Gene expansion in G. elata and microbial community analysis. a REViGO semantic similarity scatter plot of Biology Process Gene Ontology terms for expanded genes in G. elata. In semantic spaces, the proximity between circles represents relatedness (similarity) of the GO terms. Similar GO terms are close together in the plot. The axes in the plot have no intrinsic meaning, but were used to measure pairwise similarities between GO terms. Color indicates degree of enrichment for each process presented as the p-value from the hyper-geometric test. b The draft mitochondrial genome of G. elata. Nineteen contigs are manually displayed as a circle, including 12 circular contigs in orange (ornamented with stars) and 7 linear contigs (in blue). The genes are indicated in the middle circle, and are color coded as follows: trn (blue), rrn (light blue), atp (red), and other protein-coding genes (black). The duplicated atp genes and their fragments are detailed in the inner circle. The duplicated genes are suffixed with ‘b’, and the gene fragments are suffixed with ‘fragment’. c Gene expression heat map of the normalized RNA-Seq data for genes encoding the monocot mannose-binding lectin antifungal proteins (GAFP) in G. elata16. The units indicate the expression levels of different gene members of GAFP in the protocorm, juvenile tuber, immature tuber, mature tuber, and scape of G. elata (only shown where the gene expression level RPKM > 1, n = 3). d Venn diagrams showing the number of shared and unique fungal and bacterial operational taxonomic units (OTUs) based on the ITS and 16S sequence analyses in protocorms, juvenile tubers, immature tubers, and mature tubers of G. elata. OTUs showed the composition and abundance of the microbe species, which were defined at 3% dissimilarity