastating diseases. In this paper, two smut fungi strains, ZC202104 and ZC202205, were isolated from infected plants and identified as Ustilago coicis based on morphology and multi-gene phylogenetic analysis (ITS, LSU, ATP6). The two strains showed distinct genetic differentiation in morphology characteristics. ZC202205 exhibited a unique off-white colony with central fluff and lacked yeast-like folds, a feature not previously reported. Moreover, the two strains also differed in cultural features and mycelial nutrient composition. Genome sequencing revealed similar genome sizes (~22 Mb) and GC content (~53.8%) for both strains, with thousands of interspersed and tandem repeats. Cluster analysis of homologous gene families encompassed 10 species of smut fungi strains, with encoding gene counts ranging from 5,756 to 6,783. The phylogenetic clustering annalysis revealed that the Ustilago genus diverged into two clades approximately 109.2 million years ago (MYA) and Sporisorium genus were further diverged from Ustilago in about 103 million years ago. Ustilago coicis clustered with Ustilago trichophora, indicating a closer phylogenetic relationship. Gene family dynamics analysis revealed a significant trend of gene expansion in Ustilago coicis, with few genes contracted. This study integrates the biological characteristics and genomic data of Ustilago coicis to enhance the understanding of its evolutionary status, providing a foundation for elucidating the infection mechanisms of Ustilago coicis as well as its development and utilization.