The Three-Dimensional Structure of the Genome of the Dark Septate Endophyte Exophiala tremulae and Its Symbiosis Effect on Alpine Meadow Plant Growth

The establishment of artificial grassland is a good pathway for resolving serious social and economic problems in the Qinghai-Tibet Plateau. Some beneficial indigenous microbes may be used to improve productivity in artificial grassland. The genome of the indigenous dark septate fungus, <i>Exophiala tremulae</i> CICC2537, was sequenced and assembled at the chromosome level using the PacBio sequencing platform, with the assistance of the Hi-C technique for scaffolding, and its 3D genome structures were investigated. The genome size of <i>E. tremulae</i> is 51.903848 Mb, and it contains eight chromosomes. A total of 12,277 protein-coding genes were predicted, and 11,932 genes (97.19%) were annotated. As for the distribution of exon and intron number and the distribution of gene GC and CDS GC, <i>E. tremulae</i> showed similar distribution patterns to the other investigated members of the genus <i>Exophiala</i>. The analysis of carbohydrate-active enzymes showed that <i>E. tremulae</i> possesses the greatest number of enzymes with auxiliary activities and the lowest number of enzymes with carbohydrate-binding modules among the investigated fungi. The total number of candidate effector proteins was 3337, out of which cytoplasmic and apoplastic effector proteins made up 3100 and 163, respectively. The whole genome of <i>E. tremulae</i> contained 40 compartment As and 76 compartment Bs, and there was no significant difference in GC content in its compartment As and Bs. The whole genome of <i>E. tremulae</i> was predicted to contain 155 topologically associating domains (TADs), and their average length was 250,000 bp, but there were no significant differences in the numbers of genes and the GC content per bin localized within the boundaries and interiors of TADs. Comparative genome analysis showed that <i>E. tremulae</i> diverged from <i>Exophiala mesophila</i> about 34.1 (30.0-39.1) Myr ago, and from <i>Exophiala calicioides</i> about 85.6 (76.1-90.6) Myr ago. Compared with all the investigated fungi, the numbers of contraction and expansion gene families in the <i>E. tremulae</i> genome were 13 and 89, respectively, and the numbers of contraction and expansion genes were 14 and 670, respectively. Our work provides a basis for the use of the dark septate fungus in alpine artificial grassland and further research into its symbiosis mechanisms, which may improve the growth of plant species used in the Qinghai-Tibet Plateau.