Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure.
Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure.
复制标题
DOI：
10.1534/g3.117.040691
复制
发表时间：
2017-07-05
期刊：
影响因子：
--
通讯作者：
Nislow C
中科院分区：
文献类型：
--
作者：
Sinha S;Flibotte S;Neira M;Formby S;Plemenitaš A;Cimerman NG;Lenassi M;Gostinčar C;Stajich JE;Nislow C
极端生物通过突出细胞生理学如何适应极端环境来展示基本生物过程的灵活性和适应性。很少有真核极端微生物得到了很好的研究，只有少数适合实验室培养和操作。这些生物体的基因组结构的详细表征对于阐明它们如何适应环境压力是重要的。嗜极真菌的一个很好的例子是嗜盐菌Hortaea werneckii（盘菌亚门，Dothideomycetes，Capnodiales），这是一种酵母样真菌，能够在接近饱和浓度的氯化钠中茁壮成长，也能耐受紫外线照射和干燥。考虑到它独特的生活方式和最近的全基因组复制，H。werneckii为测试基因组复制的作用和对极端环境的适应性提供了机会。我们之前组装了H. werneckii使用短读测序技术，发现了显著程度的基因重复。然而，由于技术的限制，无法对整个基因组进行高置信度的注释。因此，我们重新审视了H。wernickii基因组的长读段单分子测序，并提供了一个改进的基因组组装，与转录组和核小体分析相结合，为真菌嗜盐菌基因组学提供了有用的资源。值得注意的是，250 Mb H. wernickii基因组包含15，974个基因，其中95%（7608个）是由最近的全基因组重复（WGD）形成的重复，它们之间平均有5%的蛋白质序列差异。我们发现WGD是非常新的，与酿酒酵母相比，大多数基因组的ohnologs在染色质结构的基因表达水平上没有分歧。
Extremophilic organisms demonstrate the flexibility and adaptability of basic biological processes by highlighting how cell physiology adapts to environmental extremes. Few eukaryotic extremophiles have been well studied and only a small number are amenable to laboratory cultivation and manipulation. A detailed characterization of the genome architecture of such organisms is important to illuminate how they adapt to environmental stresses. One excellent example of a fungal extremophile is the halophile Hortaea werneckii (Pezizomycotina, Dothideomycetes, Capnodiales), a yeast-like fungus able to thrive at near-saturating concentrations of sodium chloride and which is also tolerant to both UV irradiation and desiccation. Given its unique lifestyle and its remarkably recent whole genome duplication, H. werneckii provides opportunities for testing the role of genome duplications and adaptability to extreme environments. We previously assembled the genome of H. werneckii using short-read sequencing technology and found a remarkable degree of gene duplication. Technology limitations, however, precluded high-confidence annotation of the entire genome. We therefore revisited the H. wernickii genome using long-read, single-molecule sequencing and provide an improved genome assembly which, combined with transcriptome and nucleosome analysis, provides a useful resource for fungal halophile genomics. Remarkably, the ∼50 Mb H. wernickii genome contains 15,974 genes of which 95% (7608) are duplicates formed by a recent whole genome duplication (WGD), with an average of 5% protein sequence divergence between them. We found that the WGD is extraordinarily recent, and compared to Saccharomyces cerevisiae, the majority of the genome’s ohnologs have not diverged at the level of gene expression of chromatin structure.