文献类型：期刊文献

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

作者：Wu, Chu[1] Fan, Junjie[2] Hu, Die[1] Sun, Honggang[3] Lu, Guangxin[4] Wang, Yun[2] Yang, Yujie[1]

第一作者：Wu, Chu

通信作者：Hu, D[1]

机构：[1]Yangtze Univ, Coll Hort & Gardening, Jingzhou 434025, Peoples R China;[2]Yangtze Univ, Coll Life Sci, Jingzhou 434025, Peoples R China;[3]Chinese Acad Forestry, Res Inst Subtrop Forestry, Hangzhou 311400, Peoples R China;[4]Qinghai Univ, Coll Agr & Anim Husb, Xining 810016, Peoples R China

年份：2025

卷号：11

期号：4

外文期刊名：JOURNAL OF FUNGI

收录：;Scopus(收录号：2-s2.0-105003538232);WOS:【SCI-EXPANDED(收录号:WOS:001475414800001)】；

基金：The research was sponsored by the general program of the National Natural Science Foundation of China (2024-2027, grant number: U23A2043).

语种：英文

外文关键词：3D genome structure; topologically associating domains; chromatin loops; chromosome compartments; contraction and expansion gene family; alpine meadow plants

摘要：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, Exophiala tremulae 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 E. tremulae 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, E. tremulae showed similar distribution patterns to the other investigated members of the genus Exophiala. The analysis of carbohydrate-active enzymes showed that E. tremulae 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 E. tremulae 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 E. tremulae 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 E. tremulae diverged from Exophiala mesophila about 34.1 (30.0-39.1) Myr ago, and from Exophiala calicioides 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 E. tremulae 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.