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Discovering Functions of Unannotated Genes from a Transcriptome Survey of Wild Fungal Isolates

机译：从野生真菌分离株的转录组调查中发现未注释基因的功能

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Most fungal genomes are poorly annotated, and many fungal traits of industrial and biomedical relevance are not well suited to classical genetic screens. Assigning genes to phenotypes on a genomic scale thus remains an urgent need in the field. We developed an approach to infer gene function from expression profiles of wild fungal isolates, and we applied our strategy to the filamentous fungus Neurospora crassa. Using transcriptome measurements in 70 strains from two well-defined clades of this microbe, we first identified 2,247 cases in which the expression of an unannotated gene rose and fell across N.?crassa strains in parallel with the expression of well-characterized genes. We then used image analysis of hyphal morphologies, quantitative growth assays, and expression profiling to test the functions of four genes predicted from our population analyses. The results revealed two factors that influenced regulation of metabolism of nonpreferred carbon and nitrogen sources, a gene that governed hyphal architecture, and a gene that mediated amino acid starvation resistance. These findings validate the power of our population-transcriptomic approach for inference of novel gene function, and we suggest that this strategy will be of broad utility for genome-scale annotation in many fungal systems. >IMPORTANCE Some fungal species cause deadly infections in humans or crop plants, and other fungi are workhorses of industrial chemistry, including the production of biofuels. Advances in medical and industrial mycology require an understanding of the genes that control fungal traits. We developed a method to infer functions of uncharacterized genes by observing correlated expression of their mRNAs with those of known genes across wild fungal isolates. We applied this strategy to a filamentous fungus and predicted functions for thousands of unknown genes. In four cases, we experimentally validated the predictions from our method, discovering novel genes involved in the metabolism of nutrient sources relevant for biofuel production, as well as colony morphology and starvation resistance. Our strategy is straightforward, inexpensive, and applicable for predicting gene function in many fungal species.
机译：大多数真菌基因组的注释不善，许多与工业和生物医学相关的真菌性状都不太适合经典遗传筛选。因此，在基因组规模上将基因分配给表型仍然是本领域的迫切需求。我们开发了一种从野生真菌分离株的表达谱推断基因功能的方法，并将我们的策略应用于丝状真菌 Neurospora crassa 。使用来自两个明确定义的该进化枝的70个菌株的转录组测量结果，我们首先鉴定出2247例未注释基因的表达与 cr.crassa 菌株平行表达的情况充分表征的基因。然后，我们使用了菌丝形态的图像分析，定量生长分析和表达谱分析来测试根据我们的种群分析预测的四个基因的功能。结果揭示了影响非优选碳源和氮源代谢调控的两个因素，一个控制菌丝结构的基因和一个介导氨基酸饥饿抗性的基因。这些发现验证了我们的种群转录组学方法对新型基因功能的推断能力，并且我们建议这种策略在许多真菌系统中对基因组规模注释具有广泛的实用性。 >重要性：某些真菌物种会导致人类或农作物的致命感染，而其他真菌则是工业化学的主要力量，包括生物燃料的生产。医学和工业真菌学的进步要求了解控制真菌性状的基因。我们开发了一种方法，通过观察野生真菌分离株中它们的mRNA与已知基因的相关表达来推断未表征基因的功能。我们将此策略应用于丝状真菌，并预测了数千个未知基因的功能。在四种情况下，我们通过实验验证了我们方法的预测，发现了与生物燃料生产相关的营养源代谢以及菌落形态和饥饿抗性相关的新基因。我们的策略简单，便宜，可用于预测许多真菌物种的基因功能。

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