Specialized plant biochemistry drives gene clustering in fungi
Specialized plant biochemistry drives gene clustering in fungi
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DOI：
10.1038/s41396-018-0075-3
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发表时间：
2018-07-01
期刊：
影响因子：
11
通讯作者：
Slot, Jason C.
中科院分区：
文献类型：
--
作者：
Gluck-Thaler, Emile;Slot, Jason C.
原核生物和真核生物的适应性和进化受到其基因组组织的影响。特别是，基因的物理聚类可以协调基因表达，并可以防止共适应等位基因的分裂。虽然聚类可能因此导致选择表型优化和持久性，环境选择压力对真核生物基因组组织的影响很少被系统地探讨。在这里，我们研究了真菌基因的组织参与降解苯丙素类，一类植物产生的次生代谢产物，介导植物和真菌之间的许多生态相互作用。使用一种新的基因簇检测方法，我们确定了1110个基因簇和许多保守的组合簇在一组不同的真菌。我们表明，在小的空间尺度上的基因组组织的一致性往往与生态生活方式的相似性。此外，我们发现，虽然集群往往是作为独立的模块，在内容上几乎没有重叠的结构，某些基因家族合并成一个共同的网络多个模块，这表明它们是苯丙素降解策略的重要组成部分。总之，我们的研究结果表明，苯丙素类已多次选择在真菌中的基因聚类，并强调在这个古老的真核生物谱系的基因组组织和生态进化之间的相互作用。
The fitness and evolution of prokaryotes and eukaryotes are affected by the organization of their genomes. In particular, the physical clustering of genes can coordinate gene expression and can prevent the breakup of co-adapted alleles. Although clustering may thus result from selection for phenotype optimization and persistence, the impact of environmental selection pressures on eukaryotic genome organization has rarely been systematically explored. Here, we investigated the organization of fungal genes involved in the degradation of phenylpropanoids, a class of plant-produced secondary metabolites that mediate many ecological interactions between plants and fungi. Using a novel gene cluster detection method, we identified 1110 gene clusters and many conserved combinations of clusters in a diverse set of fungi. We demonstrate that congruence in genome organization over small spatial scales is often associated with similarities in ecological lifestyle. Additionally, we find that while clusters are often structured as independent modules with little overlap in content, certain gene families merge multiple modules into a common network, suggesting they are important components of phenylpropanoid degradation strategies. Together, our results suggest that phenylpropanoids have repeatedly selected for gene clustering in fungi, and highlight the interplay between genome organization and ecological evolution in this ancient eukaryotic lineage.