College of Marine Life Sciences, Ocean University of China, Yushan Road, No. 5, Qingdao, China.
Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China.
Funct Integr Genomics. 2023 Jun 19;23(3):206. doi: 10.1007/s10142-023-01127-8.
Aureobasidium melanogenum TN3-1 strain and A. melanogenum P16 strain were isolated from the natural honey and the mangrove ecosystem, respectively. The former can produce much higher pullulan from high concentration of glucose than the latter. In order to know what happened to their genomes, the PacBio sequencing and Hi-C technologies were used to create the first high-quality chromosome-level reference genome assembly of A. melanogenum TN3-1 (51.61 Mb) and A. melanogenum P16 (25.82 Mb) with the contig N50 of 2.19 Mb and 2.26 Mb, respectively. Based on the Hi-C results, a total of 93.33% contigs in the TN3-1 strain and 92.31% contigs in the P16 strain were anchored onto 24 and 12 haploid chromosomes, respectively. The genomes of the TN3-1 strain had two subgenomes A and B. Synteny analysis showed that the genomic contents of the two subgenomes were asymmetric with many structural variations. Intriguingly, the TN3-1 strain was revealed as a recent hybrid/fusion between the ancestor of A. melanogenum CBS105.22/CBS110374 and the ancestor of another unidentified strain of A. melanogenum similar to P16 strain. We estimated that the two ancient progenitors diverged around 18.38 Mya and merged around 10.66-9.98 Mya. It was found that in the TN3-1 strain, telomeres of each chromosome contained high level of long interspersed nuclear elements (LINEs), but had low level of the telomerase encoding gene. Meanwhile, there were high level of transposable elements (TEs) inserted in the chromosomes of the TN3-1 strain. In addition, the positively selected genes of the TN3-1 strain were mainly enriched in the metabolic processes related to harsh environmental adaptability. Most of the stress-related genes were found to be related to the adjacent LTRs, and the glucose derepression was caused by the mutation of the Glc7-2 in the Snf-Mig1 system. All of these could contribute to its genetic instability, genome evolution, high stress resistance, and high pullulan production from glucose.
从天然蜂蜜和红树林生态系统中分别分离出嗜热丝孢酵母 TN3-1 菌株和嗜热丝孢酵母 P16 菌株。前者能够从高浓度葡萄糖中产生更高浓度的普鲁兰多糖，而后者则不能。为了了解它们的基因组发生了什么变化，我们使用 PacBio 测序和 Hi-C 技术构建了嗜热丝孢酵母 TN3-1（51.61Mb）和嗜热丝孢酵母 P16（25.82Mb）的第一个高质量染色体水平参考基因组组装，其重叠群 N50 分别为 2.19Mb 和 2.26Mb。基于 Hi-C 结果，TN3-1 菌株的 93.33%的重叠群和 P16 菌株的 92.31%的重叠群分别锚定在 24 条和 12 条单倍体染色体上。TN3-1 菌株的基因组有两个亚基因组 A 和 B。共线性分析表明，两个亚基因组的基因组内容不对称，存在许多结构变异。有趣的是，TN3-1 菌株被揭示为嗜热丝孢酵母 CBS105.22/CBS110374 的祖先和类似于 P16 菌株的另一个未鉴定的嗜热丝孢酵母祖先之间的最近的杂种/融合体。我们估计，这两个古老的祖先是在 18.38Mya 左右分化的，大约在 10.66-9.98Mya 左右融合的。研究发现，在 TN3-1 菌株中，每条染色体的端粒都含有高水平的长散布核元件（LINEs），但端粒酶编码基因的水平较低。同时，TN3-1 菌株的染色体中插入了高水平的转座元件（TEs）。此外，TN3-1 菌株的正选择基因主要富集在与恶劣环境适应性相关的代谢过程中。大多数与应激相关的基因都与相邻的 LTRs 有关，葡萄糖去阻遏是由 Snf-Mig1 系统中的 Glc7-2 突变引起的。所有这些都有助于其遗传不稳定性、基因组进化、高应激抗性和从葡萄糖中高效生产普鲁兰多糖。
