The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi.
The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi.
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DOI：
10.1093/molbev/msaa122
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发表时间：
2020-10-01
影响因子：
10.7
通讯作者：
Slot JC
中科院分区：
文献类型：
--
作者：
Gluck-Thaler E;Haridas S;Binder M;Grigoriev IV;Crous PW;Spatafora JW;Bushley K;Slot JC
真菌的生态多样性在很大程度上是由代谢特征定义的，包括产生介导与其他生物相互作用的次级或“专门”代谢物（SM）的能力。真菌SM途径通常编码在生物合成基因簇（BGC）中，这有助于代谢途径的鉴定和表征。BGC组成的变化反映了其SM产品的多样性。最近的研究已经记录了相同真菌物种的分离株之间BGC库的惊人多样性，但很少有人知道这种群体水平的变化是如何在宏观进化时间尺度上遗传的。在这里，我们应用了一种新的基于链接的算法来揭示BGC组成，分布和101种Dothideomycetes的库中以前未探索的多样性维度，这些Dothideomycetes被认为是最具遗传多样性的真菌类，并且已知产生许多SM。与现有方法相比，我们预测了互补和重叠的聚类基因集，并确定了与已知次级代谢产物基因相关的新基因对。我们发现，在个别基因组中的BGC集之间的变化是由于非重叠的BGC组合，几个BGC有偏见的生态分布，符合生态位特异性选择。我们观察到，总BGC多样性的规模与增加的剧目大小线性，这表明次级代谢产物在个别真菌几乎没有结构冗余。我们的项目，有大量的未采样的BGC多样性在特定的家庭Dothideomycetes，这将提供一个路线图，为未来的采样工作。我们的方法和发现为BGC多样性如何在整个真菌分类学类别中产生和维持提供了新的见解。
Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or “specialized” metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. Here, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered the most phylogenetically diverse class of fungi and known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation among sets of BGCs in individual genomes is due to nonoverlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. We project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.
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影响因子：
5.9
作者：
Del Carratore，Francesco;Zych，Konrad;Breitling，Rainer
通讯作者：
Breitling，Rainer
影响因子：
6.6
作者：
Baselga, Andres;Orme, C. David L.
通讯作者：
Orme, C. David L.
影响因子：
3.5
作者：
Condon, Bradford J.;Elliott, Candace;Turgeon, B. Gillian
通讯作者：
Turgeon, B. Gillian
影响因子：
11
作者：
Gluck-Thaler, Emile;Slot, Jason C.
通讯作者：
Slot, Jason C.
DOI：
10.3390/antibiotics7010012
发表时间：
2018-02-13
期刊：
Antibiotics (Basel, Switzerland)
影响因子：
--
作者：
Choudoir MJ;Pepe-Ranney C;Buckley DH
通讯作者：
Buckley DH