Gene clusters are genomic loci that contain multiple genes that are functionally and genetically linked. Gene clusters collectively encode diverse functions, including small molecule biosynthesis, nutrient assimilation, metabolite degradation, and production of proteins essential for growth and development. Identifying gene clusters is a powerful tool for small molecule discovery and provides insight into the ecology and evolution of organisms. Current detection algorithms focus on canonical ‘core’ biosynthetic functions many gene clusters encode, while overlooking uncommon or unknown cluster classes. These overlooked clusters are a potential source of novel natural products and comprise an untold portion of overall gene cluster repertoires. Unbiased, function-agnostic detection algorithms therefore provide an opportunity to reveal novel classes of gene clusters and more precisely define genome organization. We present CLOCI (Co-occurrence Locus and Orthologous Cluster Identifier), an algorithm that identifies gene clusters using multiple proxies of selection for coordinated gene evolution. Our approach generalizes gene cluster detection and gene cluster family circumscription, improves detection of multiple known functional classes, and unveils non-canonical gene clusters. CLOCI is suitable for genome-enabled small molecule mining, and presents an easily tunable approach for delineating gene cluster families and homologous loci.

中文翻译：

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CLOCI：通过通用检测揭示神秘真菌基因簇


基因簇是包含多个在功能和遗传上相关的基因的基因组位点。基因簇共同编码多种功能，包括小分子生物合成、营养同化、代谢物降解以及生长和发育必需的蛋白质的产生。识别基因簇是发现小分子的强大工具，可以深入了解生物体的生态和进化。当前的检测算法侧重于许多基因簇编码的规范“核心”生物合成功能，而忽略了不常见或未知的簇类别。这些被忽视的基因簇是新型天然产物的潜在来源，并且构成了整个基因簇库的不为人知的部分。因此，公正、与功能无关的检测算法提供了揭示新类别基因簇并更精确地定义基因组组织的机会。我们提出了 CLOCI（共现基因座和直系同源簇标识符），这是一种使用多个选择代理来识别基因簇的算法，以协调基因进化。我们的方法概括了基因簇检测和基因簇家族限制，改进了多个已知功能类别的检测，并揭示了非规范基因簇。 CLOCI 适用于基因组支持的小分子挖掘，并提供了一种易于调整的方法来描绘基因簇家族和同源基因座。