Liu Jie, Guo Linong, Li Zongwei, Zhou Zhe, Li Zhen, Li Qian, Bo Xiaochen, Wang Shengqi, Wang Junli, Ma Shuangcheng, Zheng Jian, Yang Ying
Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, 100850 China.
Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, 100050 China.
Chin Med. 2020 Oct 6;15:107. doi: 10.1186/s13020-020-00365-3. eCollection 2020.
, which is only naturally found in the high-elevation extreme environment of the Tibetan Plateau, has been used in traditional Chinese medicine. Information concerning the evolutionary and geologic context of remains limited, however.
We constructed the high-quality genome of and provided insight into the evolution and ecology of using comparative genomics.
We mapped the whole genome of the anamorph/asexual form of using Illumina and PacBio sequencing technologies and obtained a well assembled genome of 119.2 Mbp size. Long-read Single Molecule Real Time (SMRT) sequencing technology generated an assembly with more accurate representation of repeat sequence abundances and placement. Evolutionary analyses indicated that diverged from other fungi 65.9 Mya in the Upper Cretaceous, during the uplift of the Tibetan Plateau. Gene family expansions and contractions in addition to genome inflation via long terminal repeat (LTR) retrotransposon insertions were implicated as an important driver of divergence. The insertion rate of LTR sequences into the genome peaked ~ 30-40 Mya, when the Tibetan Plateau rose rapidly. Gene Ontology (GO) enrichment analysis suggested that contained more genes related to ice binding compared to other closely related fungi, which may aid in their adaptability to the cold Tibetan Plateau. Further, heavy metal resistance genes were in low abundance in the genome, which may help to explain previous observations that tissues contain high levels of heavy metals.
Our results reveal the evolutionary, geological, and ecological context for the evolution of the genome and the factors that have contributed to the environmental adaptability of this valuable fungus. These findings suggest that genome inflation via LTR retrotransposon insertions in coincided with the uplift of the Tibetan Plateau. LTRs and the specific genetic mechanisms of contributed to its adaptation to the environment on the plateau.
[物种名称]仅自然存在于青藏高原的高海拔极端环境中，已被用于传统中药。然而，关于[物种名称]的进化和地质背景的信息仍然有限。
我们构建了[物种名称]的高质量基因组，并通过比较基因组学深入了解了[物种名称]的进化和生态。
我们使用Illumina和PacBio测序技术对[物种名称]的无性型/无性形式的全基因组进行了测序，并获得了一个大小为119.2 Mbp的组装良好的基因组。长读长单分子实时（SMRT）测序技术生成的组装结果更准确地反映了重复序列的丰度和位置。进化分析表明，[物种名称]在白垩纪晚期青藏高原隆升期间于6590万年前与其他真菌分化。基因家族的扩张和收缩以及通过长末端重复（LTR）逆转录转座子插入导致的基因组膨胀被认为是[物种名称]分化的重要驱动力。LTR序列插入[物种名称]基因组的速率在约3000 - 4000万年前达到峰值，当时青藏高原迅速隆升。基因本体（GO）富集分析表明，与其他密切相关的真菌相比，[物种名称]含有更多与冰结合相关的基因，这可能有助于它们适应寒冷的青藏高原。此外，[物种名称]基因组中重金属抗性基因的丰度较低，这可能有助于解释之前关于[物种名称]组织中含有高水平重金属的观察结果。
我们的结果揭示了[物种名称]基因组进化的进化、地质和生态背景以及促成这种珍贵真菌环境适应性的因素。这些发现表明，[物种名称]中通过LTR逆转录转座子插入导致的基因组膨胀与青藏高原的隆升同时发生。LTR和[物种名称]的特定遗传机制促成了其对高原环境的适应。
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